# HG changeset patch
# User artbio
# Date 1523096090 14400
# Node ID d33263e6e8126e7cace512cc0da84c1a87c81f7b
# Parent  a561a71bd7d72e4d17027ef14b57a90f8add597d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f

diff -r a561a71bd7d7 -r d33263e6e812 small_rna_maps.r
--- a/small_rna_maps.r	Tue Mar 06 06:11:55 2018 -0500
+++ b/small_rna_maps.r	Sat Apr 07 06:14:50 2018 -0400
@@ -1,6 +1,6 @@
 ## Setup R error handling to go to stderr
 options( show.error.messages=F,
-       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+         error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
 options(warn = -1)
 library(RColorBrewer)
 library(lattice)
@@ -11,37 +11,39 @@
 
 
 option_list <- list(
-    make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
-    make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"),
-    make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"),
-    make_option("--first_plot_method", type = "character", help="How additional data should be plotted"),
-    make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"),
-    make_option("--global", type = "character", help="data should be plotted as global size distribution"),
-    make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
-    )
- 
+  make_option(c("-i", "--ymin"), type="double", help="set min ylimit. e.g. '-100.0'"),
+  make_option(c("-a", "--ymax"), type="double", help="set max ylimit. e.g. '100.0'"),
+  make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
+  make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"),
+  make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"),
+  make_option("--first_plot_method", type = "character", help="How additional data should be plotted"),
+  make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"),
+  make_option("--global", type = "character", help="data should be plotted as global size distribution"),
+  make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
+)
+
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
 args = parse_args(parser)
- 
+
 # data frames implementation
 ## first table
 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
-    Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+  Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
 }
 n_samples=length(unique(Table$Dataset))
 samples = unique(Table$Dataset)
 if (args$normalization != "") {
-    norm_factors = as.numeric(unlist(strsplit(args$normalization, " ")))
+  norm_factors = as.numeric(unlist(strsplit(args$normalization, " ")))
 } else {
-    norm_factors = rep(1, n_samples)
+  norm_factors = rep(1, n_samples)
 }
 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size" | args$first_plot_method == "Coverage") {
-    i = 1
-    for (sample in samples) {
-        Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i]
-        i = i + 1
-    }
+  i = 1
+  for (sample in samples) {
+    Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i]
+    i = i + 1
+  }
 }
 genes=unique(Table$Chromosome)
 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
@@ -49,198 +51,202 @@
 n_genes=length(per_gene_readmap)
 # second table
 if (args$extra_plot_method != '') {
-    ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
-    if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
-        ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+  ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
+  if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
+    ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+  }
+  if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") {
+    i = 1
+    for (sample in samples) {
+      ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i]
+      i = i + 1
     }
-    if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") {
-        i = 1
-        for (sample in samples) {
-            ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i]
-            i = i + 1
-        }
-    }
-    per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
+  }
+  per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
 }
 
 ## functions
 globalbc = function(df, global="", ...) {
-    if (global == "yes") {
-        bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)),
-              data = df, origin = 0,
-              horizontal=FALSE,
-              col=c("darkblue"),
-              scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))),
-              xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85),
-              ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85),
-              main=title_first_method[[args$first_plot_method]],
-              layout = c(2, 6), newpage=T,
-              as.table=TRUE,
-              aspect=0.5,
-              strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"),
-              ...
-              )
-    } else {
-        bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)),
-              data = df, origin = 0,
-              horizontal=FALSE,
-              group=Polarity,
-              stack=TRUE,
-              col=c('red', 'blue'),
-              scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))),
-              xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85),
-              ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85),
-              main=title_first_method[[args$first_plot_method]],
-              layout = c(2, 6), newpage=T,
-              as.table=TRUE,
-              aspect=0.5,
-              strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"),
-              ...
-              )
-    }
-   return(bc)
+  if (global == "yes") {
+    bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)),
+                   data = df, origin = 0,
+                   horizontal=FALSE,
+                   col=c("darkblue"),
+                   scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))),
+                   xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85),
+                   ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85),
+                   main=title_first_method[[args$first_plot_method]],
+                   layout = c(2, 6), newpage=T,
+                   as.table=TRUE,
+                   aspect=0.5,
+                   strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"),
+                   ...
+    )
+  } else {
+    bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)),
+                   data = df, origin = 0,
+                   horizontal=FALSE,
+                   group=Polarity,
+                   stack=TRUE,
+                   col=c('red', 'blue'),
+                   scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))),
+                   xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85),
+                   ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85),
+                   main=title_first_method[[args$first_plot_method]],
+                   layout = c(2, 6), newpage=T,
+                   as.table=TRUE,
+                   aspect=0.5,
+                   strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"),
+                   ...
+    )
+  }
+  return(bc)
 }
 plot_unit = function(df, method=args$first_plot_method, ...) {
-    if (method == 'Counts') {
-        p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
-        data=df,
-        type='h',
-        lwd=1.5,
-        scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
-        xlab=NULL, main=NULL, ylab=NULL,
-        as.table=T,
-        origin = 0,
-        horizontal=FALSE,
-        group=Polarity,
-        col=c("red","blue"),
-        par.strip.text = list(cex=0.7),
-        ...)
-    } else if (method != "Size") {
-        p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
-        data=df,
-        type='p',
-        pch=19,
-        cex=0.35,
-        scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
-        xlab=NULL, main=NULL, ylab=NULL,
-        as.table=T,
-        origin = 0,
-        horizontal=FALSE,
-        group=Polarity,
-        col=c("red","blue"),
-        par.strip.text = list(cex=0.7),
-        ...)
-    } else {
-        p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
-                     horizontal=FALSE,
-                     group=Polarity,
-                     stack=TRUE,
-                     col=c('red', 'blue'),
-                     scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=0.5)),
-        xlab = NULL,
-        ylab = NULL,
-        main = NULL,
-        as.table=TRUE,
-        par.strip.text = list(cex=0.6),
-        ...)
-    }
-    combineLimits(p)
+  if (exists('ymin', where=args)){
+    min=args$ymin
+  }else{
+    min=''
+  }
+  if ((exists('ymax', where=args))){
+    max=args$ymax
+  }else{
+    max=''
+  }
+  ylimits=c(min,max)
+  if (method == 'Counts') {
+    p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+               data=df,
+               type='h',
+               lwd=1.5,
+               scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+               xlab=NULL, main=NULL, ylab=NULL, ylim=ylimits,
+               as.table=T,
+               origin = 0,
+               horizontal=FALSE,
+               group=Polarity,
+               col=c("red","blue"),
+               par.strip.text = list(cex=0.7),
+               ...)
+    p=combineLimits(p)
+  } else if (method != "Size") {
+    p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+               data=df,
+               type='p',
+               pch=19,
+               cex=0.35,
+               scales= list(relation="free", x=list(rot=0, cex=0.7, tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+               xlab=NULL, main=NULL, ylab=NULL, ylim=ylimits,
+               as.table=T,
+               origin = 0,
+               horizontal=FALSE,
+               group=Polarity,
+               col=c("red","blue"),
+               par.strip.text = list(cex=0.7),
+               ...)
+  } else {
+    p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
+                 horizontal=FALSE,
+                 group=Polarity,
+                 stack=TRUE,
+                 col=c('red', 'blue'),
+                 scales=list(y=list(rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=c(1,0))),
+                 xlab = NULL,
+                 ylab = NULL,
+                 main = NULL,
+                 as.table=TRUE,
+                 par.strip.text = list(cex=0.6),
+                 ...)
+    p=combineLimits(p)
+  }
+  return(p)
 }
 
+
 ## function parameters
 
 #par.settings.firstplot = list(layout.heights=list(top.padding=11, bottom.padding = -14))
 #par.settings.secondplot=list(layout.heights=list(top.padding=11, bottom.padding = -15), strip.background=list(col=c("lavender","deepskyblue")))
-par.settings.firstplot = list(layout.heights=list(top.padding=-2, bottom.padding=-2))
-par.settings.secondplot=list(layout.heights=list(top.padding=-1, bottom.padding=-1), strip.background=list(col=c("lavender","deepskyblue")))
-par.settings.single_plot=list(strip.background = list(col = c("lightblue", "lightgreen")))
+par.settings.firstplot = list(layout.heights=list(top.padding=-2, bottom.padding=-2),strip.background=list(col=c("lightblue","lightgreen")))
+par.settings.secondplot=list(layout.heights=list(top.padding=-1, bottom.padding=-1),strip.background=list(col=c("lightblue","lightgreen")))
 title_first_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions")
 title_extra_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions")
 legend_first_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count")
-legend_extra_method =list(Counts="Read count", Coverage="Coveragedepth", Median="Median size", Mean="Mean size", Size="Read count")
+legend_extra_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count")
 bottom_first_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads")
 bottom_extra_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads")
 
 ## Plotting Functions
 
 double_plot <- function(...) {
-    page_height = 15
-    rows_per_page = 10
-    graph_heights=c(40,30,40,30,40,30,40,30,40,30,10)
-    if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 2.3*n_samples +2.5}
-    pdf(file=args$output_pdf, paper="special", height=page_height, width=page_width)
-    for (i in seq(1,n_genes,rows_per_page/2)) {
-        start=i
-        end=i+rows_per_page/2-1
-        if (end>n_genes) {end=n_genes}
-        if (end-start+1 < 5) {graph_heights=c(rep(c(40,30),end-start+1),10,rep(c(40,30),5-(end-start+1)))}
-        first_plot.list = lapply(per_gene_readmap[start:end], function(x) plot_unit(x, strip=FALSE, par.settings=par.settings.firstplot))
-        second_plot.list = lapply(per_gene_size[start:end], function(x) plot_unit(x, method=args$extra_plot_method, par.settings=par.settings.secondplot))
-        plot.list=rbind(second_plot.list, first_plot.list)
-        args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 11)),
-                                    top=textGrob(paste(title_first_method[[args$first_plot_method]], "and", title_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, just="top"),
-                                    left=textGrob(paste(legend_first_method[[args$first_plot_method]], "/", legend_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just=0.675*(end-start-(2.2*(4/2.7))),vjust=2, rot=90),
-                                    sub=textGrob(paste(bottom_first_method[[args$first_plot_method]], "/", bottom_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just="bottom", vjust=2)
-                                    )
-                   )
-        do.call(grid.arrange, args_list)
-        }
-    devname=dev.off()
+  page_height = 15
+  rows_per_page = 10
+  graph_heights=c(40,30,40,30,40,30,40,30,40,30,10)
+  page_width=8.2677 * n_samples / 2
+  pdf(file=args$output_pdf, paper="special", height=page_height, width=page_width)
+  for (i in seq(1,n_genes,rows_per_page/2)) {
+    start=i
+    end=i+rows_per_page/2-1
+    if (end>n_genes) {end=n_genes}
+    if (end-start+1 < 5) {graph_heights=c(rep(c(40,30),end-start+1),10,rep(c(40,30),5-(end-start+1)))}
+    first_plot.list = lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings=par.settings.secondplot), strip.left=strip.custom(par.strip.text = list(cex=0.5)))))
+    second_plot.list = lapply(per_gene_size[start:end], function(x) update(useOuterStrips(plot_unit(x, method=args$extra_plot_method, par.settings=par.settings.firstplot), strip.left=strip.custom(par.strip.text = list(cex=0.5)), strip=FALSE)))
+    plot.list=rbind(first_plot.list, second_plot.list)
+    args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 11)),
+                                 top=textGrob(paste(title_first_method[[args$first_plot_method]], "and", title_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, just="top"),
+                                 left=textGrob(paste(legend_first_method[[args$first_plot_method]], "/", legend_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, hjust=0, x=1, y=(-0.38/4)*(end-start-(3.28/0.38)), rot=90),
+                                 sub=textGrob(paste(bottom_first_method[[args$first_plot_method]], "/", bottom_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just="bottom", vjust=2)
+    )
+    )
+    do.call(grid.arrange, args_list)
+  }
+  devname=dev.off()
 }
 
 
 single_plot <- function(...) {
-    width = 8.2677 * n_samples / 2
-    rows_per_page=8
-    graph_heights=c(rep(40,8),10)
-    pdf(file=args$output_pdf, paper="special", height=15, width=width)
-    for (i in seq(1,n_genes,rows_per_page)) {
-        start=i
-        end=i+rows_per_page-1
-        if (end>n_genes) {end=n_genes}
-        if (end-start+1 < 8) {graph_heights=c(rep(c(40),end-start+1),10,rep(c(40),8-(end-start+1)))}
-        first_plot.list = lapply(per_gene_readmap[start:end], function(x) plot_unit(x, par.settings=par.settings.firstplot))
-        plot.list=rbind(first_plot.list)
-        args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 9)),
-                                    top=textGrob(title_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, just="top"),
-                                    left=textGrob(legend_first_method[[args$first_plot_method]], gp=gpar(cex=1), just=(6.4/7)*(end-start-(6.2*(7/6.4))),vjust=2, rot=90),
-                                    sub=textGrob(bottom_first_method[[args$first_plot_method]], gp=gpar(cex=1), just="bottom", vjust=2)
-                                    )
-                   )
-        do.call(grid.arrange, args_list)
-        }
-    devname=dev.off()
+  width = 8.2677 * n_samples / 2
+  rows_per_page=8
+  graph_heights=c(rep(40,8),10)
+  pdf(file=args$output_pdf, paper="special", height=15, width=width)
+  for (i in seq(1,n_genes,rows_per_page)) {
+    start=i
+    end=i+rows_per_page-1
+    if (end>n_genes) {end=n_genes}
+    if (end-start+1 < 8) {graph_heights=c(rep(c(40),end-start+1),10,rep(c(40),8-(end-start+1)))}
+    first_plot.list = lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings=par.settings.firstplot),strip.left=strip.custom(par.strip.text = list(cex=0.5)))))
+    plot.list=rbind(first_plot.list)
+    args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 9)),
+                                 top=textGrob(title_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, just="top"),
+                                 left=textGrob(legend_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, hjust=0, x=1, y=(-0.41/7)*(end-start-(6.23/0.41)), rot=90),
+                                 sub=textGrob(bottom_first_method[[args$first_plot_method]], gp=gpar(cex=1), just="bottom", vjust=2)
+    )
+    )
+    do.call(grid.arrange, args_list)
+  }
+  devname=dev.off()
 }
 
 # main
 
 if (args$extra_plot_method != '') { double_plot() }
 if (args$extra_plot_method == '' & !exists('global', where=args)) {
-    single_plot()
+  single_plot()
 }
 if (exists('global', where=args)) {
-    pdf(file=args$output, paper="special", height=11.69)
-    Table <- within(Table, Counts[Polarity=="R"] <- abs(Counts[Polarity=="R"])) # retropedalage
-    library(reshape2)
-    ml = melt(Table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size"))
-    if (args$global == "nomerge") {
-        castml = dcast(ml, Dataset+Polarity+Size ~ variable, function(x) sum(x))
-        castml <- within(castml, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
-        bc = globalbc(castml, global="no")
-    } else {
-        castml = dcast(ml, Dataset+Size ~ variable, function(x) sum(x))
-        bc = globalbc(castml, global="yes")
-    }
-    plot(bc)
-    devname=dev.off()
+  pdf(file=args$output, paper="special", height=11.69)
+  Table <- within(Table, Counts[Polarity=="R"] <- abs(Counts[Polarity=="R"])) # retropedalage
+  library(reshape2)
+  ml = melt(Table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size"))
+  if (args$global == "nomerge") {
+    castml = dcast(ml, Dataset+Polarity+Size ~ variable, function(x) sum(x))
+    castml <- within(castml, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+    bc = globalbc(castml, global="no")
+  } else {
+    castml = dcast(ml, Dataset+Size ~ variable, function(x) sum(x))
+    bc = globalbc(castml, global="yes")
+  }
+  plot(bc)
+  devname=dev.off()
 }
-    
 
-
-
-
-
-
-
-
-
diff -r a561a71bd7d7 -r d33263e6e812 small_rna_maps.xml
--- a/small_rna_maps.xml	Tue Mar 06 06:11:55 2018 -0500
+++ b/small_rna_maps.xml	Sat Apr 07 06:14:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.4.3">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.5.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -13,35 +13,65 @@
       <exit_code range="1:" level="fatal" description="Tool exception" />
   </stdio>
   <command detect_errors="exit_code"><![CDATA[
-      #for $file in $inputs
-          samtools index '$file' &&
-      #end for
-      python '$__tool_directory__'/small_rna_maps.py 
-          --inputs 
-      #for $file in $inputs
-           '$file'
-      #end for
-          --sample_names
-      #for $sample in $inputs
-          '$sample.name'
-      #end for
+      #if $inputs_cond.normalize == "no":
+          #for $file in $inputs_cond.inputs
+              samtools index '$file';
+          #end for
+          python '$__tool_directory__'/small_rna_maps.py 
+              --inputs
+          #for $file in $inputs_cond.inputs
+              '$file'
+          #end for
+              --sample_names
+          #for $sample in $inputs_cond.inputs
+              '$sample.name'
+          #end for
+      #else if $inputs_cond.normalize == "yes":
+          #for $file in $inputs_cond.series
+              samtools index '$file.inputs';
+          #end for
+          python '$__tool_directory__'/small_rna_maps.py 
+              --inputs
+          #for $file in $inputs_cond.series
+              '$file.inputs'
+          #end for
+              --sample_names
+          #for $sample in $inputs_cond.series
+              '$sample.inputs.name'
+          #end for
+      #end if
           --minsize $minsize
           --maxsize $maxsize
           --cluster $cluster
       #if str($plots_options.plots_options_selector ) == "two_plot":
           --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
-          --outputs '$output_tab' '$extra_output_tab' &&
+          --outputs '$output_tab' '$extra_output_tab';
       #elif str($plots_options.plots_options_selector ) == "global":
           --plot_methods 'Size'
-          --outputs '$output_tab' &&
+          --outputs '$output_tab';
       #else:
           --plot_methods '${plots_options.first_plot}'
-          --outputs '$output_tab' &&
+          --outputs '$output_tab' ;
       #end if
       Rscript '$__tool_directory__'/small_rna_maps.r
           --first_dataframe '$output_tab' 
           --extra_dataframe '$extra_output_tab'
-          --normalization '$normalization'
+          --normalization 
+          #if $inputs_cond.normalize == "no":
+              ''
+          #else if $inputs_cond.normalize == "yes":
+              #set $norm = ""
+              #for $file in $inputs_cond.series
+                     #set $norm += str($file.normalization)+' '
+              #end for
+              #set $norm = $norm[:-1]
+              '$norm'
+          #end if
+          #if $ylimits_cond.ylimits == "no":
+              --ymin '' --ymax ''
+          #else:
+              --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
+          #end if
           #if str($plots_options.plots_options_selector ) == "two_plot":
               --first_plot_method '${plots_options.first_plot}'
               --extra_plot_method '${plots_options.extra_plot}'
@@ -56,15 +86,25 @@
               --output_pdf '$output_pdf'
   ]]></command>
  <inputs>
-    <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
-    <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
-           help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
+    <conditional name="inputs_cond">
+        <param name="normalize" type="boolean" label="Will there be normalization?" truevalue="yes" falsevalue="no" checked="false"/>
+        <when value="no">
+            <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
+        </when>
+        <when value="yes">
+            <repeat name="series" title="Normalization factors" min="1">
+                <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" />
+                <param name="normalization" type="float" label="Enter size/normalization factors."
+                       help="e.g. '0.75' '1.23'" value="1.0"/>
+            </repeat>
+        </when>
+    </conditional>
     <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
            value="0" help="default value: 0" />
     <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
            value="10000" help="default value: 10000" />
-    <param name="cluster" type="integer" label="aggregation distance in nucleotides"
-           value="0" help="if not 0, sets the distance (in nt) below which data are clustered to a single median position" />
+    <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
+           value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
     <conditional name="plots_options">
         <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
             <option value="one_plot">Just one plot per chromosome</option>
@@ -72,14 +112,14 @@
             <option value="global">Global read size distributions of aligned reads</option> 
         </param>
         <when value="two_plot">
-            <param name="first_plot" type="select" display="radio" label="Select the type of the first plot">
+            <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
                 <option value="Counts">Counts</option> 
                 <option value="Coverage">Coverage</option> 
                 <option value="Mean">Mean Sizes</option> 
                 <option value="Median">Median Sizes</option>
                 <option value="Size">Size Distributions</option>
             </param>
-            <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot">
+            <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
                 <option value="Counts">Counts</option> 
                 <option value="Coverage">Coverage</option> 
                 <option value="Mean">Mean Sizes</option> 
@@ -88,7 +128,7 @@
             </param>
         </when>
         <when value="one_plot">
-            <param name="first_plot" type="select" display="radio" label="select the type of the first plot">
+            <param name="first_plot" type="select" display="radio" label="select the type of plot">
                 <option value="Counts">Counts</option> 
                 <option value="Coverage">Coverage</option> 
                 <option value="Mean">Mean Sizes</option> 
@@ -104,6 +144,16 @@
             </param>
         </when>
     </conditional>
+    <conditional name="ylimits_cond">
+        <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
+               help="This limit won't be applied to size distribution plots"/>
+        <when value="yes">
+            <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
+            <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
+        </when>
+        <when value="no">
+        </when>
+    </conditional>
  </inputs>
 
  <outputs>
@@ -116,15 +166,100 @@
 
     <tests>
         <test>
+            <param name="inputs" value="input1.bam" ftype="bam"/>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
+            <param name="ylimits" value="yes" />
+            <param name="ymin" value="-5" />
+            <param name="ymax" value="5" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Counts" />
+            <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
+            <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam" ftype="bam"/>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="5" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Coverage" />
+            <output file="input1_coverage_cluster5.tab" name="output_tab" />
+            <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam" ftype="bam"/>
+            <param name="minsize" value="20" />
+            <param name="maxsize" value="30" />
+            <param name="cluster" value="0" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Size" />
+            <output file="input1_min20_max30_size.tab" name="output_tab" />
+            <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam" ftype="bam"/>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Mean" />
+            <output file="input1_mean.tab" name="output_tab" />
+            <output file="input1__single_plot_mean.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam" ftype="bam"/>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Median" />
+            <output file="input1_median.tab" name="output_tab" />
+            <output file="input1_single_plot_median.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="normalize" value="yes" />
+            <repeat name="series">
+                <param name="inputs" value="input1.bam" ftype="bam" />
+                <param name="normalization" value="1.0" />
+            </repeat>
+            <repeat name="series">
+                <param name="inputs" value="input2.bam" ftype="bam" />
+                <param name="normalization" value="2.0" />
+            </repeat>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Counts" />
+            <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
+            <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
+        </test>
+        <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
-            <param name="cluster" value="5" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
+            <param name="ylimits" value="yes" />
+            <param name="ymin" value="-5" />
+            <param name="ymax" value="5" />
+            <param name="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
+            <param name="extra_plot" value="Size" />
+            <output file="input1_input2_counts.tab" name="output_tab" />
+            <output file="input1_input2_size.tab" name="extra_output_tab" />
+            <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam"/>
+            <param name="minsize" value="0" />
+            <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
-            <param name="normalization" value="1 1" />
-            <param name="first_plot" value="Counts" />
-            <output file="count_cluster_5.tab" name="output_tab" />
-            <output file="count_cluster_5.pdf" name="output_pdf" />
+            <param name="first_plot" value="Coverage" />
+            <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
+            <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
         </test>
         <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
@@ -150,223 +285,33 @@
             <output file="size.tab" name="output_tab" />
             <output file="global_merge.pdf" name="output_pdf" />
         </test>
-        <test>
-            <param name="inputs" value="input1.bam" ftype="bam"/>
-            <param name="minsize" value="20" />
-            <param name="maxsize" value="30" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="global" />
-            <param name="mergestrands" value="merge" />
-            <param name="first_plot" value="Size" />
-            <param name="normalization" value="1 1" />
-            <output file="size20-30.tab" name="output_tab" />
-            <output file="global_merge_20-30.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Mean" />
-            <param name="normalization" value="1 1" />
-            <output file="count.tab" name="output_tab" />
-            <output file="mean.tab" name="extra_output_tab" />
-            <output file="count-mean.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
-            <param name="minsize" value="20" />
-            <param name="maxsize" value="30" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Mean" />
-            <param name="normalization" value="1 1" />
-            <output file="count20-30.tab" name="output_tab" />
-            <output file="mean20-30.tab" name="extra_output_tab" />
-            <output file="count-mean-20-30.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Mean" />
-            <param name="normalization" value="1 1" />
-            <output file="doubled_count.tab" name="output_tab" />
-            <output file="doubled_mean.tab" name="extra_output_tab" />
-            <output file="doubled_count-mean.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Median" />
-            <param name="normalization" value="1 1" />
-            <output file="count.tab" name="output_tab" />
-            <output file="median.tab" name="extra_output_tab" />
-            <output file="count-median.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Coverage" />
-            <param name="normalization" value="1 1" />
-            <output file="count.tab" name="output_tab" />
-            <output file="coverage.tab" name="extra_output_tab" />
-            <output file="count-coverage.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Size" />
-            <param name="normalization" value="1 1" />
-            <output file="count.tab" name="output_tab" />
-            <output file="size.tab" name="extra_output_tab" />
-            <output file="count-size.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Size" />
-            <param name="extra_plot" value="Counts" />
-            <param name="normalization" value="1 1" />
-            <output file="size.tab" name="output_tab" />
-            <output file="count.tab" name="extra_output_tab" />
-            <output file="size-count.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Size" />
-            <param name="extra_plot" value="Counts" />
-            <param name="normalization" value="1 0.75" />
-            <output file="size.tab" name="output_tab" />
-            <output file="count.tab" name="extra_output_tab" />
-            <output file="size-count_normed.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input_single_chr.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Coverage" />
-            <param name="normalization" value="1 1" />
-            <output file="count_1_chr.tab" name="output_tab" />
-            <output file="coverage_1_chr.tab" name="extra_output_tab" />
-            <output file="counts_coverage_1.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input_5_chr.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="two_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="extra_plot" value="Coverage" />
-            <param name="normalization" value="1 1" />
-            <output file="count_5_chr.tab" name="output_tab" />
-            <output file="coverage_5_chr.tab" name="extra_output_tab" />
-            <output file="counts_coverage_5.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input_single_chr.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="first_plot" value="Counts" />
-            <param name="normalization" value="1 1" />
-            <output file="count_1_chr.tab" name="output_tab" />
-            <output file="count_1.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="cluster" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="normalization" value="1 1" />
-            <param name="first_plot" value="Counts" />
-            <output file="count.tab" name="output_tab" />
-            <output file="count.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="first_plot" value="Size" />
-            <param name="normalization" value="1 1" />
-            <output file="size.tab" name="output_tab" />
-            <output file="size.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="first_plot" value="Coverage" />
-            <param name="normalization" value="1 1" />
-            <output file="coverage.tab" name="output_tab" />
-            <output file="coverage.pdf" name="output_pdf" />
-        </test>
-        <test>
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
-            <param name="minsize" value="0" />
-            <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="first_plot" value="Coverage" />
-            <param name="normalization" value="1 0.2" />
-            <output file="coverage.tab" name="output_tab" />
-            <output file="coverage_normed.pdf" name="output_pdf" />
-        </test>
     </tests>
-
-
 <help>
 
 **What it does**
 
-Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
-size read distribution along chromosome references.
+Plots mapping statistics of an alignment along the reference chromosomes :
 
-Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
-whose 5' end map to a given coordinate in a chromosome reference.
+ - counts
+ - mean sizes
+ - median sizes
+ - coverage depth
+ - size distribution
+
+Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
+in each position of a chromosome reference.
 Coverage depths are computed from the input bam alignment files using the python pysam module.
 
-The variables mentioned above (1-5) can be plotted either separately or in all possible
-pairwise combinations.
+The metrics mentioned above can be plotted either separately:
+
+.. image:: one_plot.png
 
-For comparison purpose, values from bam alignment files can be normalized by a size factor
-before plotting. If the normalization field is leaved blank, default normalization of 1
-is assumed.
+Or in all possible pairwise combinations:
+
+.. image:: two_plot.png
+
+For comparison purposes, values from bam alignment files can be normalized by a size factor
+before plotting.
 
 **Inputs**
 
@@ -374,16 +319,11 @@
 
   - single-read
   - sorted
-  - mapping to the same reference
-  
-Optionally, a space-separated list of normalization/size factors may be added before plotting.
-This list maps to the selected bam alignments from bottom to top.
+  - mapped to the same reference
 
 **Output**
 
-A pdf file generated by the R package lattice
-
-One or two dataframes used to plot data
+A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
 
 </help>
 
diff -r a561a71bd7d7 -r d33263e6e812 static/images/one_plot.png
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count-mean-20-30.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count-mean.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count-median.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count-size.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/count.tab
--- a/test-data/count.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam	FBtr0070001	72	1	F	1
-input1.bam	FBtr0070001	72	7	F	6
-input1.bam	FBtr0070001	72	8	F	3
-input1.bam	FBtr0070001	72	11	F	2
-input1.bam	FBtr0070001	72	16	F	1
-input1.bam	FBtr0070001	72	17	F	1
-input1.bam	FBtr0070001	72	18	F	1
-input1.bam	FBtr0070001	72	27	F	2
-input1.bam	FBtr0070001	72	30	F	1
-input1.bam	FBtr0070001	72	31	F	11
-input1.bam	FBtr0070001	72	32	F	27
-input1.bam	FBtr0070001	72	34	F	1
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	1
-input1.bam	FBtr0070533	72	12	F	2
-input1.bam	FBtr0070533	72	15	F	1
-input1.bam	FBtr0070533	72	19	F	5
-input1.bam	FBtr0070533	72	20	F	1
-input1.bam	FBtr0070533	72	21	F	1
-input1.bam	FBtr0070533	72	22	F	1
-input1.bam	FBtr0070533	72	25	F	1
-input1.bam	FBtr0070533	72	26	F	1
-input1.bam	FBtr0070533	72	28	F	1
-input1.bam	FBtr0070533	72	32	F	4
-input1.bam	FBtr0070533	72	35	F	1
-input1.bam	FBtr0070533	72	37	F	2
-input1.bam	FBtr0070533	72	38	F	2
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
-input1.bam	FBtr0070603	72	3	F	1
-input1.bam	FBtr0070603	72	4	F	1
-input1.bam	FBtr0070603	72	6	F	1
-input1.bam	FBtr0070603	72	7	F	7
-input1.bam	FBtr0070603	72	8	F	4
-input1.bam	FBtr0070603	72	9	F	7
-input1.bam	FBtr0070603	72	12	F	2
-input1.bam	FBtr0070603	72	13	F	1
-input1.bam	FBtr0070603	72	15	F	2
-input1.bam	FBtr0070603	72	16	F	2
-input1.bam	FBtr0070603	72	17	F	3
-input1.bam	FBtr0070603	72	18	F	1
-input1.bam	FBtr0070603	72	19	F	9
-input1.bam	FBtr0070603	72	20	F	3
-input1.bam	FBtr0070603	72	21	F	1
-input1.bam	FBtr0070603	72	22	F	3
-input1.bam	FBtr0070603	72	24	F	2
-input1.bam	FBtr0070603	72	25	F	1
-input1.bam	FBtr0070603	72	26	F	6
-input1.bam	FBtr0070603	72	27	F	3
-input1.bam	FBtr0070603	72	32	F	1
-input1.bam	FBtr0070603	72	34	F	3
-input1.bam	FBtr0070603	72	38	F	1
-input1.bam	FBtr0070603	72	42	F	1
-input1.bam	FBtr0070603	72	51	F	1
-input1.bam	FBtr0070603	72	56	F	1
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	1
-input1.bam	FBtr0070604	72	18	F	1
-input1.bam	FBtr0070604	72	22	F	1
-input1.bam	FBtr0070604	72	30	F	2
-input1.bam	FBtr0070604	72	31	F	10
-input1.bam	FBtr0070604	72	32	F	24
-input1.bam	FBtr0070604	72	57	F	1
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	1
-input1.bam	FBtr0070911	73	38	F	1
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	2
-input1.bam	FBtr0078490	72	17	F	1
-input1.bam	FBtr0078490	72	18	F	1
-input1.bam	FBtr0078490	72	25	F	1
-input1.bam	FBtr0078490	72	28	F	2
-input1.bam	FBtr0078490	72	38	F	1
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	1041
-input1.bam	FBtr0078580	72	3	F	3
-input1.bam	FBtr0078580	72	4	F	4
-input1.bam	FBtr0078580	72	5	F	5
-input1.bam	FBtr0078580	72	6	F	4
-input1.bam	FBtr0078580	72	7	F	1
-input1.bam	FBtr0078580	72	8	F	2
-input1.bam	FBtr0078580	72	11	F	1
-input1.bam	FBtr0078580	72	12	F	13
-input1.bam	FBtr0078580	72	14	F	7
-input1.bam	FBtr0078580	72	15	F	1
-input1.bam	FBtr0078580	72	16	F	4
-input1.bam	FBtr0078580	72	17	F	1
-input1.bam	FBtr0078580	72	19	F	1
-input1.bam	FBtr0078580	72	20	F	2
-input1.bam	FBtr0078580	72	21	F	5
-input1.bam	FBtr0078580	72	24	F	3
-input1.bam	FBtr0078580	72	25	F	2
-input1.bam	FBtr0078580	72	29	F	1
-input1.bam	FBtr0078580	72	31	F	1
-input1.bam	FBtr0078580	72	52	F	2
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	1
-input1.bam	FBtr0078790	73	17	F	2
-input1.bam	FBtr0078790	73	33	F	1
-input1.bam	FBtr0078790	73	42	F	4
-input1.bam	FBtr0078790	73	44	F	2
-input1.bam	FBtr0078790	73	46	F	1
-input1.bam	FBtr0078790	73	47	F	1
-input1.bam	FBtr0078790	73	52	F	1
-input1.bam	FBtr0078790	73	69	R	1
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	1
-input1.bam	FBtr0079064	72	3	F	1
-input1.bam	FBtr0079064	72	33	F	1
-input1.bam	FBtr0079064	72	52	F	1
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	2
-input1.bam	FBtr0079090	72	26	F	1
-input1.bam	FBtr0079090	72	33	F	1
-input1.bam	FBtr0079090	72	53	F	1
-input1.bam	FBtr0079090	72	56	R	1
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	1
-input1.bam	FBtr0079338	73	13	F	2
-input1.bam	FBtr0079338	73	14	F	1
-input1.bam	FBtr0079338	73	17	F	1
-input1.bam	FBtr0079338	73	25	F	1
-input1.bam	FBtr0079338	73	42	F	8
-input1.bam	FBtr0079338	73	43	F	1
-input1.bam	FBtr0079338	73	46	F	1
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	19
-input1.bam	FBtr0079528	71	3	F	55
-input1.bam	FBtr0079528	71	4	F	2
-input1.bam	FBtr0079528	71	8	F	4
-input1.bam	FBtr0079528	71	10	F	1
-input1.bam	FBtr0079528	71	11	F	2
-input1.bam	FBtr0079528	71	13	F	1
-input1.bam	FBtr0079528	71	14	F	4
-input1.bam	FBtr0079528	71	16	F	1
-input1.bam	FBtr0079528	71	17	F	4
-input1.bam	FBtr0079528	71	18	F	4
-input1.bam	FBtr0079528	71	28	F	1
-input1.bam	FBtr0079528	71	35	F	1
-input1.bam	FBtr0079528	71	36	F	1
-input1.bam	FBtr0079528	71	37	F	1
-input1.bam	FBtr0079528	71	51	F	5
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	13
-input1.bam	FBtr0079596	73	3	F	13
-input1.bam	FBtr0079596	73	4	F	31
-input1.bam	FBtr0079596	73	5	F	2
-input1.bam	FBtr0079596	73	6	F	11
-input1.bam	FBtr0079596	73	8	F	9
-input1.bam	FBtr0079596	73	9	F	12
-input1.bam	FBtr0079596	73	10	F	3
-input1.bam	FBtr0079596	73	11	F	19
-input1.bam	FBtr0079596	73	12	F	1
-input1.bam	FBtr0079596	73	13	F	20
-input1.bam	FBtr0079596	73	14	F	6
-input1.bam	FBtr0079596	73	15	F	1
-input1.bam	FBtr0079596	73	16	F	3
-input1.bam	FBtr0079596	73	17	F	2
-input1.bam	FBtr0079596	73	18	F	1
-input1.bam	FBtr0079596	73	19	F	1
-input1.bam	FBtr0079596	73	53	F	2
-input1.bam	FBtr0079596	73	54	F	2
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	1
-input1.bam	FBtr0079677	72	5	F	1
-input1.bam	FBtr0079677	72	52	F	1
-input1.bam	FBtr0079677	72	53	F	1
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	1
-input1.bam	FBtr0079690	72	22	F	1
-input1.bam	FBtr0079690	72	27	F	1
-input1.bam	FBtr0079690	72	33	F	2
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	3
-input1.bam	FBtr0079692	73	18	F	1
-input1.bam	FBtr0079692	73	25	F	1
-input1.bam	FBtr0079692	73	32	F	1
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	5
-input1.bam	FBtr0079693	72	25	F	1
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	5
-input1.bam	FBtr0079694	72	18	F	1
-input1.bam	FBtr0079694	72	52	F	1
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	1
-input1.bam	FBtr0079702	72	19	F	2
-input1.bam	FBtr0079702	72	56	F	1
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	2
-input1.bam	FBtr0079728	72	8	F	1
-input1.bam	FBtr0079728	72	19	F	1
-input1.bam	FBtr0079728	72	33	F	3
-input1.bam	FBtr0079728	72	56	F	1
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	1
-input1.bam	FBtr0079729	72	13	F	1
-input1.bam	FBtr0079729	72	52	F	1
-input1.bam	FBtr0079729	72	57	F	1
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	2
-input1.bam	FBtr0079752	72	7	F	1
-input1.bam	FBtr0079752	72	12	F	1
-input1.bam	FBtr0079752	72	33	F	2
-input1.bam	FBtr0079752	72	52	F	2
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	1
-input1.bam	FBtr0079820	74	46	F	2
-input1.bam	FBtr0079820	74	48	F	1
-input1.bam	FBtr0079820	74	49	F	1
-input1.bam	FBtr0079820	74	51	F	1
-input1.bam	FBtr0079820	74	54	F	4
-input1.bam	FBtr0079820	74	55	F	1
-input1.bam	FBtr0079820	74	56	F	2
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	13
-input1.bam	FBtr0080609	72	3	F	2
-input1.bam	FBtr0080609	72	4	F	10
-input1.bam	FBtr0080609	72	5	F	2
-input1.bam	FBtr0080609	72	7	F	19
-input1.bam	FBtr0080609	72	8	F	4
-input1.bam	FBtr0080609	72	9	F	3
-input1.bam	FBtr0080609	72	12	F	1
-input1.bam	FBtr0080609	72	15	F	1
-input1.bam	FBtr0080609	72	16	F	1
-input1.bam	FBtr0080609	72	17	F	2
-input1.bam	FBtr0080609	72	19	F	1
-input1.bam	FBtr0080609	72	20	F	1
-input1.bam	FBtr0080609	72	42	F	1
-input1.bam	FBtr0080609	72	51	F	1
-input1.bam	FBtr0080609	72	52	F	1
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	1
-input1.bam	FBtr0080644	72	4	F	2
-input1.bam	FBtr0080644	72	7	F	1
-input1.bam	FBtr0080644	72	12	F	2
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
-input1.bam	FBtr0080646	72	6	F	1
-input1.bam	FBtr0080646	72	7	F	1
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	3
-input1.bam	FBtr0080647	72	3	F	1
-input1.bam	FBtr0080647	72	6	F	2
-input1.bam	FBtr0080647	72	8	F	1
-input1.bam	FBtr0080647	72	11	F	2
-input1.bam	FBtr0080647	72	12	F	1
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	7	F	3
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
-input1.bam	FBtr0080663	71	3	F	56
-input1.bam	FBtr0080663	71	4	F	4
-input1.bam	FBtr0080663	71	7	F	1
-input1.bam	FBtr0080663	71	8	F	4
-input1.bam	FBtr0080663	71	12	F	2
-input1.bam	FBtr0080663	71	14	F	2
-input1.bam	FBtr0080663	71	15	F	1
-input1.bam	FBtr0080663	71	16	F	3
-input1.bam	FBtr0080663	71	17	F	7
-input1.bam	FBtr0080663	71	26	F	1
-input1.bam	FBtr0080663	71	32	F	2
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	9
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
-input1.bam	FBtr0080664	71	3	F	56
-input1.bam	FBtr0080664	71	4	F	4
-input1.bam	FBtr0080664	71	6	F	1
-input1.bam	FBtr0080664	71	7	F	1
-input1.bam	FBtr0080664	71	8	F	4
-input1.bam	FBtr0080664	71	9	F	1
-input1.bam	FBtr0080664	71	11	F	3
-input1.bam	FBtr0080664	71	12	F	3
-input1.bam	FBtr0080664	71	13	F	2
-input1.bam	FBtr0080664	71	14	F	3
-input1.bam	FBtr0080664	71	16	F	2
-input1.bam	FBtr0080664	71	17	F	10
-input1.bam	FBtr0080664	71	18	F	1
-input1.bam	FBtr0080664	71	21	F	1
-input1.bam	FBtr0080664	71	28	F	2
-input1.bam	FBtr0080664	71	32	F	1
-input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	34	F	1
-input1.bam	FBtr0080664	71	35	F	1
-input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	37	F	1
-input1.bam	FBtr0080664	71	38	F	1
-input1.bam	FBtr0080664	71	50	F	2
-input1.bam	FBtr0080664	71	51	F	7
-input1.bam	FBtr0080664	71	52	F	1
-input1.bam	FBtr0080664	71	56	F	1
-input1.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0070001	72	1	F	1
-input2.bam	FBtr0070001	72	12	F	1
-input2.bam	FBtr0070001	72	13	F	1
-input2.bam	FBtr0070001	72	18	F	1
-input2.bam	FBtr0070001	72	19	F	1
-input2.bam	FBtr0070001	72	28	F	1
-input2.bam	FBtr0070001	72	32	F	3
-input2.bam	FBtr0070001	72	53	F	2
-input2.bam	FBtr0070001	72	56	F	2
-input2.bam	FBtr0070001	72	57	F	1
-input2.bam	FBtr0070001	72	58	F	10
-input2.bam	FBtr0070001	72	72	F	0
-input2.bam	FBtr0070533	72	1	F	0
-input2.bam	FBtr0070533	72	15	F	1
-input2.bam	FBtr0070533	72	16	F	2
-input2.bam	FBtr0070533	72	17	F	2
-input2.bam	FBtr0070533	72	19	F	1
-input2.bam	FBtr0070533	72	20	F	1
-input2.bam	FBtr0070533	72	21	F	4
-input2.bam	FBtr0070533	72	22	F	20
-input2.bam	FBtr0070533	72	23	F	1
-input2.bam	FBtr0070533	72	24	F	6
-input2.bam	FBtr0070533	72	25	F	5
-input2.bam	FBtr0070533	72	27	F	1
-input2.bam	FBtr0070533	72	39	F	1
-input2.bam	FBtr0070533	72	72	F	0
-input2.bam	FBtr0070603	72	1	F	0
-input2.bam	FBtr0070603	72	12	F	2
-input2.bam	FBtr0070603	72	17	F	6
-input2.bam	FBtr0070603	72	19	F	3
-input2.bam	FBtr0070603	72	20	F	2
-input2.bam	FBtr0070603	72	21	F	1
-input2.bam	FBtr0070603	72	22	F	21
-input2.bam	FBtr0070603	72	25	F	1
-input2.bam	FBtr0070603	72	27	F	2
-input2.bam	FBtr0070603	72	28	F	2
-input2.bam	FBtr0070603	72	30	F	2
-input2.bam	FBtr0070603	72	31	F	2
-input2.bam	FBtr0070603	72	34	F	4
-input2.bam	FBtr0070603	72	35	F	2
-input2.bam	FBtr0070603	72	37	F	2
-input2.bam	FBtr0070603	72	38	F	2
-input2.bam	FBtr0070603	72	41	F	3
-input2.bam	FBtr0070603	72	51	F	2
-input2.bam	FBtr0070603	72	53	F	2
-input2.bam	FBtr0070603	72	72	F	0
-input2.bam	FBtr0070604	72	1	F	0
-input2.bam	FBtr0070604	72	3	F	1
-input2.bam	FBtr0070604	72	31	F	1
-input2.bam	FBtr0070604	72	32	F	5
-input2.bam	FBtr0070604	72	40	F	1
-input2.bam	FBtr0070604	72	53	F	3
-input2.bam	FBtr0070604	72	56	F	4
-input2.bam	FBtr0070604	72	57	F	18
-input2.bam	FBtr0070604	72	58	F	22
-input2.bam	FBtr0070604	72	72	F	0
-input2.bam	FBtr0070911	73	1	F	0
-input2.bam	FBtr0070911	73	11	F	1
-input2.bam	FBtr0070911	73	32	F	1
-input2.bam	FBtr0070911	73	48	F	1
-input2.bam	FBtr0070911	73	73	F	0
-input2.bam	FBtr0078490	72	1	F	3
-input2.bam	FBtr0078490	72	13	F	2
-input2.bam	FBtr0078490	72	14	F	4
-input2.bam	FBtr0078490	72	20	F	1
-input2.bam	FBtr0078490	72	30	F	1
-input2.bam	FBtr0078490	72	38	F	2
-input2.bam	FBtr0078490	72	41	F	1
-input2.bam	FBtr0078490	72	72	F	0
-input2.bam	FBtr0078580	72	1	F	146
-input2.bam	FBtr0078580	72	11	F	1
-input2.bam	FBtr0078580	72	13	F	1
-input2.bam	FBtr0078580	72	15	F	3
-input2.bam	FBtr0078580	72	16	F	5
-input2.bam	FBtr0078580	72	17	F	2
-input2.bam	FBtr0078580	72	18	F	9
-input2.bam	FBtr0078580	72	19	F	20
-input2.bam	FBtr0078580	72	20	F	21
-input2.bam	FBtr0078580	72	21	F	55
-input2.bam	FBtr0078580	72	22	F	1
-input2.bam	FBtr0078580	72	23	F	11
-input2.bam	FBtr0078580	72	24	F	24
-input2.bam	FBtr0078580	72	25	F	20
-input2.bam	FBtr0078580	72	26	F	19
-input2.bam	FBtr0078580	72	27	F	9
-input2.bam	FBtr0078580	72	28	F	2
-input2.bam	FBtr0078580	72	29	F	9
-input2.bam	FBtr0078580	72	30	F	2
-input2.bam	FBtr0078580	72	31	F	1
-input2.bam	FBtr0078580	72	40	F	5
-input2.bam	FBtr0078580	72	43	F	1
-input2.bam	FBtr0078580	72	52	F	3
-input2.bam	FBtr0078580	72	72	F	0
-input2.bam	FBtr0078790	73	1	F	0
-input2.bam	FBtr0078790	73	17	F	1
-input2.bam	FBtr0078790	73	41	F	2
-input2.bam	FBtr0078790	73	42	F	1
-input2.bam	FBtr0078790	73	46	F	1
-input2.bam	FBtr0078790	73	51	F	1
-input2.bam	FBtr0078790	73	52	F	2
-input2.bam	FBtr0078790	73	54	F	2
-input2.bam	FBtr0078790	73	73	F	0
-input2.bam	FBtr0079064	72	1	F	3
-input2.bam	FBtr0079064	72	52	F	2
-input2.bam	FBtr0079064	72	72	F	0
-input2.bam	FBtr0079090	72	1	F	1
-input2.bam	FBtr0079090	72	16	F	1
-input2.bam	FBtr0079090	72	20	F	1
-input2.bam	FBtr0079090	72	33	F	1
-input2.bam	FBtr0079090	72	35	F	1
-input2.bam	FBtr0079090	72	52	F	2
-input2.bam	FBtr0079090	72	72	F	0
-input2.bam	FBtr0079338	73	1	F	0
-input2.bam	FBtr0079338	73	12	F	2
-input2.bam	FBtr0079338	73	13	F	4
-input2.bam	FBtr0079338	73	14	F	6
-input2.bam	FBtr0079338	73	16	F	4
-input2.bam	FBtr0079338	73	17	F	2
-input2.bam	FBtr0079338	73	18	F	1
-input2.bam	FBtr0079338	73	39	F	1
-input2.bam	FBtr0079338	73	41	F	2
-input2.bam	FBtr0079338	73	42	F	1
-input2.bam	FBtr0079338	73	73	F	0
-input2.bam	FBtr0079528	71	1	F	2
-input2.bam	FBtr0079528	71	3	F	1
-input2.bam	FBtr0079528	71	10	F	4
-input2.bam	FBtr0079528	71	11	F	3
-input2.bam	FBtr0079528	71	13	F	4
-input2.bam	FBtr0079528	71	14	F	17
-input2.bam	FBtr0079528	71	15	F	19
-input2.bam	FBtr0079528	71	16	F	10
-input2.bam	FBtr0079528	71	17	F	12
-input2.bam	FBtr0079528	71	18	F	13
-input2.bam	FBtr0079528	71	19	F	6
-input2.bam	FBtr0079528	71	20	F	7
-input2.bam	FBtr0079528	71	21	F	13
-input2.bam	FBtr0079528	71	22	F	5
-input2.bam	FBtr0079528	71	23	F	1
-input2.bam	FBtr0079528	71	30	F	1
-input2.bam	FBtr0079528	71	31	F	2
-input2.bam	FBtr0079528	71	32	F	39
-input2.bam	FBtr0079528	71	33	F	4
-input2.bam	FBtr0079528	71	34	F	27
-input2.bam	FBtr0079528	71	35	F	122
-input2.bam	FBtr0079528	71	36	F	6
-input2.bam	FBtr0079528	71	37	F	21
-input2.bam	FBtr0079528	71	38	F	12
-input2.bam	FBtr0079528	71	43	F	1
-input2.bam	FBtr0079528	71	46	F	1
-input2.bam	FBtr0079528	71	50	F	2
-input2.bam	FBtr0079528	71	51	F	4
-input2.bam	FBtr0079528	71	53	F	1
-input2.bam	FBtr0079528	71	56	F	2
-input2.bam	FBtr0079528	71	57	F	3
-input2.bam	FBtr0079528	71	71	F	0
-input2.bam	FBtr0079596	73	1	F	22
-input2.bam	FBtr0079596	73	2	F	1
-input2.bam	FBtr0079596	73	3	F	8
-input2.bam	FBtr0079596	73	4	F	5
-input2.bam	FBtr0079596	73	5	F	9
-input2.bam	FBtr0079596	73	6	F	1
-input2.bam	FBtr0079596	73	8	F	2
-input2.bam	FBtr0079596	73	9	F	2
-input2.bam	FBtr0079596	73	11	F	18
-input2.bam	FBtr0079596	73	12	F	44
-input2.bam	FBtr0079596	73	13	F	40
-input2.bam	FBtr0079596	73	14	F	36
-input2.bam	FBtr0079596	73	15	F	81
-input2.bam	FBtr0079596	73	16	F	13
-input2.bam	FBtr0079596	73	17	F	11
-input2.bam	FBtr0079596	73	18	F	12
-input2.bam	FBtr0079596	73	19	F	4
-input2.bam	FBtr0079596	73	22	F	2
-input2.bam	FBtr0079596	73	42	F	1
-input2.bam	FBtr0079596	73	53	F	3
-input2.bam	FBtr0079596	73	59	R	1
-input2.bam	FBtr0079596	73	73	F	0
-input2.bam	FBtr0079677	72	1	F	2
-input2.bam	FBtr0079677	72	15	F	1
-input2.bam	FBtr0079677	72	24	F	1
-input2.bam	FBtr0079677	72	43	F	1
-input2.bam	FBtr0079677	72	52	F	1
-input2.bam	FBtr0079677	72	54	F	1
-input2.bam	FBtr0079677	72	72	F	0
-input2.bam	FBtr0079690	72	1	F	1
-input2.bam	FBtr0079690	72	15	F	1
-input2.bam	FBtr0079690	72	17	F	1
-input2.bam	FBtr0079690	72	19	F	1
-input2.bam	FBtr0079690	72	21	F	1
-input2.bam	FBtr0079690	72	72	F	0
-input2.bam	FBtr0079692	73	1	F	0
-input2.bam	FBtr0079692	73	4	F	1
-input2.bam	FBtr0079692	73	7	F	1
-input2.bam	FBtr0079692	73	12	F	1
-input2.bam	FBtr0079692	73	15	F	1
-input2.bam	FBtr0079692	73	73	F	0
-input2.bam	FBtr0079693	72	1	F	3
-input2.bam	FBtr0079693	72	17	F	2
-input2.bam	FBtr0079693	72	20	F	1
-input2.bam	FBtr0079693	72	45	F	1
-input2.bam	FBtr0079693	72	52	F	1
-input2.bam	FBtr0079693	72	54	F	1
-input2.bam	FBtr0079693	72	72	F	0
-input2.bam	FBtr0079694	72	1	F	2
-input2.bam	FBtr0079694	72	16	F	1
-input2.bam	FBtr0079694	72	17	F	1
-input2.bam	FBtr0079694	72	18	F	1
-input2.bam	FBtr0079694	72	52	F	1
-input2.bam	FBtr0079694	72	72	F	0
-input2.bam	FBtr0079702	72	1	F	2
-input2.bam	FBtr0079702	72	52	F	2
-input2.bam	FBtr0079702	72	72	F	0
-input2.bam	FBtr0079728	72	1	F	3
-input2.bam	FBtr0079728	72	20	F	1
-input2.bam	FBtr0079728	72	52	F	2
-input2.bam	FBtr0079728	72	72	F	0
-input2.bam	FBtr0079729	72	1	F	1
-input2.bam	FBtr0079729	72	19	F	1
-input2.bam	FBtr0079729	72	33	F	1
-input2.bam	FBtr0079729	72	53	F	1
-input2.bam	FBtr0079729	72	72	F	0
-input2.bam	FBtr0079752	72	1	F	0
-input2.bam	FBtr0079752	72	49	F	1
-input2.bam	FBtr0079752	72	52	F	1
-input2.bam	FBtr0079752	72	72	F	0
-input2.bam	FBtr0079820	74	1	F	0
-input2.bam	FBtr0079820	74	39	F	1
-input2.bam	FBtr0079820	74	52	F	1
-input2.bam	FBtr0079820	74	53	F	28
-input2.bam	FBtr0079820	74	54	F	26
-input2.bam	FBtr0079820	74	55	F	10
-input2.bam	FBtr0079820	74	56	F	2
-input2.bam	FBtr0079820	74	57	F	6
-input2.bam	FBtr0079820	74	58	F	5
-input2.bam	FBtr0079820	74	59	F	11
-input2.bam	FBtr0079820	74	60	F	19
-input2.bam	FBtr0079820	74	74	F	0
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	20	F	1
-input2.bam	FBtr0080609	72	21	F	2
-input2.bam	FBtr0080609	72	22	F	1
-input2.bam	FBtr0080609	72	33	F	1
-input2.bam	FBtr0080609	72	39	F	1
-input2.bam	FBtr0080609	72	52	F	1
-input2.bam	FBtr0080609	72	53	F	1
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	57	F	1
-input2.bam	FBtr0080644	72	58	F	7
-input2.bam	FBtr0080644	72	72	F	0
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	1
-input2.bam	FBtr0080646	72	57	F	2
-input2.bam	FBtr0080646	72	58	F	9
-input2.bam	FBtr0080646	72	72	F	0
-input2.bam	FBtr0080647	72	1	F	1
-input2.bam	FBtr0080647	72	57	F	4
-input2.bam	FBtr0080647	72	58	F	7
-input2.bam	FBtr0080647	72	72	F	0
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	11
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	2
-input2.bam	FBtr0080663	71	11	F	1
-input2.bam	FBtr0080663	71	12	F	4
-input2.bam	FBtr0080663	71	13	F	4
-input2.bam	FBtr0080663	71	14	F	22
-input2.bam	FBtr0080663	71	15	F	14
-input2.bam	FBtr0080663	71	16	F	5
-input2.bam	FBtr0080663	71	17	F	12
-input2.bam	FBtr0080663	71	18	F	5
-input2.bam	FBtr0080663	71	19	F	6
-input2.bam	FBtr0080663	71	20	F	6
-input2.bam	FBtr0080663	71	21	F	13
-input2.bam	FBtr0080663	71	22	F	3
-input2.bam	FBtr0080663	71	31	F	1
-input2.bam	FBtr0080663	71	50	F	2
-input2.bam	FBtr0080663	71	51	F	1
-input2.bam	FBtr0080663	71	52	F	2
-input2.bam	FBtr0080663	71	57	F	3
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	3	F	2
-input2.bam	FBtr0080664	71	10	F	1
-input2.bam	FBtr0080664	71	11	F	2
-input2.bam	FBtr0080664	71	12	F	3
-input2.bam	FBtr0080664	71	13	F	11
-input2.bam	FBtr0080664	71	14	F	11
-input2.bam	FBtr0080664	71	15	F	17
-input2.bam	FBtr0080664	71	16	F	15
-input2.bam	FBtr0080664	71	17	F	13
-input2.bam	FBtr0080664	71	18	F	10
-input2.bam	FBtr0080664	71	19	F	8
-input2.bam	FBtr0080664	71	20	F	1
-input2.bam	FBtr0080664	71	21	F	15
-input2.bam	FBtr0080664	71	22	F	6
-input2.bam	FBtr0080664	71	24	F	1
-input2.bam	FBtr0080664	71	30	F	1
-input2.bam	FBtr0080664	71	31	F	3
-input2.bam	FBtr0080664	71	32	F	39
-input2.bam	FBtr0080664	71	33	F	4
-input2.bam	FBtr0080664	71	34	F	37
-input2.bam	FBtr0080664	71	35	F	135
-input2.bam	FBtr0080664	71	36	F	8
-input2.bam	FBtr0080664	71	37	F	25
-input2.bam	FBtr0080664	71	38	F	8
-input2.bam	FBtr0080664	71	39	F	1
-input2.bam	FBtr0080664	71	42	F	1
-input2.bam	FBtr0080664	71	47	F	1
-input2.bam	FBtr0080664	71	50	F	2
-input2.bam	FBtr0080664	71	52	F	1
-input2.bam	FBtr0080664	71	53	F	1
-input2.bam	FBtr0080664	71	56	F	1
-input2.bam	FBtr0080664	71	57	F	2
-input2.bam	FBtr0080664	71	62	R	1
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count20-30.tab
--- a/test-data/count20-30.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,350 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input2.bam	FBtr0070001	72	1	F	0
-input2.bam	FBtr0070001	72	13	F	1
-input2.bam	FBtr0070001	72	19	F	1
-input2.bam	FBtr0070001	72	28	F	1
-input2.bam	FBtr0070001	72	32	F	3
-input2.bam	FBtr0070001	72	53	F	1
-input2.bam	FBtr0070001	72	72	F	0
-input2.bam	FBtr0070533	72	1	F	0
-input2.bam	FBtr0070533	72	16	F	1
-input2.bam	FBtr0070533	72	19	F	1
-input2.bam	FBtr0070533	72	20	F	1
-input2.bam	FBtr0070533	72	21	F	2
-input2.bam	FBtr0070533	72	22	F	10
-input2.bam	FBtr0070533	72	72	F	0
-input2.bam	FBtr0070603	72	1	F	0
-input2.bam	FBtr0070603	72	17	F	4
-input2.bam	FBtr0070603	72	19	F	2
-input2.bam	FBtr0070603	72	20	F	1
-input2.bam	FBtr0070603	72	22	F	9
-input2.bam	FBtr0070603	72	27	F	1
-input2.bam	FBtr0070603	72	28	F	2
-input2.bam	FBtr0070603	72	30	F	1
-input2.bam	FBtr0070603	72	31	F	1
-input2.bam	FBtr0070603	72	34	F	2
-input2.bam	FBtr0070603	72	35	F	1
-input2.bam	FBtr0070603	72	37	F	1
-input2.bam	FBtr0070603	72	41	F	1
-input2.bam	FBtr0070603	72	51	F	2
-input2.bam	FBtr0070603	72	72	F	0
-input2.bam	FBtr0070604	72	1	F	0
-input2.bam	FBtr0070604	72	31	F	1
-input2.bam	FBtr0070604	72	32	F	5
-input2.bam	FBtr0070604	72	53	F	2
-input2.bam	FBtr0070604	72	72	F	0
-input2.bam	FBtr0070911	73	1	F	0
-input2.bam	FBtr0070911	73	32	F	1
-input2.bam	FBtr0070911	73	73	F	0
-input2.bam	FBtr0078490	72	1	F	3
-input2.bam	FBtr0078490	72	13	F	1
-input2.bam	FBtr0078490	72	20	F	1
-input2.bam	FBtr0078490	72	30	F	1
-input2.bam	FBtr0078490	72	72	F	0
-input2.bam	FBtr0078580	72	1	F	3
-input2.bam	FBtr0078580	72	11	F	1
-input2.bam	FBtr0078580	72	13	F	1
-input2.bam	FBtr0078580	72	15	F	2
-input2.bam	FBtr0078580	72	16	F	3
-input2.bam	FBtr0078580	72	17	F	2
-input2.bam	FBtr0078580	72	18	F	9
-input2.bam	FBtr0078580	72	19	F	19
-input2.bam	FBtr0078580	72	20	F	19
-input2.bam	FBtr0078580	72	21	F	39
-input2.bam	FBtr0078580	72	25	F	1
-input2.bam	FBtr0078580	72	26	F	1
-input2.bam	FBtr0078580	72	28	F	2
-input2.bam	FBtr0078580	72	29	F	1
-input2.bam	FBtr0078580	72	40	F	1
-input2.bam	FBtr0078580	72	72	F	0
-input2.bam	FBtr0078790	73	1	F	0
-input2.bam	FBtr0078790	73	42	F	1
-input2.bam	FBtr0078790	73	51	F	1
-input2.bam	FBtr0078790	73	52	F	2
-input2.bam	FBtr0078790	73	73	F	0
-input2.bam	FBtr0079064	72	1	F	0
-input2.bam	FBtr0079064	72	72	F	0
-input2.bam	FBtr0079090	72	1	F	0
-input2.bam	FBtr0079090	72	16	F	1
-input2.bam	FBtr0079090	72	72	F	0
-input2.bam	FBtr0079338	73	1	F	0
-input2.bam	FBtr0079338	73	41	F	2
-input2.bam	FBtr0079338	73	42	F	1
-input2.bam	FBtr0079338	73	73	F	0
-input2.bam	FBtr0079528	71	1	F	0
-input2.bam	FBtr0079528	71	3	F	1
-input2.bam	FBtr0079528	71	10	F	4
-input2.bam	FBtr0079528	71	11	F	3
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-input1.bam	FBtr0079596	73	3	F	11
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-input1.bam	FBtr0080644	72	1	F	1
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-input1.bam	FBtr0080646	72	1	F	0
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-input1.bam	FBtr0080660	72	1	F	0
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-input1.bam	FBtr0080660	72	7	F	2
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-input1.bam	FBtr0080663	71	1	F	6
-input1.bam	FBtr0080663	71	3	F	56
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-input1.bam	FBtr0080663	71	8	F	2
-input1.bam	FBtr0080663	71	51	F	1
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-input1.bam	FBtr0080664	71	1	F	6
-input1.bam	FBtr0080664	71	3	F	56
-input1.bam	FBtr0080664	71	4	F	4
-input1.bam	FBtr0080664	71	6	F	1
-input1.bam	FBtr0080664	71	7	F	1
-input1.bam	FBtr0080664	71	8	F	3
-input1.bam	FBtr0080664	71	9	F	1
-input1.bam	FBtr0080664	71	12	F	1
-input1.bam	FBtr0080664	71	13	F	2
-input1.bam	FBtr0080664	71	33	F	1
-input1.bam	FBtr0080664	71	36	F	1
-input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_1.pdf
Binary file test-data/count_1.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_1_chr.tab
--- a/test-data/count_1_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input_single_chr.bam	1	80	1	F	1
-input_single_chr.bam	1	80	80	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_5_chr.tab
--- a/test-data/count_5_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input_5_chr.bam	1	80	1	F	1
-input_5_chr.bam	1	80	80	F	0
-input_5_chr.bam	2	80	1	F	1
-input_5_chr.bam	2	80	80	F	0
-input_5_chr.bam	3	80	1	F	1
-input_5_chr.bam	3	80	80	F	0
-input_5_chr.bam	4	80	1	F	1
-input_5_chr.bam	4	80	80	F	0
-input_5_chr.bam	5	80	1	F	1
-input_5_chr.bam	5	80	80	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_cluster_5.pdf
Binary file test-data/count_cluster_5.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_cluster_5.tab
--- a/test-data/count_cluster_5.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,265 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
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-input1.bam	FBtr0070603	72	21	F	68
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-input1.bam	FBtr0070604	72	1	F	1
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-input1.bam	FBtr0070604	72	31	F	36
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-input1.bam	FBtr0070911	73	1	F	0
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-input1.bam	FBtr0078490	72	26	F	3
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-input1.bam	FBtr0078580	72	1	F	0
-input1.bam	FBtr0078580	72	16	F	1102
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-input1.bam	FBtr0079338	73	1	F	0
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-input1.bam	FBtr0079528	71	1	F	0
-input1.bam	FBtr0079528	71	9	F	97
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-input1.bam	FBtr0079596	73	1	F	0
-input1.bam	FBtr0079596	73	10	F	148
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-input2.bam	FBtr0079090	72	34	F	2
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-input2.bam	FBtr0079338	73	1	F	0
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-input2.bam	FBtr0079528	71	1	F	0
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-input2.bam	FBtr0079596	73	1	F	0
-input2.bam	FBtr0079596	73	11	F	311
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-input2.bam	FBtr0079596	73	59	R	1
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-input2.bam	FBtr0079677	72	1	F	2
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-input2.bam	FBtr0079694	72	1	F	2
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-input2.bam	FBtr0080647	72	1	F	1
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-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	11
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	2
-input2.bam	FBtr0080663	71	16	F	95
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-input2.bam	FBtr0080663	71	53	F	8
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-input2.bam	FBtr0080664	71	1	F	0
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-input2.bam	FBtr0080664	71	43	F	270
-input2.bam	FBtr0080664	71	62	R	1
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-input2.bam	FBtr0080664	71	71	R	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/count_single_chr.tab
--- a/test-data/count_single_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input_single_chr.bam	Anopheles_C_Virus|KU169878	8919	1	F	0
-input_single_chr.bam	Anopheles_C_Virus|KU169878	8919	749	R	1
-input_single_chr.bam	Anopheles_C_Virus|KU169878	8919	8919	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/counts_coverage_1.pdf
Binary file test-data/counts_coverage_1.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/counts_coverage_5.pdf
Binary file test-data/counts_coverage_5.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/coverage.pdf
Binary file test-data/coverage.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/coverage.tab
--- a/test-data/coverage.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3109 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
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-input1.bam	FBtr0070001	72	3	F	1
-input1.bam	FBtr0070001	72	4	F	1
-input1.bam	FBtr0070001	72	5	F	1
-input1.bam	FBtr0070001	72	6	F	1
-input1.bam	FBtr0070001	72	7	F	7
-input1.bam	FBtr0070001	72	8	F	10
-input1.bam	FBtr0070001	72	9	F	10
-input1.bam	FBtr0070001	72	10	F	10
-input1.bam	FBtr0070001	72	11	F	12
-input1.bam	FBtr0070001	72	12	F	12
-input1.bam	FBtr0070001	72	13	F	12
-input1.bam	FBtr0070001	72	14	F	12
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-input1.bam	FBtr0070001	72	16	F	13
-input1.bam	FBtr0070001	72	17	F	14
-input1.bam	FBtr0070001	72	18	F	14
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-input1.bam	FBtr0070001	72	72	F	0
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-input1.bam	FBtr0070533	72	6	F	1
-input1.bam	FBtr0070533	72	7	F	1
-input1.bam	FBtr0070533	72	8	F	1
-input1.bam	FBtr0070533	72	9	F	1
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-input1.bam	FBtr0070533	72	11	F	1
-input1.bam	FBtr0070533	72	12	F	3
-input1.bam	FBtr0070533	72	13	F	3
-input1.bam	FBtr0070533	72	14	F	3
-input1.bam	FBtr0070533	72	15	F	4
-input1.bam	FBtr0070533	72	16	F	3
-input1.bam	FBtr0070533	72	17	F	3
-input1.bam	FBtr0070533	72	18	F	3
-input1.bam	FBtr0070533	72	19	F	8
-input1.bam	FBtr0070533	72	20	F	9
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-input1.bam	FBtr0070533	72	22	F	11
-input1.bam	FBtr0070533	72	23	F	11
-input1.bam	FBtr0070533	72	24	F	11
-input1.bam	FBtr0070533	72	25	F	12
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-input1.bam	FBtr0070533	72	28	F	14
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-input1.bam	FBtr0070533	72	34	F	15
-input1.bam	FBtr0070533	72	35	F	16
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-input1.bam	FBtr0070533	72	40	F	17
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-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	2
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-input1.bam	FBtr0070603	72	3	F	3
-input1.bam	FBtr0070603	72	4	F	4
-input1.bam	FBtr0070603	72	5	F	4
-input1.bam	FBtr0070603	72	6	F	5
-input1.bam	FBtr0070603	72	7	F	12
-input1.bam	FBtr0070603	72	8	F	16
-input1.bam	FBtr0070603	72	9	F	23
-input1.bam	FBtr0070603	72	10	F	23
-input1.bam	FBtr0070603	72	11	F	23
-input1.bam	FBtr0070603	72	12	F	25
-input1.bam	FBtr0070603	72	13	F	26
-input1.bam	FBtr0070603	72	14	F	26
-input1.bam	FBtr0070603	72	15	F	28
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-input1.bam	FBtr0070603	72	17	F	32
-input1.bam	FBtr0070603	72	18	F	33
-input1.bam	FBtr0070603	72	19	F	41
-input1.bam	FBtr0070603	72	20	F	44
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-input1.bam	FBtr0070603	72	23	F	48
-input1.bam	FBtr0070603	72	24	F	30
-input1.bam	FBtr0070603	72	25	F	30
-input1.bam	FBtr0070603	72	26	F	36
-input1.bam	FBtr0070603	72	27	F	39
-input1.bam	FBtr0070603	72	28	F	39
-input1.bam	FBtr0070603	72	29	F	38
-input1.bam	FBtr0070603	72	30	F	38
-input1.bam	FBtr0070603	72	31	F	38
-input1.bam	FBtr0070603	72	32	F	38
-input1.bam	FBtr0070603	72	33	F	37
-input1.bam	FBtr0070603	72	34	F	39
-input1.bam	FBtr0070603	72	35	F	35
-input1.bam	FBtr0070603	72	36	F	34
-input1.bam	FBtr0070603	72	37	F	34
-input1.bam	FBtr0070603	72	38	F	35
-input1.bam	FBtr0070603	72	39	F	34
-input1.bam	FBtr0070603	72	40	F	33
-input1.bam	FBtr0070603	72	41	F	32
-input1.bam	FBtr0070603	72	42	F	21
-input1.bam	FBtr0070603	72	43	F	21
-input1.bam	FBtr0070603	72	44	F	20
-input1.bam	FBtr0070603	72	45	F	18
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-input1.bam	FBtr0070603	72	48	F	15
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-input2.bam	FBtr0079752	72	59	F	2
-input2.bam	FBtr0079752	72	60	F	2
-input2.bam	FBtr0079752	72	61	F	2
-input2.bam	FBtr0079752	72	62	F	2
-input2.bam	FBtr0079752	72	63	F	2
-input2.bam	FBtr0079752	72	64	F	2
-input2.bam	FBtr0079752	72	65	F	2
-input2.bam	FBtr0079752	72	66	F	2
-input2.bam	FBtr0079752	72	67	F	2
-input2.bam	FBtr0079752	72	68	F	2
-input2.bam	FBtr0079752	72	69	F	1
-input2.bam	FBtr0079752	72	70	F	1
-input2.bam	FBtr0079752	72	71	F	1
-input2.bam	FBtr0079752	72	72	F	1
-input2.bam	FBtr0079820	74	1	F	0
-input2.bam	FBtr0079820	74	39	F	1
-input2.bam	FBtr0079820	74	40	F	1
-input2.bam	FBtr0079820	74	41	F	1
-input2.bam	FBtr0079820	74	42	F	1
-input2.bam	FBtr0079820	74	43	F	1
-input2.bam	FBtr0079820	74	44	F	1
-input2.bam	FBtr0079820	74	45	F	1
-input2.bam	FBtr0079820	74	46	F	1
-input2.bam	FBtr0079820	74	47	F	1
-input2.bam	FBtr0079820	74	48	F	1
-input2.bam	FBtr0079820	74	49	F	1
-input2.bam	FBtr0079820	74	50	F	1
-input2.bam	FBtr0079820	74	51	F	1
-input2.bam	FBtr0079820	74	52	F	2
-input2.bam	FBtr0079820	74	53	F	30
-input2.bam	FBtr0079820	74	54	F	56
-input2.bam	FBtr0079820	74	55	F	65
-input2.bam	FBtr0079820	74	56	F	67
-input2.bam	FBtr0079820	74	57	F	73
-input2.bam	FBtr0079820	74	58	F	78
-input2.bam	FBtr0079820	74	59	F	89
-input2.bam	FBtr0079820	74	60	F	108
-input2.bam	FBtr0079820	74	61	F	108
-input2.bam	FBtr0079820	74	62	F	108
-input2.bam	FBtr0079820	74	63	F	108
-input2.bam	FBtr0079820	74	64	F	108
-input2.bam	FBtr0079820	74	65	F	108
-input2.bam	FBtr0079820	74	66	F	108
-input2.bam	FBtr0079820	74	67	F	108
-input2.bam	FBtr0079820	74	68	F	108
-input2.bam	FBtr0079820	74	69	F	108
-input2.bam	FBtr0079820	74	70	F	107
-input2.bam	FBtr0079820	74	71	F	105
-input2.bam	FBtr0079820	74	72	F	103
-input2.bam	FBtr0079820	74	73	F	54
-input2.bam	FBtr0079820	74	74	F	30
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	20	F	1
-input2.bam	FBtr0080609	72	21	F	3
-input2.bam	FBtr0080609	72	22	F	4
-input2.bam	FBtr0080609	72	23	F	4
-input2.bam	FBtr0080609	72	24	F	4
-input2.bam	FBtr0080609	72	25	F	4
-input2.bam	FBtr0080609	72	26	F	4
-input2.bam	FBtr0080609	72	27	F	4
-input2.bam	FBtr0080609	72	28	F	4
-input2.bam	FBtr0080609	72	29	F	4
-input2.bam	FBtr0080609	72	30	F	4
-input2.bam	FBtr0080609	72	31	F	4
-input2.bam	FBtr0080609	72	32	F	4
-input2.bam	FBtr0080609	72	33	F	5
-input2.bam	FBtr0080609	72	34	F	5
-input2.bam	FBtr0080609	72	35	F	5
-input2.bam	FBtr0080609	72	36	F	5
-input2.bam	FBtr0080609	72	37	F	5
-input2.bam	FBtr0080609	72	38	F	4
-input2.bam	FBtr0080609	72	39	F	4
-input2.bam	FBtr0080609	72	40	F	4
-input2.bam	FBtr0080609	72	41	F	4
-input2.bam	FBtr0080609	72	42	F	4
-input2.bam	FBtr0080609	72	43	F	4
-input2.bam	FBtr0080609	72	44	F	4
-input2.bam	FBtr0080609	72	45	F	3
-input2.bam	FBtr0080609	72	46	F	2
-input2.bam	FBtr0080609	72	47	F	2
-input2.bam	FBtr0080609	72	48	F	2
-input2.bam	FBtr0080609	72	49	F	2
-input2.bam	FBtr0080609	72	50	F	2
-input2.bam	FBtr0080609	72	51	F	2
-input2.bam	FBtr0080609	72	52	F	3
-input2.bam	FBtr0080609	72	53	F	4
-input2.bam	FBtr0080609	72	54	F	4
-input2.bam	FBtr0080609	72	55	F	3
-input2.bam	FBtr0080609	72	56	F	2
-input2.bam	FBtr0080609	72	57	F	2
-input2.bam	FBtr0080609	72	58	F	2
-input2.bam	FBtr0080609	72	59	F	2
-input2.bam	FBtr0080609	72	60	F	2
-input2.bam	FBtr0080609	72	61	F	2
-input2.bam	FBtr0080609	72	62	F	2
-input2.bam	FBtr0080609	72	63	F	2
-input2.bam	FBtr0080609	72	64	F	2
-input2.bam	FBtr0080609	72	65	F	2
-input2.bam	FBtr0080609	72	66	F	2
-input2.bam	FBtr0080609	72	67	F	2
-input2.bam	FBtr0080609	72	68	F	2
-input2.bam	FBtr0080609	72	69	F	2
-input2.bam	FBtr0080609	72	70	F	1
-input2.bam	FBtr0080609	72	71	F	1
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	57	F	1
-input2.bam	FBtr0080644	72	58	F	8
-input2.bam	FBtr0080644	72	59	F	8
-input2.bam	FBtr0080644	72	60	F	8
-input2.bam	FBtr0080644	72	61	F	8
-input2.bam	FBtr0080644	72	62	F	8
-input2.bam	FBtr0080644	72	63	F	8
-input2.bam	FBtr0080644	72	64	F	8
-input2.bam	FBtr0080644	72	65	F	8
-input2.bam	FBtr0080644	72	66	F	8
-input2.bam	FBtr0080644	72	67	F	8
-input2.bam	FBtr0080644	72	68	F	8
-input2.bam	FBtr0080644	72	69	F	8
-input2.bam	FBtr0080644	72	70	F	8
-input2.bam	FBtr0080644	72	71	F	8
-input2.bam	FBtr0080644	72	72	F	7
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	1
-input2.bam	FBtr0080646	72	52	F	1
-input2.bam	FBtr0080646	72	53	F	1
-input2.bam	FBtr0080646	72	54	F	1
-input2.bam	FBtr0080646	72	55	F	1
-input2.bam	FBtr0080646	72	56	F	1
-input2.bam	FBtr0080646	72	57	F	3
-input2.bam	FBtr0080646	72	58	F	12
-input2.bam	FBtr0080646	72	59	F	12
-input2.bam	FBtr0080646	72	60	F	12
-input2.bam	FBtr0080646	72	61	F	12
-input2.bam	FBtr0080646	72	62	F	12
-input2.bam	FBtr0080646	72	63	F	12
-input2.bam	FBtr0080646	72	64	F	12
-input2.bam	FBtr0080646	72	65	F	12
-input2.bam	FBtr0080646	72	66	F	12
-input2.bam	FBtr0080646	72	67	F	12
-input2.bam	FBtr0080646	72	68	F	12
-input2.bam	FBtr0080646	72	69	F	12
-input2.bam	FBtr0080646	72	70	F	12
-input2.bam	FBtr0080646	72	71	F	12
-input2.bam	FBtr0080646	72	72	F	10
-input2.bam	FBtr0080647	72	1	F	1
-input2.bam	FBtr0080647	72	2	F	1
-input2.bam	FBtr0080647	72	3	F	1
-input2.bam	FBtr0080647	72	4	F	1
-input2.bam	FBtr0080647	72	5	F	1
-input2.bam	FBtr0080647	72	6	F	1
-input2.bam	FBtr0080647	72	7	F	1
-input2.bam	FBtr0080647	72	8	F	1
-input2.bam	FBtr0080647	72	9	F	1
-input2.bam	FBtr0080647	72	10	F	1
-input2.bam	FBtr0080647	72	11	F	1
-input2.bam	FBtr0080647	72	12	F	1
-input2.bam	FBtr0080647	72	13	F	1
-input2.bam	FBtr0080647	72	14	F	1
-input2.bam	FBtr0080647	72	15	F	1
-input2.bam	FBtr0080647	72	16	F	1
-input2.bam	FBtr0080647	72	17	F	1
-input2.bam	FBtr0080647	72	18	F	1
-input2.bam	FBtr0080647	72	57	F	4
-input2.bam	FBtr0080647	72	58	F	11
-input2.bam	FBtr0080647	72	59	F	11
-input2.bam	FBtr0080647	72	60	F	11
-input2.bam	FBtr0080647	72	61	F	11
-input2.bam	FBtr0080647	72	62	F	11
-input2.bam	FBtr0080647	72	63	F	11
-input2.bam	FBtr0080647	72	64	F	11
-input2.bam	FBtr0080647	72	65	F	11
-input2.bam	FBtr0080647	72	66	F	11
-input2.bam	FBtr0080647	72	67	F	11
-input2.bam	FBtr0080647	72	68	F	11
-input2.bam	FBtr0080647	72	69	F	11
-input2.bam	FBtr0080647	72	70	F	11
-input2.bam	FBtr0080647	72	71	F	11
-input2.bam	FBtr0080647	72	72	F	9
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	11
-input2.bam	FBtr0080660	72	59	F	11
-input2.bam	FBtr0080660	72	60	F	11
-input2.bam	FBtr0080660	72	61	F	11
-input2.bam	FBtr0080660	72	62	F	11
-input2.bam	FBtr0080660	72	63	F	11
-input2.bam	FBtr0080660	72	64	F	11
-input2.bam	FBtr0080660	72	65	F	11
-input2.bam	FBtr0080660	72	66	F	11
-input2.bam	FBtr0080660	72	67	F	11
-input2.bam	FBtr0080660	72	68	F	11
-input2.bam	FBtr0080660	72	69	F	11
-input2.bam	FBtr0080660	72	70	F	11
-input2.bam	FBtr0080660	72	71	F	11
-input2.bam	FBtr0080660	72	72	F	11
-input2.bam	FBtr0080663	71	1	F	2
-input2.bam	FBtr0080663	71	2	F	2
-input2.bam	FBtr0080663	71	3	F	2
-input2.bam	FBtr0080663	71	4	F	2
-input2.bam	FBtr0080663	71	5	F	2
-input2.bam	FBtr0080663	71	6	F	2
-input2.bam	FBtr0080663	71	7	F	2
-input2.bam	FBtr0080663	71	8	F	2
-input2.bam	FBtr0080663	71	9	F	2
-input2.bam	FBtr0080663	71	10	F	2
-input2.bam	FBtr0080663	71	11	F	3
-input2.bam	FBtr0080663	71	12	F	7
-input2.bam	FBtr0080663	71	13	F	11
-input2.bam	FBtr0080663	71	14	F	33
-input2.bam	FBtr0080663	71	15	F	47
-input2.bam	FBtr0080663	71	16	F	52
-input2.bam	FBtr0080663	71	17	F	64
-input2.bam	FBtr0080663	71	18	F	69
-input2.bam	FBtr0080663	71	19	F	75
-input2.bam	FBtr0080663	71	20	F	81
-input2.bam	FBtr0080663	71	21	F	94
-input2.bam	FBtr0080663	71	22	F	97
-input2.bam	FBtr0080663	71	23	F	95
-input2.bam	FBtr0080663	71	24	F	95
-input2.bam	FBtr0080663	71	25	F	95
-input2.bam	FBtr0080663	71	26	F	95
-input2.bam	FBtr0080663	71	27	F	95
-input2.bam	FBtr0080663	71	28	F	95
-input2.bam	FBtr0080663	71	29	F	95
-input2.bam	FBtr0080663	71	30	F	95
-input2.bam	FBtr0080663	71	31	F	96
-input2.bam	FBtr0080663	71	32	F	62
-input2.bam	FBtr0080663	71	33	F	41
-input2.bam	FBtr0080663	71	34	F	40
-input2.bam	FBtr0080663	71	35	F	34
-input2.bam	FBtr0080663	71	36	F	12
-input2.bam	FBtr0080663	71	37	F	6
-input2.bam	FBtr0080663	71	38	F	5
-input2.bam	FBtr0080663	71	39	F	4
-input2.bam	FBtr0080663	71	40	F	3
-input2.bam	FBtr0080663	71	41	F	2
-input2.bam	FBtr0080663	71	42	F	1
-input2.bam	FBtr0080663	71	43	F	1
-input2.bam	FBtr0080663	71	44	F	1
-input2.bam	FBtr0080663	71	45	F	1
-input2.bam	FBtr0080663	71	46	F	1
-input2.bam	FBtr0080663	71	47	F	1
-input2.bam	FBtr0080663	71	50	F	2
-input2.bam	FBtr0080663	71	51	F	3
-input2.bam	FBtr0080663	71	52	F	5
-input2.bam	FBtr0080663	71	53	F	5
-input2.bam	FBtr0080663	71	54	F	5
-input2.bam	FBtr0080663	71	55	F	5
-input2.bam	FBtr0080663	71	56	F	5
-input2.bam	FBtr0080663	71	57	F	8
-input2.bam	FBtr0080663	71	58	F	8
-input2.bam	FBtr0080663	71	59	F	8
-input2.bam	FBtr0080663	71	60	F	8
-input2.bam	FBtr0080663	71	61	F	8
-input2.bam	FBtr0080663	71	62	F	8
-input2.bam	FBtr0080663	71	63	F	8
-input2.bam	FBtr0080663	71	64	F	8
-input2.bam	FBtr0080663	71	65	F	7
-input2.bam	FBtr0080663	71	66	F	6
-input2.bam	FBtr0080663	71	67	F	4
-input2.bam	FBtr0080663	71	68	F	4
-input2.bam	FBtr0080663	71	69	F	4
-input2.bam	FBtr0080663	71	70	F	3
-input2.bam	FBtr0080663	71	71	F	3
-input2.bam	FBtr0080664	71	1	F	1
-input2.bam	FBtr0080664	71	2	F	1
-input2.bam	FBtr0080664	71	3	F	3
-input2.bam	FBtr0080664	71	4	F	3
-input2.bam	FBtr0080664	71	5	F	3
-input2.bam	FBtr0080664	71	6	F	3
-input2.bam	FBtr0080664	71	7	F	3
-input2.bam	FBtr0080664	71	8	F	3
-input2.bam	FBtr0080664	71	9	F	3
-input2.bam	FBtr0080664	71	10	F	4
-input2.bam	FBtr0080664	71	11	F	6
-input2.bam	FBtr0080664	71	12	F	9
-input2.bam	FBtr0080664	71	13	F	20
-input2.bam	FBtr0080664	71	14	F	31
-input2.bam	FBtr0080664	71	15	F	48
-input2.bam	FBtr0080664	71	16	F	63
-input2.bam	FBtr0080664	71	17	F	76
-input2.bam	FBtr0080664	71	18	F	86
-input2.bam	FBtr0080664	71	19	F	94
-input2.bam	FBtr0080664	71	20	F	95
-input2.bam	FBtr0080664	71	21	F	110
-input2.bam	FBtr0080664	71	22	F	116
-input2.bam	FBtr0080664	71	23	F	114
-input2.bam	FBtr0080664	71	24	F	115
-input2.bam	FBtr0080664	71	25	F	115
-input2.bam	FBtr0080664	71	26	F	115
-input2.bam	FBtr0080664	71	27	F	115
-input2.bam	FBtr0080664	71	28	F	115
-input2.bam	FBtr0080664	71	29	F	113
-input2.bam	FBtr0080664	71	30	F	113
-input2.bam	FBtr0080664	71	31	F	117
-input2.bam	FBtr0080664	71	32	F	127
-input2.bam	FBtr0080664	71	33	F	97
-input2.bam	FBtr0080664	71	34	F	134
-input2.bam	FBtr0080664	71	35	F	265
-input2.bam	FBtr0080664	71	36	F	249
-input2.bam	FBtr0080664	71	37	F	266
-input2.bam	FBtr0080664	71	38	F	268
-input2.bam	FBtr0080664	71	39	F	263
-input2.bam	FBtr0080664	71	40	F	263
-input2.bam	FBtr0080664	71	41	F	262
-input2.bam	FBtr0080664	71	42	F	262
-input2.bam	FBtr0080664	71	43	F	260
-input2.bam	FBtr0080664	71	44	F	263
-input2.bam	FBtr0080664	71	45	F	263
-input2.bam	FBtr0080664	71	46	F	263
-input2.bam	FBtr0080664	71	47	F	264
-input2.bam	FBtr0080664	71	48	F	264
-input2.bam	FBtr0080664	71	49	F	254
-input2.bam	FBtr0080664	71	50	F	72
-input2.bam	FBtr0080664	71	51	F	63
-input2.bam	FBtr0080664	71	52	F	61
-input2.bam	FBtr0080664	71	53	F	31
-input2.bam	FBtr0080664	71	54	F	30
-input2.bam	FBtr0080664	71	55	F	21
-input2.bam	FBtr0080664	71	56	F	16
-input2.bam	FBtr0080664	71	57	F	18
-input2.bam	FBtr0080664	71	58	F	18
-input2.bam	FBtr0080664	71	59	F	18
-input2.bam	FBtr0080664	71	60	F	17
-input2.bam	FBtr0080664	71	61	F	16
-input2.bam	FBtr0080664	71	62	F	12
-input2.bam	FBtr0080664	71	62	R	12
-input2.bam	FBtr0080664	71	63	F	8
-input2.bam	FBtr0080664	71	64	F	8
-input2.bam	FBtr0080664	71	65	F	7
-input2.bam	FBtr0080664	71	66	F	6
-input2.bam	FBtr0080664	71	67	F	6
-input2.bam	FBtr0080664	71	68	F	5
-input2.bam	FBtr0080664	71	69	F	5
-input2.bam	FBtr0080664	71	70	F	5
-input2.bam	FBtr0080664	71	71	F	5
-input2.bam	FBtr0080664	71	71	R	5
diff -r a561a71bd7d7 -r d33263e6e812 test-data/coverage_1_chr.tab
--- a/test-data/coverage_1_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input_single_chr.bam	1	80	1	F	1
-input_single_chr.bam	1	80	2	F	1
-input_single_chr.bam	1	80	3	F	1
-input_single_chr.bam	1	80	4	F	1
-input_single_chr.bam	1	80	5	F	1
-input_single_chr.bam	1	80	6	F	1
-input_single_chr.bam	1	80	7	F	1
-input_single_chr.bam	1	80	8	F	1
-input_single_chr.bam	1	80	9	F	1
-input_single_chr.bam	1	80	10	F	1
-input_single_chr.bam	1	80	11	F	1
-input_single_chr.bam	1	80	12	F	1
-input_single_chr.bam	1	80	13	F	1
-input_single_chr.bam	1	80	14	F	1
-input_single_chr.bam	1	80	15	F	1
-input_single_chr.bam	1	80	16	F	1
-input_single_chr.bam	1	80	17	F	1
-input_single_chr.bam	1	80	18	F	1
-input_single_chr.bam	1	80	19	F	1
-input_single_chr.bam	1	80	20	F	1
-input_single_chr.bam	1	80	21	F	1
-input_single_chr.bam	1	80	22	F	1
-input_single_chr.bam	1	80	23	F	1
-input_single_chr.bam	1	80	24	F	1
-input_single_chr.bam	1	80	25	F	1
-input_single_chr.bam	1	80	26	F	1
-input_single_chr.bam	1	80	27	F	1
-input_single_chr.bam	1	80	28	F	1
-input_single_chr.bam	1	80	29	F	1
-input_single_chr.bam	1	80	30	F	1
-input_single_chr.bam	1	80	31	F	1
-input_single_chr.bam	1	80	32	F	1
-input_single_chr.bam	1	80	33	F	1
-input_single_chr.bam	1	80	34	F	1
-input_single_chr.bam	1	80	35	F	1
-input_single_chr.bam	1	80	36	F	1
-input_single_chr.bam	1	80	37	F	1
-input_single_chr.bam	1	80	38	F	1
-input_single_chr.bam	1	80	39	F	1
-input_single_chr.bam	1	80	40	F	1
-input_single_chr.bam	1	80	41	F	1
-input_single_chr.bam	1	80	42	F	1
-input_single_chr.bam	1	80	43	F	1
-input_single_chr.bam	1	80	44	F	1
-input_single_chr.bam	1	80	45	F	1
-input_single_chr.bam	1	80	46	F	1
-input_single_chr.bam	1	80	47	F	1
-input_single_chr.bam	1	80	48	F	1
-input_single_chr.bam	1	80	49	F	1
-input_single_chr.bam	1	80	50	F	1
-input_single_chr.bam	1	80	51	F	1
-input_single_chr.bam	1	80	52	F	1
-input_single_chr.bam	1	80	53	F	1
-input_single_chr.bam	1	80	54	F	1
-input_single_chr.bam	1	80	55	F	1
-input_single_chr.bam	1	80	56	F	1
-input_single_chr.bam	1	80	57	F	1
-input_single_chr.bam	1	80	58	F	1
-input_single_chr.bam	1	80	59	F	1
-input_single_chr.bam	1	80	60	F	1
-input_single_chr.bam	1	80	61	F	1
-input_single_chr.bam	1	80	62	F	1
-input_single_chr.bam	1	80	63	F	1
-input_single_chr.bam	1	80	64	F	1
-input_single_chr.bam	1	80	65	F	1
-input_single_chr.bam	1	80	66	F	1
-input_single_chr.bam	1	80	67	F	1
-input_single_chr.bam	1	80	68	F	1
-input_single_chr.bam	1	80	69	F	1
-input_single_chr.bam	1	80	70	F	1
-input_single_chr.bam	1	80	71	F	1
-input_single_chr.bam	1	80	72	F	1
-input_single_chr.bam	1	80	73	F	1
-input_single_chr.bam	1	80	74	F	1
-input_single_chr.bam	1	80	75	F	1
-input_single_chr.bam	1	80	76	F	1
-input_single_chr.bam	1	80	77	F	1
-input_single_chr.bam	1	80	78	F	1
-input_single_chr.bam	1	80	79	F	1
-input_single_chr.bam	1	80	80	F	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/coverage_5_chr.tab
--- a/test-data/coverage_5_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,401 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
-input_5_chr.bam	1	80	1	F	1
-input_5_chr.bam	1	80	2	F	1
-input_5_chr.bam	1	80	3	F	1
-input_5_chr.bam	1	80	4	F	1
-input_5_chr.bam	1	80	5	F	1
-input_5_chr.bam	1	80	6	F	1
-input_5_chr.bam	1	80	7	F	1
-input_5_chr.bam	1	80	8	F	1
-input_5_chr.bam	1	80	9	F	1
-input_5_chr.bam	1	80	10	F	1
-input_5_chr.bam	1	80	11	F	1
-input_5_chr.bam	1	80	12	F	1
-input_5_chr.bam	1	80	13	F	1
-input_5_chr.bam	1	80	14	F	1
-input_5_chr.bam	1	80	15	F	1
-input_5_chr.bam	1	80	16	F	1
-input_5_chr.bam	1	80	17	F	1
-input_5_chr.bam	1	80	18	F	1
-input_5_chr.bam	1	80	19	F	1
-input_5_chr.bam	1	80	20	F	1
-input_5_chr.bam	1	80	21	F	1
-input_5_chr.bam	1	80	22	F	1
-input_5_chr.bam	1	80	23	F	1
-input_5_chr.bam	1	80	24	F	1
-input_5_chr.bam	1	80	25	F	1
-input_5_chr.bam	1	80	26	F	1
-input_5_chr.bam	1	80	27	F	1
-input_5_chr.bam	1	80	28	F	1
-input_5_chr.bam	1	80	29	F	1
-input_5_chr.bam	1	80	30	F	1
-input_5_chr.bam	1	80	31	F	1
-input_5_chr.bam	1	80	32	F	1
-input_5_chr.bam	1	80	33	F	1
-input_5_chr.bam	1	80	34	F	1
-input_5_chr.bam	1	80	35	F	1
-input_5_chr.bam	1	80	36	F	1
-input_5_chr.bam	1	80	37	F	1
-input_5_chr.bam	1	80	38	F	1
-input_5_chr.bam	1	80	39	F	1
-input_5_chr.bam	1	80	40	F	1
-input_5_chr.bam	1	80	41	F	1
-input_5_chr.bam	1	80	42	F	1
-input_5_chr.bam	1	80	43	F	1
-input_5_chr.bam	1	80	44	F	1
-input_5_chr.bam	1	80	45	F	1
-input_5_chr.bam	1	80	46	F	1
-input_5_chr.bam	1	80	47	F	1
-input_5_chr.bam	1	80	48	F	1
-input_5_chr.bam	1	80	49	F	1
-input_5_chr.bam	1	80	50	F	1
-input_5_chr.bam	1	80	51	F	1
-input_5_chr.bam	1	80	52	F	1
-input_5_chr.bam	1	80	53	F	1
-input_5_chr.bam	1	80	54	F	1
-input_5_chr.bam	1	80	55	F	1
-input_5_chr.bam	1	80	56	F	1
-input_5_chr.bam	1	80	57	F	1
-input_5_chr.bam	1	80	58	F	1
-input_5_chr.bam	1	80	59	F	1
-input_5_chr.bam	1	80	60	F	1
-input_5_chr.bam	1	80	61	F	1
-input_5_chr.bam	1	80	62	F	1
-input_5_chr.bam	1	80	63	F	1
-input_5_chr.bam	1	80	64	F	1
-input_5_chr.bam	1	80	65	F	1
-input_5_chr.bam	1	80	66	F	1
-input_5_chr.bam	1	80	67	F	1
-input_5_chr.bam	1	80	68	F	1
-input_5_chr.bam	1	80	69	F	1
-input_5_chr.bam	1	80	70	F	1
-input_5_chr.bam	1	80	71	F	1
-input_5_chr.bam	1	80	72	F	1
-input_5_chr.bam	1	80	73	F	1
-input_5_chr.bam	1	80	74	F	1
-input_5_chr.bam	1	80	75	F	1
-input_5_chr.bam	1	80	76	F	1
-input_5_chr.bam	1	80	77	F	1
-input_5_chr.bam	1	80	78	F	1
-input_5_chr.bam	1	80	79	F	1
-input_5_chr.bam	1	80	80	F	1
-input_5_chr.bam	2	80	1	F	1
-input_5_chr.bam	2	80	2	F	1
-input_5_chr.bam	2	80	3	F	1
-input_5_chr.bam	2	80	4	F	1
-input_5_chr.bam	2	80	5	F	1
-input_5_chr.bam	2	80	6	F	1
-input_5_chr.bam	2	80	7	F	1
-input_5_chr.bam	2	80	8	F	1
-input_5_chr.bam	2	80	9	F	1
-input_5_chr.bam	2	80	10	F	1
-input_5_chr.bam	2	80	11	F	1
-input_5_chr.bam	2	80	12	F	1
-input_5_chr.bam	2	80	13	F	1
-input_5_chr.bam	2	80	14	F	1
-input_5_chr.bam	2	80	15	F	1
-input_5_chr.bam	2	80	16	F	1
-input_5_chr.bam	2	80	17	F	1
-input_5_chr.bam	2	80	18	F	1
-input_5_chr.bam	2	80	19	F	1
-input_5_chr.bam	2	80	20	F	1
-input_5_chr.bam	2	80	21	F	1
-input_5_chr.bam	2	80	22	F	1
-input_5_chr.bam	2	80	23	F	1
-input_5_chr.bam	2	80	24	F	1
-input_5_chr.bam	2	80	25	F	1
-input_5_chr.bam	2	80	26	F	1
-input_5_chr.bam	2	80	27	F	1
-input_5_chr.bam	2	80	28	F	1
-input_5_chr.bam	2	80	29	F	1
-input_5_chr.bam	2	80	30	F	1
-input_5_chr.bam	2	80	31	F	1
-input_5_chr.bam	2	80	32	F	1
-input_5_chr.bam	2	80	33	F	1
-input_5_chr.bam	2	80	34	F	1
-input_5_chr.bam	2	80	35	F	1
-input_5_chr.bam	2	80	36	F	1
-input_5_chr.bam	2	80	37	F	1
-input_5_chr.bam	2	80	38	F	1
-input_5_chr.bam	2	80	39	F	1
-input_5_chr.bam	2	80	40	F	1
-input_5_chr.bam	2	80	41	F	1
-input_5_chr.bam	2	80	42	F	1
-input_5_chr.bam	2	80	43	F	1
-input_5_chr.bam	2	80	44	F	1
-input_5_chr.bam	2	80	45	F	1
-input_5_chr.bam	2	80	46	F	1
-input_5_chr.bam	2	80	47	F	1
-input_5_chr.bam	2	80	48	F	1
-input_5_chr.bam	2	80	49	F	1
-input_5_chr.bam	2	80	50	F	1
-input_5_chr.bam	2	80	51	F	1
-input_5_chr.bam	2	80	52	F	1
-input_5_chr.bam	2	80	53	F	1
-input_5_chr.bam	2	80	54	F	1
-input_5_chr.bam	2	80	55	F	1
-input_5_chr.bam	2	80	56	F	1
-input_5_chr.bam	2	80	57	F	1
-input_5_chr.bam	2	80	58	F	1
-input_5_chr.bam	2	80	59	F	1
-input_5_chr.bam	2	80	60	F	1
-input_5_chr.bam	2	80	61	F	1
-input_5_chr.bam	2	80	62	F	1
-input_5_chr.bam	2	80	63	F	1
-input_5_chr.bam	2	80	64	F	1
-input_5_chr.bam	2	80	65	F	1
-input_5_chr.bam	2	80	66	F	1
-input_5_chr.bam	2	80	67	F	1
-input_5_chr.bam	2	80	68	F	1
-input_5_chr.bam	2	80	69	F	1
-input_5_chr.bam	2	80	70	F	1
-input_5_chr.bam	2	80	71	F	1
-input_5_chr.bam	2	80	72	F	1
-input_5_chr.bam	2	80	73	F	1
-input_5_chr.bam	2	80	74	F	1
-input_5_chr.bam	2	80	75	F	1
-input_5_chr.bam	2	80	76	F	1
-input_5_chr.bam	2	80	77	F	1
-input_5_chr.bam	2	80	78	F	1
-input_5_chr.bam	2	80	79	F	1
-input_5_chr.bam	2	80	80	F	1
-input_5_chr.bam	3	80	1	F	1
-input_5_chr.bam	3	80	2	F	1
-input_5_chr.bam	3	80	3	F	1
-input_5_chr.bam	3	80	4	F	1
-input_5_chr.bam	3	80	5	F	1
-input_5_chr.bam	3	80	6	F	1
-input_5_chr.bam	3	80	7	F	1
-input_5_chr.bam	3	80	8	F	1
-input_5_chr.bam	3	80	9	F	1
-input_5_chr.bam	3	80	10	F	1
-input_5_chr.bam	3	80	11	F	1
-input_5_chr.bam	3	80	12	F	1
-input_5_chr.bam	3	80	13	F	1
-input_5_chr.bam	3	80	14	F	1
-input_5_chr.bam	3	80	15	F	1
-input_5_chr.bam	3	80	16	F	1
-input_5_chr.bam	3	80	17	F	1
-input_5_chr.bam	3	80	18	F	1
-input_5_chr.bam	3	80	19	F	1
-input_5_chr.bam	3	80	20	F	1
-input_5_chr.bam	3	80	21	F	1
-input_5_chr.bam	3	80	22	F	1
-input_5_chr.bam	3	80	23	F	1
-input_5_chr.bam	3	80	24	F	1
-input_5_chr.bam	3	80	25	F	1
-input_5_chr.bam	3	80	26	F	1
-input_5_chr.bam	3	80	27	F	1
-input_5_chr.bam	3	80	28	F	1
-input_5_chr.bam	3	80	29	F	1
-input_5_chr.bam	3	80	30	F	1
-input_5_chr.bam	3	80	31	F	1
-input_5_chr.bam	3	80	32	F	1
-input_5_chr.bam	3	80	33	F	1
-input_5_chr.bam	3	80	34	F	1
-input_5_chr.bam	3	80	35	F	1
-input_5_chr.bam	3	80	36	F	1
-input_5_chr.bam	3	80	37	F	1
-input_5_chr.bam	3	80	38	F	1
-input_5_chr.bam	3	80	39	F	1
-input_5_chr.bam	3	80	40	F	1
-input_5_chr.bam	3	80	41	F	1
-input_5_chr.bam	3	80	42	F	1
-input_5_chr.bam	3	80	43	F	1
-input_5_chr.bam	3	80	44	F	1
-input_5_chr.bam	3	80	45	F	1
-input_5_chr.bam	3	80	46	F	1
-input_5_chr.bam	3	80	47	F	1
-input_5_chr.bam	3	80	48	F	1
-input_5_chr.bam	3	80	49	F	1
-input_5_chr.bam	3	80	50	F	1
-input_5_chr.bam	3	80	51	F	1
-input_5_chr.bam	3	80	52	F	1
-input_5_chr.bam	3	80	53	F	1
-input_5_chr.bam	3	80	54	F	1
-input_5_chr.bam	3	80	55	F	1
-input_5_chr.bam	3	80	56	F	1
-input_5_chr.bam	3	80	57	F	1
-input_5_chr.bam	3	80	58	F	1
-input_5_chr.bam	3	80	59	F	1
-input_5_chr.bam	3	80	60	F	1
-input_5_chr.bam	3	80	61	F	1
-input_5_chr.bam	3	80	62	F	1
-input_5_chr.bam	3	80	63	F	1
-input_5_chr.bam	3	80	64	F	1
-input_5_chr.bam	3	80	65	F	1
-input_5_chr.bam	3	80	66	F	1
-input_5_chr.bam	3	80	67	F	1
-input_5_chr.bam	3	80	68	F	1
-input_5_chr.bam	3	80	69	F	1
-input_5_chr.bam	3	80	70	F	1
-input_5_chr.bam	3	80	71	F	1
-input_5_chr.bam	3	80	72	F	1
-input_5_chr.bam	3	80	73	F	1
-input_5_chr.bam	3	80	74	F	1
-input_5_chr.bam	3	80	75	F	1
-input_5_chr.bam	3	80	76	F	1
-input_5_chr.bam	3	80	77	F	1
-input_5_chr.bam	3	80	78	F	1
-input_5_chr.bam	3	80	79	F	1
-input_5_chr.bam	3	80	80	F	1
-input_5_chr.bam	4	80	1	F	1
-input_5_chr.bam	4	80	2	F	1
-input_5_chr.bam	4	80	3	F	1
-input_5_chr.bam	4	80	4	F	1
-input_5_chr.bam	4	80	5	F	1
-input_5_chr.bam	4	80	6	F	1
-input_5_chr.bam	4	80	7	F	1
-input_5_chr.bam	4	80	8	F	1
-input_5_chr.bam	4	80	9	F	1
-input_5_chr.bam	4	80	10	F	1
-input_5_chr.bam	4	80	11	F	1
-input_5_chr.bam	4	80	12	F	1
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-input_5_chr.bam	4	80	15	F	1
-input_5_chr.bam	4	80	16	F	1
-input_5_chr.bam	4	80	17	F	1
-input_5_chr.bam	4	80	18	F	1
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-input_5_chr.bam	5	80	19	F	1
-input_5_chr.bam	5	80	20	F	1
-input_5_chr.bam	5	80	21	F	1
-input_5_chr.bam	5	80	22	F	1
-input_5_chr.bam	5	80	23	F	1
-input_5_chr.bam	5	80	24	F	1
-input_5_chr.bam	5	80	25	F	1
-input_5_chr.bam	5	80	26	F	1
-input_5_chr.bam	5	80	27	F	1
-input_5_chr.bam	5	80	28	F	1
-input_5_chr.bam	5	80	29	F	1
-input_5_chr.bam	5	80	30	F	1
-input_5_chr.bam	5	80	31	F	1
-input_5_chr.bam	5	80	32	F	1
-input_5_chr.bam	5	80	33	F	1
-input_5_chr.bam	5	80	34	F	1
-input_5_chr.bam	5	80	35	F	1
-input_5_chr.bam	5	80	36	F	1
-input_5_chr.bam	5	80	37	F	1
-input_5_chr.bam	5	80	38	F	1
-input_5_chr.bam	5	80	39	F	1
-input_5_chr.bam	5	80	40	F	1
-input_5_chr.bam	5	80	41	F	1
-input_5_chr.bam	5	80	42	F	1
-input_5_chr.bam	5	80	43	F	1
-input_5_chr.bam	5	80	44	F	1
-input_5_chr.bam	5	80	45	F	1
-input_5_chr.bam	5	80	46	F	1
-input_5_chr.bam	5	80	47	F	1
-input_5_chr.bam	5	80	48	F	1
-input_5_chr.bam	5	80	49	F	1
-input_5_chr.bam	5	80	50	F	1
-input_5_chr.bam	5	80	51	F	1
-input_5_chr.bam	5	80	52	F	1
-input_5_chr.bam	5	80	53	F	1
-input_5_chr.bam	5	80	54	F	1
-input_5_chr.bam	5	80	55	F	1
-input_5_chr.bam	5	80	56	F	1
-input_5_chr.bam	5	80	57	F	1
-input_5_chr.bam	5	80	58	F	1
-input_5_chr.bam	5	80	59	F	1
-input_5_chr.bam	5	80	60	F	1
-input_5_chr.bam	5	80	61	F	1
-input_5_chr.bam	5	80	62	F	1
-input_5_chr.bam	5	80	63	F	1
-input_5_chr.bam	5	80	64	F	1
-input_5_chr.bam	5	80	65	F	1
-input_5_chr.bam	5	80	66	F	1
-input_5_chr.bam	5	80	67	F	1
-input_5_chr.bam	5	80	68	F	1
-input_5_chr.bam	5	80	69	F	1
-input_5_chr.bam	5	80	70	F	1
-input_5_chr.bam	5	80	71	F	1
-input_5_chr.bam	5	80	72	F	1
-input_5_chr.bam	5	80	73	F	1
-input_5_chr.bam	5	80	74	F	1
-input_5_chr.bam	5	80	75	F	1
-input_5_chr.bam	5	80	76	F	1
-input_5_chr.bam	5	80	77	F	1
-input_5_chr.bam	5	80	78	F	1
-input_5_chr.bam	5	80	79	F	1
-input_5_chr.bam	5	80	80	F	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/coverage_normed.pdf
Binary file test-data/coverage_normed.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/doubled_count-mean.pdf
Binary file test-data/doubled_count-mean.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/doubled_count.tab
--- a/test-data/doubled_count.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,599 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
-input1.bam_0	FBtr0070001	72	1	F	1
-input1.bam_0	FBtr0070001	72	7	F	6
-input1.bam_0	FBtr0070001	72	8	F	3
-input1.bam_0	FBtr0070001	72	11	F	2
-input1.bam_0	FBtr0070001	72	16	F	1
-input1.bam_0	FBtr0070001	72	17	F	1
-input1.bam_0	FBtr0070001	72	18	F	1
-input1.bam_0	FBtr0070001	72	27	F	2
-input1.bam_0	FBtr0070001	72	30	F	1
-input1.bam_0	FBtr0070001	72	31	F	11
-input1.bam_0	FBtr0070001	72	32	F	27
-input1.bam_0	FBtr0070001	72	34	F	1
-input1.bam_0	FBtr0070001	72	72	F	0
-input1.bam_0	FBtr0070533	72	1	F	1
-input1.bam_0	FBtr0070533	72	12	F	2
-input1.bam_0	FBtr0070533	72	15	F	1
-input1.bam_0	FBtr0070533	72	19	F	5
-input1.bam_0	FBtr0070533	72	20	F	1
-input1.bam_0	FBtr0070533	72	21	F	1
-input1.bam_0	FBtr0070533	72	22	F	1
-input1.bam_0	FBtr0070533	72	25	F	1
-input1.bam_0	FBtr0070533	72	26	F	1
-input1.bam_0	FBtr0070533	72	28	F	1
-input1.bam_0	FBtr0070533	72	32	F	4
-input1.bam_0	FBtr0070533	72	35	F	1
-input1.bam_0	FBtr0070533	72	37	F	2
-input1.bam_0	FBtr0070533	72	38	F	2
-input1.bam_0	FBtr0070533	72	72	F	0
-input1.bam_0	FBtr0070603	72	1	F	2
-input1.bam_0	FBtr0070603	72	3	F	1
-input1.bam_0	FBtr0070603	72	4	F	1
-input1.bam_0	FBtr0070603	72	6	F	1
-input1.bam_0	FBtr0070603	72	7	F	7
-input1.bam_0	FBtr0070603	72	8	F	4
-input1.bam_0	FBtr0070603	72	9	F	7
-input1.bam_0	FBtr0070603	72	12	F	2
-input1.bam_0	FBtr0070603	72	13	F	1
-input1.bam_0	FBtr0070603	72	15	F	2
-input1.bam_0	FBtr0070603	72	16	F	2
-input1.bam_0	FBtr0070603	72	17	F	3
-input1.bam_0	FBtr0070603	72	18	F	1
-input1.bam_0	FBtr0070603	72	19	F	9
-input1.bam_0	FBtr0070603	72	20	F	3
-input1.bam_0	FBtr0070603	72	21	F	1
-input1.bam_0	FBtr0070603	72	22	F	3
-input1.bam_0	FBtr0070603	72	24	F	2
-input1.bam_0	FBtr0070603	72	25	F	1
-input1.bam_0	FBtr0070603	72	26	F	6
-input1.bam_0	FBtr0070603	72	27	F	3
-input1.bam_0	FBtr0070603	72	32	F	1
-input1.bam_0	FBtr0070603	72	34	F	3
-input1.bam_0	FBtr0070603	72	38	F	1
-input1.bam_0	FBtr0070603	72	42	F	1
-input1.bam_0	FBtr0070603	72	51	F	1
-input1.bam_0	FBtr0070603	72	56	F	1
-input1.bam_0	FBtr0070603	72	72	F	0
-input1.bam_0	FBtr0070604	72	1	F	1
-input1.bam_0	FBtr0070604	72	18	F	1
-input1.bam_0	FBtr0070604	72	22	F	1
-input1.bam_0	FBtr0070604	72	30	F	2
-input1.bam_0	FBtr0070604	72	31	F	10
-input1.bam_0	FBtr0070604	72	32	F	24
-input1.bam_0	FBtr0070604	72	57	F	1
-input1.bam_0	FBtr0070604	72	72	F	0
-input1.bam_0	FBtr0070911	73	1	F	0
-input1.bam_0	FBtr0070911	73	15	F	1
-input1.bam_0	FBtr0070911	73	38	F	1
-input1.bam_0	FBtr0070911	73	73	F	0
-input1.bam_0	FBtr0078490	72	1	F	0
-input1.bam_0	FBtr0078490	72	13	F	2
-input1.bam_0	FBtr0078490	72	17	F	1
-input1.bam_0	FBtr0078490	72	18	F	1
-input1.bam_0	FBtr0078490	72	25	F	1
-input1.bam_0	FBtr0078490	72	28	F	2
-input1.bam_0	FBtr0078490	72	38	F	1
-input1.bam_0	FBtr0078490	72	72	F	0
-input1.bam_0	FBtr0078580	72	1	F	1041
-input1.bam_0	FBtr0078580	72	3	F	3
-input1.bam_0	FBtr0078580	72	4	F	4
-input1.bam_0	FBtr0078580	72	5	F	5
-input1.bam_0	FBtr0078580	72	6	F	4
-input1.bam_0	FBtr0078580	72	7	F	1
-input1.bam_0	FBtr0078580	72	8	F	2
-input1.bam_0	FBtr0078580	72	11	F	1
-input1.bam_0	FBtr0078580	72	12	F	13
-input1.bam_0	FBtr0078580	72	14	F	7
-input1.bam_0	FBtr0078580	72	15	F	1
-input1.bam_0	FBtr0078580	72	16	F	4
-input1.bam_0	FBtr0078580	72	17	F	1
-input1.bam_0	FBtr0078580	72	19	F	1
-input1.bam_0	FBtr0078580	72	20	F	2
-input1.bam_0	FBtr0078580	72	21	F	5
-input1.bam_0	FBtr0078580	72	24	F	3
-input1.bam_0	FBtr0078580	72	25	F	2
-input1.bam_0	FBtr0078580	72	29	F	1
-input1.bam_0	FBtr0078580	72	31	F	1
-input1.bam_0	FBtr0078580	72	52	F	2
-input1.bam_0	FBtr0078580	72	72	F	0
-input1.bam_0	FBtr0078790	73	1	F	1
-input1.bam_0	FBtr0078790	73	17	F	2
-input1.bam_0	FBtr0078790	73	33	F	1
-input1.bam_0	FBtr0078790	73	42	F	4
-input1.bam_0	FBtr0078790	73	44	F	2
-input1.bam_0	FBtr0078790	73	46	F	1
-input1.bam_0	FBtr0078790	73	47	F	1
-input1.bam_0	FBtr0078790	73	52	F	1
-input1.bam_0	FBtr0078790	73	69	R	1
-input1.bam_0	FBtr0078790	73	73	F	0
-input1.bam_0	FBtr0079064	72	1	F	1
-input1.bam_0	FBtr0079064	72	3	F	1
-input1.bam_0	FBtr0079064	72	33	F	1
-input1.bam_0	FBtr0079064	72	52	F	1
-input1.bam_0	FBtr0079064	72	72	F	0
-input1.bam_0	FBtr0079090	72	1	F	2
-input1.bam_0	FBtr0079090	72	26	F	1
-input1.bam_0	FBtr0079090	72	33	F	1
-input1.bam_0	FBtr0079090	72	53	F	1
-input1.bam_0	FBtr0079090	72	56	R	1
-input1.bam_0	FBtr0079090	72	72	F	0
-input1.bam_0	FBtr0079338	73	1	F	0
-input1.bam_0	FBtr0079338	73	12	F	1
-input1.bam_0	FBtr0079338	73	13	F	2
-input1.bam_0	FBtr0079338	73	14	F	1
-input1.bam_0	FBtr0079338	73	17	F	1
-input1.bam_0	FBtr0079338	73	25	F	1
-input1.bam_0	FBtr0079338	73	42	F	8
-input1.bam_0	FBtr0079338	73	43	F	1
-input1.bam_0	FBtr0079338	73	46	F	1
-input1.bam_0	FBtr0079338	73	73	F	0
-input1.bam_0	FBtr0079528	71	1	F	19
-input1.bam_0	FBtr0079528	71	3	F	55
-input1.bam_0	FBtr0079528	71	4	F	2
-input1.bam_0	FBtr0079528	71	8	F	4
-input1.bam_0	FBtr0079528	71	10	F	1
-input1.bam_0	FBtr0079528	71	11	F	2
-input1.bam_0	FBtr0079528	71	13	F	1
-input1.bam_0	FBtr0079528	71	14	F	4
-input1.bam_0	FBtr0079528	71	16	F	1
-input1.bam_0	FBtr0079528	71	17	F	4
-input1.bam_0	FBtr0079528	71	18	F	4
-input1.bam_0	FBtr0079528	71	28	F	1
-input1.bam_0	FBtr0079528	71	35	F	1
-input1.bam_0	FBtr0079528	71	36	F	1
-input1.bam_0	FBtr0079528	71	37	F	1
-input1.bam_0	FBtr0079528	71	51	F	5
-input1.bam_0	FBtr0079528	71	71	F	0
-input1.bam_0	FBtr0079596	73	1	F	13
-input1.bam_0	FBtr0079596	73	3	F	13
-input1.bam_0	FBtr0079596	73	4	F	31
-input1.bam_0	FBtr0079596	73	5	F	2
-input1.bam_0	FBtr0079596	73	6	F	11
-input1.bam_0	FBtr0079596	73	8	F	9
-input1.bam_0	FBtr0079596	73	9	F	12
-input1.bam_0	FBtr0079596	73	10	F	3
-input1.bam_0	FBtr0079596	73	11	F	19
-input1.bam_0	FBtr0079596	73	12	F	1
-input1.bam_0	FBtr0079596	73	13	F	20
-input1.bam_0	FBtr0079596	73	14	F	6
-input1.bam_0	FBtr0079596	73	15	F	1
-input1.bam_0	FBtr0079596	73	16	F	3
-input1.bam_0	FBtr0079596	73	17	F	2
-input1.bam_0	FBtr0079596	73	18	F	1
-input1.bam_0	FBtr0079596	73	19	F	1
-input1.bam_0	FBtr0079596	73	53	F	2
-input1.bam_0	FBtr0079596	73	54	F	2
-input1.bam_0	FBtr0079596	73	73	F	0
-input1.bam_0	FBtr0079677	72	1	F	1
-input1.bam_0	FBtr0079677	72	5	F	1
-input1.bam_0	FBtr0079677	72	52	F	1
-input1.bam_0	FBtr0079677	72	53	F	1
-input1.bam_0	FBtr0079677	72	72	F	0
-input1.bam_0	FBtr0079690	72	1	F	1
-input1.bam_0	FBtr0079690	72	22	F	1
-input1.bam_0	FBtr0079690	72	27	F	1
-input1.bam_0	FBtr0079690	72	33	F	2
-input1.bam_0	FBtr0079690	72	72	F	0
-input1.bam_0	FBtr0079692	73	1	F	3
-input1.bam_0	FBtr0079692	73	18	F	1
-input1.bam_0	FBtr0079692	73	25	F	1
-input1.bam_0	FBtr0079692	73	32	F	1
-input1.bam_0	FBtr0079692	73	73	F	0
-input1.bam_0	FBtr0079693	72	1	F	5
-input1.bam_0	FBtr0079693	72	25	F	1
-input1.bam_0	FBtr0079693	72	72	F	0
-input1.bam_0	FBtr0079694	72	1	F	5
-input1.bam_0	FBtr0079694	72	18	F	1
-input1.bam_0	FBtr0079694	72	52	F	1
-input1.bam_0	FBtr0079694	72	72	F	0
-input1.bam_0	FBtr0079702	72	1	F	1
-input1.bam_0	FBtr0079702	72	19	F	2
-input1.bam_0	FBtr0079702	72	56	F	1
-input1.bam_0	FBtr0079702	72	72	F	0
-input1.bam_0	FBtr0079728	72	1	F	2
-input1.bam_0	FBtr0079728	72	8	F	1
-input1.bam_0	FBtr0079728	72	19	F	1
-input1.bam_0	FBtr0079728	72	33	F	3
-input1.bam_0	FBtr0079728	72	56	F	1
-input1.bam_0	FBtr0079728	72	72	F	0
-input1.bam_0	FBtr0079729	72	1	F	1
-input1.bam_0	FBtr0079729	72	13	F	1
-input1.bam_0	FBtr0079729	72	52	F	1
-input1.bam_0	FBtr0079729	72	57	F	1
-input1.bam_0	FBtr0079729	72	72	F	0
-input1.bam_0	FBtr0079752	72	1	F	2
-input1.bam_0	FBtr0079752	72	7	F	1
-input1.bam_0	FBtr0079752	72	12	F	1
-input1.bam_0	FBtr0079752	72	33	F	2
-input1.bam_0	FBtr0079752	72	52	F	2
-input1.bam_0	FBtr0079752	72	72	F	0
-input1.bam_0	FBtr0079820	74	1	F	0
-input1.bam_0	FBtr0079820	74	45	F	1
-input1.bam_0	FBtr0079820	74	46	F	2
-input1.bam_0	FBtr0079820	74	48	F	1
-input1.bam_0	FBtr0079820	74	49	F	1
-input1.bam_0	FBtr0079820	74	51	F	1
-input1.bam_0	FBtr0079820	74	54	F	4
-input1.bam_0	FBtr0079820	74	55	F	1
-input1.bam_0	FBtr0079820	74	56	F	2
-input1.bam_0	FBtr0079820	74	74	F	0
-input1.bam_0	FBtr0080609	72	1	F	13
-input1.bam_0	FBtr0080609	72	3	F	2
-input1.bam_0	FBtr0080609	72	4	F	10
-input1.bam_0	FBtr0080609	72	5	F	2
-input1.bam_0	FBtr0080609	72	7	F	19
-input1.bam_0	FBtr0080609	72	8	F	4
-input1.bam_0	FBtr0080609	72	9	F	3
-input1.bam_0	FBtr0080609	72	12	F	1
-input1.bam_0	FBtr0080609	72	15	F	1
-input1.bam_0	FBtr0080609	72	16	F	1
-input1.bam_0	FBtr0080609	72	17	F	2
-input1.bam_0	FBtr0080609	72	19	F	1
-input1.bam_0	FBtr0080609	72	20	F	1
-input1.bam_0	FBtr0080609	72	42	F	1
-input1.bam_0	FBtr0080609	72	51	F	1
-input1.bam_0	FBtr0080609	72	52	F	1
-input1.bam_0	FBtr0080609	72	72	F	0
-input1.bam_0	FBtr0080644	72	1	F	1
-input1.bam_0	FBtr0080644	72	4	F	2
-input1.bam_0	FBtr0080644	72	7	F	1
-input1.bam_0	FBtr0080644	72	12	F	2
-input1.bam_0	FBtr0080644	72	72	F	0
-input1.bam_0	FBtr0080646	72	1	F	1
-input1.bam_0	FBtr0080646	72	6	F	1
-input1.bam_0	FBtr0080646	72	7	F	1
-input1.bam_0	FBtr0080646	72	72	F	0
-input1.bam_0	FBtr0080647	72	1	F	3
-input1.bam_0	FBtr0080647	72	3	F	1
-input1.bam_0	FBtr0080647	72	6	F	2
-input1.bam_0	FBtr0080647	72	8	F	1
-input1.bam_0	FBtr0080647	72	11	F	2
-input1.bam_0	FBtr0080647	72	12	F	1
-input1.bam_0	FBtr0080647	72	72	F	0
-input1.bam_0	FBtr0080660	72	1	F	0
-input1.bam_0	FBtr0080660	72	4	F	4
-input1.bam_0	FBtr0080660	72	7	F	3
-input1.bam_0	FBtr0080660	72	72	F	0
-input1.bam_0	FBtr0080663	71	1	F	22
-input1.bam_0	FBtr0080663	71	3	F	56
-input1.bam_0	FBtr0080663	71	4	F	4
-input1.bam_0	FBtr0080663	71	7	F	1
-input1.bam_0	FBtr0080663	71	8	F	4
-input1.bam_0	FBtr0080663	71	12	F	2
-input1.bam_0	FBtr0080663	71	14	F	2
-input1.bam_0	FBtr0080663	71	15	F	1
-input1.bam_0	FBtr0080663	71	16	F	3
-input1.bam_0	FBtr0080663	71	17	F	7
-input1.bam_0	FBtr0080663	71	26	F	1
-input1.bam_0	FBtr0080663	71	32	F	2
-input1.bam_0	FBtr0080663	71	50	F	1
-input1.bam_0	FBtr0080663	71	51	F	9
-input1.bam_0	FBtr0080663	71	71	F	0
-input1.bam_0	FBtr0080664	71	1	F	16
-input1.bam_0	FBtr0080664	71	3	F	56
-input1.bam_0	FBtr0080664	71	4	F	4
-input1.bam_0	FBtr0080664	71	6	F	1
-input1.bam_0	FBtr0080664	71	7	F	1
-input1.bam_0	FBtr0080664	71	8	F	4
-input1.bam_0	FBtr0080664	71	9	F	1
-input1.bam_0	FBtr0080664	71	11	F	3
-input1.bam_0	FBtr0080664	71	12	F	3
-input1.bam_0	FBtr0080664	71	13	F	2
-input1.bam_0	FBtr0080664	71	14	F	3
-input1.bam_0	FBtr0080664	71	16	F	2
-input1.bam_0	FBtr0080664	71	17	F	10
-input1.bam_0	FBtr0080664	71	18	F	1
-input1.bam_0	FBtr0080664	71	21	F	1
-input1.bam_0	FBtr0080664	71	28	F	2
-input1.bam_0	FBtr0080664	71	32	F	1
-input1.bam_0	FBtr0080664	71	33	F	1
-input1.bam_0	FBtr0080664	71	34	F	1
-input1.bam_0	FBtr0080664	71	35	F	1
-input1.bam_0	FBtr0080664	71	36	F	1
-input1.bam_0	FBtr0080664	71	37	F	1
-input1.bam_0	FBtr0080664	71	38	F	1
-input1.bam_0	FBtr0080664	71	50	F	2
-input1.bam_0	FBtr0080664	71	51	F	7
-input1.bam_0	FBtr0080664	71	52	F	1
-input1.bam_0	FBtr0080664	71	56	F	1
-input1.bam_0	FBtr0080664	71	71	F	0
-input1.bam_1	FBtr0070001	72	1	F	1
-input1.bam_1	FBtr0070001	72	7	F	6
-input1.bam_1	FBtr0070001	72	8	F	3
-input1.bam_1	FBtr0070001	72	11	F	2
-input1.bam_1	FBtr0070001	72	16	F	1
-input1.bam_1	FBtr0070001	72	17	F	1
-input1.bam_1	FBtr0070001	72	18	F	1
-input1.bam_1	FBtr0070001	72	27	F	2
-input1.bam_1	FBtr0070001	72	30	F	1
-input1.bam_1	FBtr0070001	72	31	F	11
-input1.bam_1	FBtr0070001	72	32	F	27
-input1.bam_1	FBtr0070001	72	34	F	1
-input1.bam_1	FBtr0070001	72	72	F	0
-input1.bam_1	FBtr0070533	72	1	F	1
-input1.bam_1	FBtr0070533	72	12	F	2
-input1.bam_1	FBtr0070533	72	15	F	1
-input1.bam_1	FBtr0070533	72	19	F	5
-input1.bam_1	FBtr0070533	72	20	F	1
-input1.bam_1	FBtr0070533	72	21	F	1
-input1.bam_1	FBtr0070533	72	22	F	1
-input1.bam_1	FBtr0070533	72	25	F	1
-input1.bam_1	FBtr0070533	72	26	F	1
-input1.bam_1	FBtr0070533	72	28	F	1
-input1.bam_1	FBtr0070533	72	32	F	4
-input1.bam_1	FBtr0070533	72	35	F	1
-input1.bam_1	FBtr0070533	72	37	F	2
-input1.bam_1	FBtr0070533	72	38	F	2
-input1.bam_1	FBtr0070533	72	72	F	0
-input1.bam_1	FBtr0070603	72	1	F	2
-input1.bam_1	FBtr0070603	72	3	F	1
-input1.bam_1	FBtr0070603	72	4	F	1
-input1.bam_1	FBtr0070603	72	6	F	1
-input1.bam_1	FBtr0070603	72	7	F	7
-input1.bam_1	FBtr0070603	72	8	F	4
-input1.bam_1	FBtr0070603	72	9	F	7
-input1.bam_1	FBtr0070603	72	12	F	2
-input1.bam_1	FBtr0070603	72	13	F	1
-input1.bam_1	FBtr0070603	72	15	F	2
-input1.bam_1	FBtr0070603	72	16	F	2
-input1.bam_1	FBtr0070603	72	17	F	3
-input1.bam_1	FBtr0070603	72	18	F	1
-input1.bam_1	FBtr0070603	72	19	F	9
-input1.bam_1	FBtr0070603	72	20	F	3
-input1.bam_1	FBtr0070603	72	21	F	1
-input1.bam_1	FBtr0070603	72	22	F	3
-input1.bam_1	FBtr0070603	72	24	F	2
-input1.bam_1	FBtr0070603	72	25	F	1
-input1.bam_1	FBtr0070603	72	26	F	6
-input1.bam_1	FBtr0070603	72	27	F	3
-input1.bam_1	FBtr0070603	72	32	F	1
-input1.bam_1	FBtr0070603	72	34	F	3
-input1.bam_1	FBtr0070603	72	38	F	1
-input1.bam_1	FBtr0070603	72	42	F	1
-input1.bam_1	FBtr0070603	72	51	F	1
-input1.bam_1	FBtr0070603	72	56	F	1
-input1.bam_1	FBtr0070603	72	72	F	0
-input1.bam_1	FBtr0070604	72	1	F	1
-input1.bam_1	FBtr0070604	72	18	F	1
-input1.bam_1	FBtr0070604	72	22	F	1
-input1.bam_1	FBtr0070604	72	30	F	2
-input1.bam_1	FBtr0070604	72	31	F	10
-input1.bam_1	FBtr0070604	72	32	F	24
-input1.bam_1	FBtr0070604	72	57	F	1
-input1.bam_1	FBtr0070604	72	72	F	0
-input1.bam_1	FBtr0070911	73	1	F	0
-input1.bam_1	FBtr0070911	73	15	F	1
-input1.bam_1	FBtr0070911	73	38	F	1
-input1.bam_1	FBtr0070911	73	73	F	0
-input1.bam_1	FBtr0078490	72	1	F	0
-input1.bam_1	FBtr0078490	72	13	F	2
-input1.bam_1	FBtr0078490	72	17	F	1
-input1.bam_1	FBtr0078490	72	18	F	1
-input1.bam_1	FBtr0078490	72	25	F	1
-input1.bam_1	FBtr0078490	72	28	F	2
-input1.bam_1	FBtr0078490	72	38	F	1
-input1.bam_1	FBtr0078490	72	72	F	0
-input1.bam_1	FBtr0078580	72	1	F	1041
-input1.bam_1	FBtr0078580	72	3	F	3
-input1.bam_1	FBtr0078580	72	4	F	4
-input1.bam_1	FBtr0078580	72	5	F	5
-input1.bam_1	FBtr0078580	72	6	F	4
-input1.bam_1	FBtr0078580	72	7	F	1
-input1.bam_1	FBtr0078580	72	8	F	2
-input1.bam_1	FBtr0078580	72	11	F	1
-input1.bam_1	FBtr0078580	72	12	F	13
-input1.bam_1	FBtr0078580	72	14	F	7
-input1.bam_1	FBtr0078580	72	15	F	1
-input1.bam_1	FBtr0078580	72	16	F	4
-input1.bam_1	FBtr0078580	72	17	F	1
-input1.bam_1	FBtr0078580	72	19	F	1
-input1.bam_1	FBtr0078580	72	20	F	2
-input1.bam_1	FBtr0078580	72	21	F	5
-input1.bam_1	FBtr0078580	72	24	F	3
-input1.bam_1	FBtr0078580	72	25	F	2
-input1.bam_1	FBtr0078580	72	29	F	1
-input1.bam_1	FBtr0078580	72	31	F	1
-input1.bam_1	FBtr0078580	72	52	F	2
-input1.bam_1	FBtr0078580	72	72	F	0
-input1.bam_1	FBtr0078790	73	1	F	1
-input1.bam_1	FBtr0078790	73	17	F	2
-input1.bam_1	FBtr0078790	73	33	F	1
-input1.bam_1	FBtr0078790	73	42	F	4
-input1.bam_1	FBtr0078790	73	44	F	2
-input1.bam_1	FBtr0078790	73	46	F	1
-input1.bam_1	FBtr0078790	73	47	F	1
-input1.bam_1	FBtr0078790	73	52	F	1
-input1.bam_1	FBtr0078790	73	69	R	1
-input1.bam_1	FBtr0078790	73	73	F	0
-input1.bam_1	FBtr0079064	72	1	F	1
-input1.bam_1	FBtr0079064	72	3	F	1
-input1.bam_1	FBtr0079064	72	33	F	1
-input1.bam_1	FBtr0079064	72	52	F	1
-input1.bam_1	FBtr0079064	72	72	F	0
-input1.bam_1	FBtr0079090	72	1	F	2
-input1.bam_1	FBtr0079090	72	26	F	1
-input1.bam_1	FBtr0079090	72	33	F	1
-input1.bam_1	FBtr0079090	72	53	F	1
-input1.bam_1	FBtr0079090	72	56	R	1
-input1.bam_1	FBtr0079090	72	72	F	0
-input1.bam_1	FBtr0079338	73	1	F	0
-input1.bam_1	FBtr0079338	73	12	F	1
-input1.bam_1	FBtr0079338	73	13	F	2
-input1.bam_1	FBtr0079338	73	14	F	1
-input1.bam_1	FBtr0079338	73	17	F	1
-input1.bam_1	FBtr0079338	73	25	F	1
-input1.bam_1	FBtr0079338	73	42	F	8
-input1.bam_1	FBtr0079338	73	43	F	1
-input1.bam_1	FBtr0079338	73	46	F	1
-input1.bam_1	FBtr0079338	73	73	F	0
-input1.bam_1	FBtr0079528	71	1	F	19
-input1.bam_1	FBtr0079528	71	3	F	55
-input1.bam_1	FBtr0079528	71	4	F	2
-input1.bam_1	FBtr0079528	71	8	F	4
-input1.bam_1	FBtr0079528	71	10	F	1
-input1.bam_1	FBtr0079528	71	11	F	2
-input1.bam_1	FBtr0079528	71	13	F	1
-input1.bam_1	FBtr0079528	71	14	F	4
-input1.bam_1	FBtr0079528	71	16	F	1
-input1.bam_1	FBtr0079528	71	17	F	4
-input1.bam_1	FBtr0079528	71	18	F	4
-input1.bam_1	FBtr0079528	71	28	F	1
-input1.bam_1	FBtr0079528	71	35	F	1
-input1.bam_1	FBtr0079528	71	36	F	1
-input1.bam_1	FBtr0079528	71	37	F	1
-input1.bam_1	FBtr0079528	71	51	F	5
-input1.bam_1	FBtr0079528	71	71	F	0
-input1.bam_1	FBtr0079596	73	1	F	13
-input1.bam_1	FBtr0079596	73	3	F	13
-input1.bam_1	FBtr0079596	73	4	F	31
-input1.bam_1	FBtr0079596	73	5	F	2
-input1.bam_1	FBtr0079596	73	6	F	11
-input1.bam_1	FBtr0079596	73	8	F	9
-input1.bam_1	FBtr0079596	73	9	F	12
-input1.bam_1	FBtr0079596	73	10	F	3
-input1.bam_1	FBtr0079596	73	11	F	19
-input1.bam_1	FBtr0079596	73	12	F	1
-input1.bam_1	FBtr0079596	73	13	F	20
-input1.bam_1	FBtr0079596	73	14	F	6
-input1.bam_1	FBtr0079596	73	15	F	1
-input1.bam_1	FBtr0079596	73	16	F	3
-input1.bam_1	FBtr0079596	73	17	F	2
-input1.bam_1	FBtr0079596	73	18	F	1
-input1.bam_1	FBtr0079596	73	19	F	1
-input1.bam_1	FBtr0079596	73	53	F	2
-input1.bam_1	FBtr0079596	73	54	F	2
-input1.bam_1	FBtr0079596	73	73	F	0
-input1.bam_1	FBtr0079677	72	1	F	1
-input1.bam_1	FBtr0079677	72	5	F	1
-input1.bam_1	FBtr0079677	72	52	F	1
-input1.bam_1	FBtr0079677	72	53	F	1
-input1.bam_1	FBtr0079677	72	72	F	0
-input1.bam_1	FBtr0079690	72	1	F	1
-input1.bam_1	FBtr0079690	72	22	F	1
-input1.bam_1	FBtr0079690	72	27	F	1
-input1.bam_1	FBtr0079690	72	33	F	2
-input1.bam_1	FBtr0079690	72	72	F	0
-input1.bam_1	FBtr0079692	73	1	F	3
-input1.bam_1	FBtr0079692	73	18	F	1
-input1.bam_1	FBtr0079692	73	25	F	1
-input1.bam_1	FBtr0079692	73	32	F	1
-input1.bam_1	FBtr0079692	73	73	F	0
-input1.bam_1	FBtr0079693	72	1	F	5
-input1.bam_1	FBtr0079693	72	25	F	1
-input1.bam_1	FBtr0079693	72	72	F	0
-input1.bam_1	FBtr0079694	72	1	F	5
-input1.bam_1	FBtr0079694	72	18	F	1
-input1.bam_1	FBtr0079694	72	52	F	1
-input1.bam_1	FBtr0079694	72	72	F	0
-input1.bam_1	FBtr0079702	72	1	F	1
-input1.bam_1	FBtr0079702	72	19	F	2
-input1.bam_1	FBtr0079702	72	56	F	1
-input1.bam_1	FBtr0079702	72	72	F	0
-input1.bam_1	FBtr0079728	72	1	F	2
-input1.bam_1	FBtr0079728	72	8	F	1
-input1.bam_1	FBtr0079728	72	19	F	1
-input1.bam_1	FBtr0079728	72	33	F	3
-input1.bam_1	FBtr0079728	72	56	F	1
-input1.bam_1	FBtr0079728	72	72	F	0
-input1.bam_1	FBtr0079729	72	1	F	1
-input1.bam_1	FBtr0079729	72	13	F	1
-input1.bam_1	FBtr0079729	72	52	F	1
-input1.bam_1	FBtr0079729	72	57	F	1
-input1.bam_1	FBtr0079729	72	72	F	0
-input1.bam_1	FBtr0079752	72	1	F	2
-input1.bam_1	FBtr0079752	72	7	F	1
-input1.bam_1	FBtr0079752	72	12	F	1
-input1.bam_1	FBtr0079752	72	33	F	2
-input1.bam_1	FBtr0079752	72	52	F	2
-input1.bam_1	FBtr0079752	72	72	F	0
-input1.bam_1	FBtr0079820	74	1	F	0
-input1.bam_1	FBtr0079820	74	45	F	1
-input1.bam_1	FBtr0079820	74	46	F	2
-input1.bam_1	FBtr0079820	74	48	F	1
-input1.bam_1	FBtr0079820	74	49	F	1
-input1.bam_1	FBtr0079820	74	51	F	1
-input1.bam_1	FBtr0079820	74	54	F	4
-input1.bam_1	FBtr0079820	74	55	F	1
-input1.bam_1	FBtr0079820	74	56	F	2
-input1.bam_1	FBtr0079820	74	74	F	0
-input1.bam_1	FBtr0080609	72	1	F	13
-input1.bam_1	FBtr0080609	72	3	F	2
-input1.bam_1	FBtr0080609	72	4	F	10
-input1.bam_1	FBtr0080609	72	5	F	2
-input1.bam_1	FBtr0080609	72	7	F	19
-input1.bam_1	FBtr0080609	72	8	F	4
-input1.bam_1	FBtr0080609	72	9	F	3
-input1.bam_1	FBtr0080609	72	12	F	1
-input1.bam_1	FBtr0080609	72	15	F	1
-input1.bam_1	FBtr0080609	72	16	F	1
-input1.bam_1	FBtr0080609	72	17	F	2
-input1.bam_1	FBtr0080609	72	19	F	1
-input1.bam_1	FBtr0080609	72	20	F	1
-input1.bam_1	FBtr0080609	72	42	F	1
-input1.bam_1	FBtr0080609	72	51	F	1
-input1.bam_1	FBtr0080609	72	52	F	1
-input1.bam_1	FBtr0080609	72	72	F	0
-input1.bam_1	FBtr0080644	72	1	F	1
-input1.bam_1	FBtr0080644	72	4	F	2
-input1.bam_1	FBtr0080644	72	7	F	1
-input1.bam_1	FBtr0080644	72	12	F	2
-input1.bam_1	FBtr0080644	72	72	F	0
-input1.bam_1	FBtr0080646	72	1	F	1
-input1.bam_1	FBtr0080646	72	6	F	1
-input1.bam_1	FBtr0080646	72	7	F	1
-input1.bam_1	FBtr0080646	72	72	F	0
-input1.bam_1	FBtr0080647	72	1	F	3
-input1.bam_1	FBtr0080647	72	3	F	1
-input1.bam_1	FBtr0080647	72	6	F	2
-input1.bam_1	FBtr0080647	72	8	F	1
-input1.bam_1	FBtr0080647	72	11	F	2
-input1.bam_1	FBtr0080647	72	12	F	1
-input1.bam_1	FBtr0080647	72	72	F	0
-input1.bam_1	FBtr0080660	72	1	F	0
-input1.bam_1	FBtr0080660	72	4	F	4
-input1.bam_1	FBtr0080660	72	7	F	3
-input1.bam_1	FBtr0080660	72	72	F	0
-input1.bam_1	FBtr0080663	71	1	F	22
-input1.bam_1	FBtr0080663	71	3	F	56
-input1.bam_1	FBtr0080663	71	4	F	4
-input1.bam_1	FBtr0080663	71	7	F	1
-input1.bam_1	FBtr0080663	71	8	F	4
-input1.bam_1	FBtr0080663	71	12	F	2
-input1.bam_1	FBtr0080663	71	14	F	2
-input1.bam_1	FBtr0080663	71	15	F	1
-input1.bam_1	FBtr0080663	71	16	F	3
-input1.bam_1	FBtr0080663	71	17	F	7
-input1.bam_1	FBtr0080663	71	26	F	1
-input1.bam_1	FBtr0080663	71	32	F	2
-input1.bam_1	FBtr0080663	71	50	F	1
-input1.bam_1	FBtr0080663	71	51	F	9
-input1.bam_1	FBtr0080663	71	71	F	0
-input1.bam_1	FBtr0080664	71	1	F	16
-input1.bam_1	FBtr0080664	71	3	F	56
-input1.bam_1	FBtr0080664	71	4	F	4
-input1.bam_1	FBtr0080664	71	6	F	1
-input1.bam_1	FBtr0080664	71	7	F	1
-input1.bam_1	FBtr0080664	71	8	F	4
-input1.bam_1	FBtr0080664	71	9	F	1
-input1.bam_1	FBtr0080664	71	11	F	3
-input1.bam_1	FBtr0080664	71	12	F	3
-input1.bam_1	FBtr0080664	71	13	F	2
-input1.bam_1	FBtr0080664	71	14	F	3
-input1.bam_1	FBtr0080664	71	16	F	2
-input1.bam_1	FBtr0080664	71	17	F	10
-input1.bam_1	FBtr0080664	71	18	F	1
-input1.bam_1	FBtr0080664	71	21	F	1
-input1.bam_1	FBtr0080664	71	28	F	2
-input1.bam_1	FBtr0080664	71	32	F	1
-input1.bam_1	FBtr0080664	71	33	F	1
-input1.bam_1	FBtr0080664	71	34	F	1
-input1.bam_1	FBtr0080664	71	35	F	1
-input1.bam_1	FBtr0080664	71	36	F	1
-input1.bam_1	FBtr0080664	71	37	F	1
-input1.bam_1	FBtr0080664	71	38	F	1
-input1.bam_1	FBtr0080664	71	50	F	2
-input1.bam_1	FBtr0080664	71	51	F	7
-input1.bam_1	FBtr0080664	71	52	F	1
-input1.bam_1	FBtr0080664	71	56	F	1
-input1.bam_1	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/doubled_mean.tab
--- a/test-data/doubled_mean.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,599 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input1.bam_0	FBtr0070001	72	1	F	17.0
-input1.bam_0	FBtr0070001	72	7	F	20.3
-input1.bam_0	FBtr0070001	72	8	F	21.3
-input1.bam_0	FBtr0070001	72	11	F	20.5
-input1.bam_0	FBtr0070001	72	16	F	19.0
-input1.bam_0	FBtr0070001	72	17	F	23.0
-input1.bam_0	FBtr0070001	72	18	F	16.0
-input1.bam_0	FBtr0070001	72	27	F	23.5
-input1.bam_0	FBtr0070001	72	30	F	23.0
-input1.bam_0	FBtr0070001	72	31	F	23.0
-input1.bam_0	FBtr0070001	72	32	F	22.0
-input1.bam_0	FBtr0070001	72	34	F	20.0
-input1.bam_0	FBtr0070001	72	72	F	0
-input1.bam_0	FBtr0070533	72	1	F	15.0
-input1.bam_0	FBtr0070533	72	12	F	18.0
-input1.bam_0	FBtr0070533	72	15	F	15.0
-input1.bam_0	FBtr0070533	72	19	F	21.8
-input1.bam_0	FBtr0070533	72	20	F	23.0
-input1.bam_0	FBtr0070533	72	21	F	18.0
-input1.bam_0	FBtr0070533	72	22	F	20.0
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-input1.bam_1	FBtr0070603	72	17	F	24.0
-input1.bam_1	FBtr0070603	72	18	F	16.0
-input1.bam_1	FBtr0070603	72	19	F	22.6
-input1.bam_1	FBtr0070603	72	20	F	21.0
-input1.bam_1	FBtr0070603	72	21	F	25.0
-input1.bam_1	FBtr0070603	72	22	F	20.7
-input1.bam_1	FBtr0070603	72	24	F	19.5
-input1.bam_1	FBtr0070603	72	25	F	23.0
-input1.bam_1	FBtr0070603	72	26	F	25.8
-input1.bam_1	FBtr0070603	72	27	F	26.3
-input1.bam_1	FBtr0070603	72	32	F	20.0
-input1.bam_1	FBtr0070603	72	34	F	19.3
-input1.bam_1	FBtr0070603	72	38	F	18.0
-input1.bam_1	FBtr0070603	72	42	F	21.0
-input1.bam_1	FBtr0070603	72	51	F	18.0
-input1.bam_1	FBtr0070603	72	56	F	16.0
-input1.bam_1	FBtr0070603	72	72	F	0
-input1.bam_1	FBtr0070604	72	1	F	15.0
-input1.bam_1	FBtr0070604	72	18	F	23.0
-input1.bam_1	FBtr0070604	72	22	F	19.0
-input1.bam_1	FBtr0070604	72	30	F	18.0
-input1.bam_1	FBtr0070604	72	31	F	22.6
-input1.bam_1	FBtr0070604	72	32	F	22.0
-input1.bam_1	FBtr0070604	72	57	F	15.0
-input1.bam_1	FBtr0070604	72	72	F	0
-input1.bam_1	FBtr0070911	73	1	F	0
-input1.bam_1	FBtr0070911	73	15	F	21.0
-input1.bam_1	FBtr0070911	73	38	F	15.0
-input1.bam_1	FBtr0070911	73	73	F	0
-input1.bam_1	FBtr0078490	72	1	F	0
-input1.bam_1	FBtr0078490	72	13	F	16.0
-input1.bam_1	FBtr0078490	72	17	F	16.0
-input1.bam_1	FBtr0078490	72	18	F	15.0
-input1.bam_1	FBtr0078490	72	25	F	15.0
-input1.bam_1	FBtr0078490	72	28	F	19.0
-input1.bam_1	FBtr0078490	72	38	F	18.0
-input1.bam_1	FBtr0078490	72	72	F	0
-input1.bam_1	FBtr0078580	72	1	F	18.9
-input1.bam_1	FBtr0078580	72	3	F	22.0
-input1.bam_1	FBtr0078580	72	4	F	25.3
-input1.bam_1	FBtr0078580	72	5	F	21.0
-input1.bam_1	FBtr0078580	72	6	F	19.0
-input1.bam_1	FBtr0078580	72	7	F	22.0
-input1.bam_1	FBtr0078580	72	8	F	18.0
-input1.bam_1	FBtr0078580	72	11	F	23.0
-input1.bam_1	FBtr0078580	72	12	F	18.0
-input1.bam_1	FBtr0078580	72	14	F	15.3
-input1.bam_1	FBtr0078580	72	15	F	16.0
-input1.bam_1	FBtr0078580	72	16	F	19.0
-input1.bam_1	FBtr0078580	72	17	F	17.0
-input1.bam_1	FBtr0078580	72	19	F	24.0
-input1.bam_1	FBtr0078580	72	20	F	21.0
-input1.bam_1	FBtr0078580	72	21	F	19.4
-input1.bam_1	FBtr0078580	72	24	F	17.0
-input1.bam_1	FBtr0078580	72	25	F	27.5
-input1.bam_1	FBtr0078580	72	29	F	17.0
-input1.bam_1	FBtr0078580	72	31	F	17.0
-input1.bam_1	FBtr0078580	72	52	F	16.0
-input1.bam_1	FBtr0078580	72	72	F	0
-input1.bam_1	FBtr0078790	73	1	F	19.0
-input1.bam_1	FBtr0078790	73	17	F	16.0
-input1.bam_1	FBtr0078790	73	33	F	23.0
-input1.bam_1	FBtr0078790	73	42	F	18.5
-input1.bam_1	FBtr0078790	73	44	F	19.5
-input1.bam_1	FBtr0078790	73	46	F	17.0
-input1.bam_1	FBtr0078790	73	47	F	18.0
-input1.bam_1	FBtr0078790	73	52	F	20.0
-input1.bam_1	FBtr0078790	73	69	R	15.0
-input1.bam_1	FBtr0078790	73	73	F	0
-input1.bam_1	FBtr0079064	72	1	F	15.0
-input1.bam_1	FBtr0079064	72	3	F	21.0
-input1.bam_1	FBtr0079064	72	33	F	15.0
-input1.bam_1	FBtr0079064	72	52	F	17.0
-input1.bam_1	FBtr0079064	72	72	F	0
-input1.bam_1	FBtr0079090	72	1	F	21.5
-input1.bam_1	FBtr0079090	72	26	F	24.0
-input1.bam_1	FBtr0079090	72	33	F	16.0
-input1.bam_1	FBtr0079090	72	53	F	18.0
-input1.bam_1	FBtr0079090	72	56	R	21.0
-input1.bam_1	FBtr0079090	72	72	F	0
-input1.bam_1	FBtr0079338	73	1	F	0
-input1.bam_1	FBtr0079338	73	12	F	17.0
-input1.bam_1	FBtr0079338	73	13	F	17.5
-input1.bam_1	FBtr0079338	73	14	F	15.0
-input1.bam_1	FBtr0079338	73	17	F	15.0
-input1.bam_1	FBtr0079338	73	25	F	16.0
-input1.bam_1	FBtr0079338	73	42	F	21.8
-input1.bam_1	FBtr0079338	73	43	F	21.0
-input1.bam_1	FBtr0079338	73	46	F	18.0
-input1.bam_1	FBtr0079338	73	73	F	0
-input1.bam_1	FBtr0079528	71	1	F	20.8
-input1.bam_1	FBtr0079528	71	3	F	23.6
-input1.bam_1	FBtr0079528	71	4	F	24.0
-input1.bam_1	FBtr0079528	71	8	F	20.3
-input1.bam_1	FBtr0079528	71	10	F	21.0
-input1.bam_1	FBtr0079528	71	11	F	19.0
-input1.bam_1	FBtr0079528	71	13	F	16.0
-input1.bam_1	FBtr0079528	71	14	F	18.5
-input1.bam_1	FBtr0079528	71	16	F	15.0
-input1.bam_1	FBtr0079528	71	17	F	15.3
-input1.bam_1	FBtr0079528	71	18	F	19.8
-input1.bam_1	FBtr0079528	71	28	F	16.0
-input1.bam_1	FBtr0079528	71	35	F	15.0
-input1.bam_1	FBtr0079528	71	36	F	20.0
-input1.bam_1	FBtr0079528	71	37	F	18.0
-input1.bam_1	FBtr0079528	71	51	F	15.0
-input1.bam_1	FBtr0079528	71	71	F	0
-input1.bam_1	FBtr0079596	73	1	F	16.2
-input1.bam_1	FBtr0079596	73	3	F	21.8
-input1.bam_1	FBtr0079596	73	4	F	21.5
-input1.bam_1	FBtr0079596	73	5	F	18.5
-input1.bam_1	FBtr0079596	73	6	F	17.5
-input1.bam_1	FBtr0079596	73	8	F	16.6
-input1.bam_1	FBtr0079596	73	9	F	16.1
-input1.bam_1	FBtr0079596	73	10	F	15.3
-input1.bam_1	FBtr0079596	73	11	F	15.2
-input1.bam_1	FBtr0079596	73	12	F	17.0
-input1.bam_1	FBtr0079596	73	13	F	16.1
-input1.bam_1	FBtr0079596	73	14	F	15.0
-input1.bam_1	FBtr0079596	73	15	F	18.0
-input1.bam_1	FBtr0079596	73	16	F	16.7
-input1.bam_1	FBtr0079596	73	17	F	16.0
-input1.bam_1	FBtr0079596	73	18	F	15.0
-input1.bam_1	FBtr0079596	73	19	F	15.0
-input1.bam_1	FBtr0079596	73	53	F	18.5
-input1.bam_1	FBtr0079596	73	54	F	19.5
-input1.bam_1	FBtr0079596	73	73	F	0
-input1.bam_1	FBtr0079677	72	1	F	23.0
-input1.bam_1	FBtr0079677	72	5	F	19.0
-input1.bam_1	FBtr0079677	72	52	F	19.0
-input1.bam_1	FBtr0079677	72	53	F	18.0
-input1.bam_1	FBtr0079677	72	72	F	0
-input1.bam_1	FBtr0079690	72	1	F	15.0
-input1.bam_1	FBtr0079690	72	22	F	15.0
-input1.bam_1	FBtr0079690	72	27	F	25.0
-input1.bam_1	FBtr0079690	72	33	F	16.0
-input1.bam_1	FBtr0079690	72	72	F	0
-input1.bam_1	FBtr0079692	73	1	F	19.3
-input1.bam_1	FBtr0079692	73	18	F	18.0
-input1.bam_1	FBtr0079692	73	25	F	17.0
-input1.bam_1	FBtr0079692	73	32	F	20.0
-input1.bam_1	FBtr0079692	73	73	F	0
-input1.bam_1	FBtr0079693	72	1	F	17.2
-input1.bam_1	FBtr0079693	72	25	F	23.0
-input1.bam_1	FBtr0079693	72	72	F	0
-input1.bam_1	FBtr0079694	72	1	F	20.4
-input1.bam_1	FBtr0079694	72	18	F	19.0
-input1.bam_1	FBtr0079694	72	52	F	17.0
-input1.bam_1	FBtr0079694	72	72	F	0
-input1.bam_1	FBtr0079702	72	1	F	15.0
-input1.bam_1	FBtr0079702	72	19	F	18.0
-input1.bam_1	FBtr0079702	72	56	F	15.0
-input1.bam_1	FBtr0079702	72	72	F	0
-input1.bam_1	FBtr0079728	72	1	F	16.0
-input1.bam_1	FBtr0079728	72	8	F	20.0
-input1.bam_1	FBtr0079728	72	19	F	24.0
-input1.bam_1	FBtr0079728	72	33	F	15.7
-input1.bam_1	FBtr0079728	72	56	F	15.0
-input1.bam_1	FBtr0079728	72	72	F	0
-input1.bam_1	FBtr0079729	72	1	F	15.0
-input1.bam_1	FBtr0079729	72	13	F	22.0
-input1.bam_1	FBtr0079729	72	52	F	18.0
-input1.bam_1	FBtr0079729	72	57	F	16.0
-input1.bam_1	FBtr0079729	72	72	F	0
-input1.bam_1	FBtr0079752	72	1	F	19.5
-input1.bam_1	FBtr0079752	72	7	F	20.0
-input1.bam_1	FBtr0079752	72	12	F	16.0
-input1.bam_1	FBtr0079752	72	33	F	16.0
-input1.bam_1	FBtr0079752	72	52	F	19.5
-input1.bam_1	FBtr0079752	72	72	F	0
-input1.bam_1	FBtr0079820	74	1	F	0
-input1.bam_1	FBtr0079820	74	45	F	20.0
-input1.bam_1	FBtr0079820	74	46	F	17.0
-input1.bam_1	FBtr0079820	74	48	F	18.0
-input1.bam_1	FBtr0079820	74	49	F	24.0
-input1.bam_1	FBtr0079820	74	51	F	20.0
-input1.bam_1	FBtr0079820	74	54	F	17.0
-input1.bam_1	FBtr0079820	74	55	F	18.0
-input1.bam_1	FBtr0079820	74	56	F	18.5
-input1.bam_1	FBtr0079820	74	74	F	0
-input1.bam_1	FBtr0080609	72	1	F	18.8
-input1.bam_1	FBtr0080609	72	3	F	21.0
-input1.bam_1	FBtr0080609	72	4	F	20.0
-input1.bam_1	FBtr0080609	72	5	F	19.0
-input1.bam_1	FBtr0080609	72	7	F	17.1
-input1.bam_1	FBtr0080609	72	8	F	16.0
-input1.bam_1	FBtr0080609	72	9	F	15.0
-input1.bam_1	FBtr0080609	72	12	F	23.0
-input1.bam_1	FBtr0080609	72	15	F	19.0
-input1.bam_1	FBtr0080609	72	16	F	23.0
-input1.bam_1	FBtr0080609	72	17	F	20.5
-input1.bam_1	FBtr0080609	72	19	F	26.0
-input1.bam_1	FBtr0080609	72	20	F	25.0
-input1.bam_1	FBtr0080609	72	42	F	21.0
-input1.bam_1	FBtr0080609	72	51	F	18.0
-input1.bam_1	FBtr0080609	72	52	F	15.0
-input1.bam_1	FBtr0080609	72	72	F	0
-input1.bam_1	FBtr0080644	72	1	F	27.0
-input1.bam_1	FBtr0080644	72	4	F	20.5
-input1.bam_1	FBtr0080644	72	7	F	16.0
-input1.bam_1	FBtr0080644	72	12	F	16.0
-input1.bam_1	FBtr0080644	72	72	F	0
-input1.bam_1	FBtr0080646	72	1	F	16.0
-input1.bam_1	FBtr0080646	72	6	F	22.0
-input1.bam_1	FBtr0080646	72	7	F	21.0
-input1.bam_1	FBtr0080646	72	72	F	0
-input1.bam_1	FBtr0080647	72	1	F	16.3
-input1.bam_1	FBtr0080647	72	3	F	16.0
-input1.bam_1	FBtr0080647	72	6	F	19.0
-input1.bam_1	FBtr0080647	72	8	F	20.0
-input1.bam_1	FBtr0080647	72	11	F	17.0
-input1.bam_1	FBtr0080647	72	12	F	16.0
-input1.bam_1	FBtr0080647	72	72	F	0
-input1.bam_1	FBtr0080660	72	1	F	0
-input1.bam_1	FBtr0080660	72	4	F	24.0
-input1.bam_1	FBtr0080660	72	7	F	19.3
-input1.bam_1	FBtr0080660	72	72	F	0
-input1.bam_1	FBtr0080663	71	1	F	18.8
-input1.bam_1	FBtr0080663	71	3	F	23.7
-input1.bam_1	FBtr0080663	71	4	F	23.3
-input1.bam_1	FBtr0080663	71	7	F	16.0
-input1.bam_1	FBtr0080663	71	8	F	19.3
-input1.bam_1	FBtr0080663	71	12	F	16.0
-input1.bam_1	FBtr0080663	71	14	F	19.0
-input1.bam_1	FBtr0080663	71	15	F	17.0
-input1.bam_1	FBtr0080663	71	16	F	15.7
-input1.bam_1	FBtr0080663	71	17	F	15.6
-input1.bam_1	FBtr0080663	71	26	F	18.0
-input1.bam_1	FBtr0080663	71	32	F	15.5
-input1.bam_1	FBtr0080663	71	50	F	17.0
-input1.bam_1	FBtr0080663	71	51	F	15.6
-input1.bam_1	FBtr0080663	71	71	F	0
-input1.bam_1	FBtr0080664	71	1	F	19.5
-input1.bam_1	FBtr0080664	71	3	F	23.8
-input1.bam_1	FBtr0080664	71	4	F	23.5
-input1.bam_1	FBtr0080664	71	6	F	23.0
-input1.bam_1	FBtr0080664	71	7	F	21.0
-input1.bam_1	FBtr0080664	71	8	F	20.5
-input1.bam_1	FBtr0080664	71	9	F	20.0
-input1.bam_1	FBtr0080664	71	11	F	16.7
-input1.bam_1	FBtr0080664	71	12	F	18.0
-input1.bam_1	FBtr0080664	71	13	F	20.0
-input1.bam_1	FBtr0080664	71	14	F	18.3
-input1.bam_1	FBtr0080664	71	16	F	15.0
-input1.bam_1	FBtr0080664	71	17	F	15.8
-input1.bam_1	FBtr0080664	71	18	F	15.0
-input1.bam_1	FBtr0080664	71	21	F	15.0
-input1.bam_1	FBtr0080664	71	28	F	16.0
-input1.bam_1	FBtr0080664	71	32	F	15.0
-input1.bam_1	FBtr0080664	71	33	F	20.0
-input1.bam_1	FBtr0080664	71	34	F	16.0
-input1.bam_1	FBtr0080664	71	35	F	15.0
-input1.bam_1	FBtr0080664	71	36	F	21.0
-input1.bam_1	FBtr0080664	71	37	F	18.0
-input1.bam_1	FBtr0080664	71	38	F	15.0
-input1.bam_1	FBtr0080664	71	50	F	16.0
-input1.bam_1	FBtr0080664	71	51	F	15.0
-input1.bam_1	FBtr0080664	71	52	F	15.0
-input1.bam_1	FBtr0080664	71	56	F	16.0
-input1.bam_1	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/global_merge.pdf
Binary file test-data/global_merge.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/global_merge.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/global_merge.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,1045 @@
+Dataset	Chromosome	Polarity	Size	Counts
+input1.bam	FBtr0070001	F	16	2
+input1.bam	FBtr0070001	F	17	1
+input1.bam	FBtr0070001	F	18	0
+input1.bam	FBtr0070001	F	19	1
+input1.bam	FBtr0070001	F	20	4
+input1.bam	FBtr0070001	F	21	4
+input1.bam	FBtr0070001	F	22	29
+input1.bam	FBtr0070001	F	23	15
+input1.bam	FBtr0070001	F	24	1
+input1.bam	FBtr0070001	R	16	0
+input1.bam	FBtr0070001	R	17	0
+input1.bam	FBtr0070001	R	18	0
+input1.bam	FBtr0070001	R	19	0
+input1.bam	FBtr0070001	R	20	0
+input1.bam	FBtr0070001	R	21	0
+input1.bam	FBtr0070001	R	22	0
+input1.bam	FBtr0070001	R	23	0
+input1.bam	FBtr0070001	R	24	0
+input1.bam	FBtr0070533	F	15	2
+input1.bam	FBtr0070533	F	16	1
+input1.bam	FBtr0070533	F	17	1
+input1.bam	FBtr0070533	F	18	6
+input1.bam	FBtr0070533	F	19	3
+input1.bam	FBtr0070533	F	20	2
+input1.bam	FBtr0070533	F	21	2
+input1.bam	FBtr0070533	F	22	4
+input1.bam	FBtr0070533	F	23	2
+input1.bam	FBtr0070533	F	24	0
+input1.bam	FBtr0070533	F	25	1
+input1.bam	FBtr0070533	R	15	0
+input1.bam	FBtr0070533	R	16	0
+input1.bam	FBtr0070533	R	17	0
+input1.bam	FBtr0070533	R	18	0
+input1.bam	FBtr0070533	R	19	0
+input1.bam	FBtr0070533	R	20	0
+input1.bam	FBtr0070533	R	21	0
+input1.bam	FBtr0070533	R	22	0
+input1.bam	FBtr0070533	R	23	0
+input1.bam	FBtr0070533	R	24	0
+input1.bam	FBtr0070533	R	25	0
+input1.bam	FBtr0070603	F	15	9
+input1.bam	FBtr0070603	F	16	6
+input1.bam	FBtr0070603	F	17	10
+input1.bam	FBtr0070603	F	18	7
+input1.bam	FBtr0070603	F	19	1
+input1.bam	FBtr0070603	F	20	6
+input1.bam	FBtr0070603	F	21	3
+input1.bam	FBtr0070603	F	22	3
+input1.bam	FBtr0070603	F	23	10
+input1.bam	FBtr0070603	F	24	2
+input1.bam	FBtr0070603	F	25	5
+input1.bam	FBtr0070603	F	26	5
+input1.bam	FBtr0070603	F	27	3
+input1.bam	FBtr0070603	R	15	0
+input1.bam	FBtr0070603	R	16	0
+input1.bam	FBtr0070603	R	17	0
+input1.bam	FBtr0070603	R	18	0
+input1.bam	FBtr0070603	R	19	0
+input1.bam	FBtr0070603	R	20	0
+input1.bam	FBtr0070603	R	21	0
+input1.bam	FBtr0070603	R	22	0
+input1.bam	FBtr0070603	R	23	0
+input1.bam	FBtr0070603	R	24	0
+input1.bam	FBtr0070603	R	25	0
+input1.bam	FBtr0070603	R	26	0
+input1.bam	FBtr0070603	R	27	0
+input1.bam	FBtr0070604	F	15	2
+input1.bam	FBtr0070604	F	16	0
+input1.bam	FBtr0070604	F	17	0
+input1.bam	FBtr0070604	F	18	2
+input1.bam	FBtr0070604	F	19	2
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+input2.bam	FBtr0079694	F	19	1
+input2.bam	FBtr0079694	R	15	0
+input2.bam	FBtr0079694	R	16	0
+input2.bam	FBtr0079694	R	17	0
+input2.bam	FBtr0079694	R	18	0
+input2.bam	FBtr0079694	R	19	0
+input2.bam	FBtr0079702	F	15	2
+input2.bam	FBtr0079702	F	16	0
+input2.bam	FBtr0079702	F	17	1
+input2.bam	FBtr0079702	F	18	1
+input2.bam	FBtr0079702	R	15	0
+input2.bam	FBtr0079702	R	16	0
+input2.bam	FBtr0079702	R	17	0
+input2.bam	FBtr0079702	R	18	0
+input2.bam	FBtr0079728	F	15	3
+input2.bam	FBtr0079728	F	16	1
+input2.bam	FBtr0079728	F	17	1
+input2.bam	FBtr0079728	F	18	1
+input2.bam	FBtr0079728	R	15	0
+input2.bam	FBtr0079728	R	16	0
+input2.bam	FBtr0079728	R	17	0
+input2.bam	FBtr0079728	R	18	0
+input2.bam	FBtr0079729	F	15	1
+input2.bam	FBtr0079729	F	16	2
+input2.bam	FBtr0079729	F	17	1
+input2.bam	FBtr0079729	R	15	0
+input2.bam	FBtr0079729	R	16	0
+input2.bam	FBtr0079729	R	17	0
+input2.bam	FBtr0079752	F	17	1
+input2.bam	FBtr0079752	F	18	0
+input2.bam	FBtr0079752	F	19	0
+input2.bam	FBtr0079752	F	20	0
+input2.bam	FBtr0079752	F	21	0
+input2.bam	FBtr0079752	F	22	0
+input2.bam	FBtr0079752	F	23	0
+input2.bam	FBtr0079752	F	24	1
+input2.bam	FBtr0079752	R	17	0
+input2.bam	FBtr0079752	R	18	0
+input2.bam	FBtr0079752	R	19	0
+input2.bam	FBtr0079752	R	20	0
+input2.bam	FBtr0079752	R	21	0
+input2.bam	FBtr0079752	R	22	0
+input2.bam	FBtr0079752	R	23	0
+input2.bam	FBtr0079752	R	24	0
+input2.bam	FBtr0079820	F	15	27
+input2.bam	FBtr0079820	F	16	10
+input2.bam	FBtr0079820	F	17	7
+input2.bam	FBtr0079820	F	18	8
+input2.bam	FBtr0079820	F	19	25
+input2.bam	FBtr0079820	F	20	24
+input2.bam	FBtr0079820	F	21	7
+input2.bam	FBtr0079820	F	22	1
+input2.bam	FBtr0079820	R	15	0
+input2.bam	FBtr0079820	R	16	0
+input2.bam	FBtr0079820	R	17	0
+input2.bam	FBtr0079820	R	18	0
+input2.bam	FBtr0079820	R	19	0
+input2.bam	FBtr0079820	R	20	0
+input2.bam	FBtr0079820	R	21	0
+input2.bam	FBtr0079820	R	22	0
+input2.bam	FBtr0080609	F	17	2
+input2.bam	FBtr0080609	F	18	1
+input2.bam	FBtr0080609	F	19	2
+input2.bam	FBtr0080609	F	20	0
+input2.bam	FBtr0080609	F	21	0
+input2.bam	FBtr0080609	F	22	1
+input2.bam	FBtr0080609	F	23	1
+input2.bam	FBtr0080609	F	24	0
+input2.bam	FBtr0080609	F	25	1
+input2.bam	FBtr0080609	R	17	0
+input2.bam	FBtr0080609	R	18	0
+input2.bam	FBtr0080609	R	19	0
+input2.bam	FBtr0080609	R	20	0
+input2.bam	FBtr0080609	R	21	0
+input2.bam	FBtr0080609	R	22	0
+input2.bam	FBtr0080609	R	23	0
+input2.bam	FBtr0080609	R	24	0
+input2.bam	FBtr0080609	R	25	0
+input2.bam	FBtr0080644	F	15	8
+input2.bam	FBtr0080644	R	15	0
+input2.bam	FBtr0080646	F	15	10
+input2.bam	FBtr0080646	F	16	1
+input2.bam	FBtr0080646	F	17	0
+input2.bam	FBtr0080646	F	18	0
+input2.bam	FBtr0080646	F	19	0
+input2.bam	FBtr0080646	F	20	0
+input2.bam	FBtr0080646	F	21	1
+input2.bam	FBtr0080646	R	15	0
+input2.bam	FBtr0080646	R	16	0
+input2.bam	FBtr0080646	R	17	0
+input2.bam	FBtr0080646	R	18	0
+input2.bam	FBtr0080646	R	19	0
+input2.bam	FBtr0080646	R	20	0
+input2.bam	FBtr0080646	R	21	0
+input2.bam	FBtr0080647	F	15	9
+input2.bam	FBtr0080647	F	16	2
+input2.bam	FBtr0080647	F	17	0
+input2.bam	FBtr0080647	F	18	1
+input2.bam	FBtr0080647	R	15	0
+input2.bam	FBtr0080647	R	16	0
+input2.bam	FBtr0080647	R	17	0
+input2.bam	FBtr0080647	R	18	0
+input2.bam	FBtr0080660	F	15	11
+input2.bam	FBtr0080660	R	15	0
+input2.bam	FBtr0080663	F	15	26
+input2.bam	FBtr0080663	F	16	14
+input2.bam	FBtr0080663	F	17	14
+input2.bam	FBtr0080663	F	18	26
+input2.bam	FBtr0080663	F	19	9
+input2.bam	FBtr0080663	F	20	7
+input2.bam	FBtr0080663	F	21	4
+input2.bam	FBtr0080663	F	22	5
+input2.bam	FBtr0080663	F	23	0
+input2.bam	FBtr0080663	F	24	1
+input2.bam	FBtr0080663	R	15	0
+input2.bam	FBtr0080663	R	16	0
+input2.bam	FBtr0080663	R	17	0
+input2.bam	FBtr0080663	R	18	0
+input2.bam	FBtr0080663	R	19	0
+input2.bam	FBtr0080663	R	20	0
+input2.bam	FBtr0080663	R	21	0
+input2.bam	FBtr0080663	R	22	0
+input2.bam	FBtr0080663	R	23	0
+input2.bam	FBtr0080663	R	24	0
+input2.bam	FBtr0080664	F	15	165
+input2.bam	FBtr0080664	F	16	59
+input2.bam	FBtr0080664	F	17	20
+input2.bam	FBtr0080664	F	18	75
+input2.bam	FBtr0080664	F	19	24
+input2.bam	FBtr0080664	F	20	21
+input2.bam	FBtr0080664	F	21	8
+input2.bam	FBtr0080664	F	22	4
+input2.bam	FBtr0080664	F	23	4
+input2.bam	FBtr0080664	F	24	0
+input2.bam	FBtr0080664	F	25	3
+input2.bam	FBtr0080664	F	26	4
+input2.bam	FBtr0080664	R	15	0
+input2.bam	FBtr0080664	R	16	0
+input2.bam	FBtr0080664	R	17	0
+input2.bam	FBtr0080664	R	18	0
+input2.bam	FBtr0080664	R	19	0
+input2.bam	FBtr0080664	R	20	0
+input2.bam	FBtr0080664	R	21	0
+input2.bam	FBtr0080664	R	22	1
+input2.bam	FBtr0080664	R	23	1
+input2.bam	FBtr0080664	R	24	0
+input2.bam	FBtr0080664	R	25	0
+input2.bam	FBtr0080664	R	26	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/global_nomerge.pdf
Binary file test-data/global_nomerge.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/global_nomerge.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/global_nomerge.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,1045 @@
+Dataset	Chromosome	Polarity	Size	Counts
+input1.bam	FBtr0070001	F	16	2
+input1.bam	FBtr0070001	F	17	1
+input1.bam	FBtr0070001	F	18	0
+input1.bam	FBtr0070001	F	19	1
+input1.bam	FBtr0070001	F	20	4
+input1.bam	FBtr0070001	F	21	4
+input1.bam	FBtr0070001	F	22	29
+input1.bam	FBtr0070001	F	23	15
+input1.bam	FBtr0070001	F	24	1
+input1.bam	FBtr0070001	R	16	0
+input1.bam	FBtr0070001	R	17	0
+input1.bam	FBtr0070001	R	18	0
+input1.bam	FBtr0070001	R	19	0
+input1.bam	FBtr0070001	R	20	0
+input1.bam	FBtr0070001	R	21	0
+input1.bam	FBtr0070001	R	22	0
+input1.bam	FBtr0070001	R	23	0
+input1.bam	FBtr0070001	R	24	0
+input1.bam	FBtr0070533	F	15	2
+input1.bam	FBtr0070533	F	16	1
+input1.bam	FBtr0070533	F	17	1
+input1.bam	FBtr0070533	F	18	6
+input1.bam	FBtr0070533	F	19	3
+input1.bam	FBtr0070533	F	20	2
+input1.bam	FBtr0070533	F	21	2
+input1.bam	FBtr0070533	F	22	4
+input1.bam	FBtr0070533	F	23	2
+input1.bam	FBtr0070533	F	24	0
+input1.bam	FBtr0070533	F	25	1
+input1.bam	FBtr0070533	R	15	0
+input1.bam	FBtr0070533	R	16	0
+input1.bam	FBtr0070533	R	17	0
+input1.bam	FBtr0070533	R	18	0
+input1.bam	FBtr0070533	R	19	0
+input1.bam	FBtr0070533	R	20	0
+input1.bam	FBtr0070533	R	21	0
+input1.bam	FBtr0070533	R	22	0
+input1.bam	FBtr0070533	R	23	0
+input1.bam	FBtr0070533	R	24	0
+input1.bam	FBtr0070533	R	25	0
+input1.bam	FBtr0070603	F	15	9
+input1.bam	FBtr0070603	F	16	6
+input1.bam	FBtr0070603	F	17	10
+input1.bam	FBtr0070603	F	18	7
+input1.bam	FBtr0070603	F	19	1
+input1.bam	FBtr0070603	F	20	6
+input1.bam	FBtr0070603	F	21	3
+input1.bam	FBtr0070603	F	22	3
+input1.bam	FBtr0070603	F	23	10
+input1.bam	FBtr0070603	F	24	2
+input1.bam	FBtr0070603	F	25	5
+input1.bam	FBtr0070603	F	26	5
+input1.bam	FBtr0070603	F	27	3
+input1.bam	FBtr0070603	R	15	0
+input1.bam	FBtr0070603	R	16	0
+input1.bam	FBtr0070603	R	17	0
+input1.bam	FBtr0070603	R	18	0
+input1.bam	FBtr0070603	R	19	0
+input1.bam	FBtr0070603	R	20	0
+input1.bam	FBtr0070603	R	21	0
+input1.bam	FBtr0070603	R	22	0
+input1.bam	FBtr0070603	R	23	0
+input1.bam	FBtr0070603	R	24	0
+input1.bam	FBtr0070603	R	25	0
+input1.bam	FBtr0070603	R	26	0
+input1.bam	FBtr0070603	R	27	0
+input1.bam	FBtr0070604	F	15	2
+input1.bam	FBtr0070604	F	16	0
+input1.bam	FBtr0070604	F	17	0
+input1.bam	FBtr0070604	F	18	2
+input1.bam	FBtr0070604	F	19	2
+input1.bam	FBtr0070604	F	20	0
+input1.bam	FBtr0070604	F	21	1
+input1.bam	FBtr0070604	F	22	23
+input1.bam	FBtr0070604	F	23	10
+input1.bam	FBtr0070604	R	15	0
+input1.bam	FBtr0070604	R	16	0
+input1.bam	FBtr0070604	R	17	0
+input1.bam	FBtr0070604	R	18	0
+input1.bam	FBtr0070604	R	19	0
+input1.bam	FBtr0070604	R	20	0
+input1.bam	FBtr0070604	R	21	0
+input1.bam	FBtr0070604	R	22	0
+input1.bam	FBtr0070604	R	23	0
+input1.bam	FBtr0070911	F	15	1
+input1.bam	FBtr0070911	F	16	0
+input1.bam	FBtr0070911	F	17	0
+input1.bam	FBtr0070911	F	18	0
+input1.bam	FBtr0070911	F	19	0
+input1.bam	FBtr0070911	F	20	0
+input1.bam	FBtr0070911	F	21	1
+input1.bam	FBtr0070911	R	15	0
+input1.bam	FBtr0070911	R	16	0
+input1.bam	FBtr0070911	R	17	0
+input1.bam	FBtr0070911	R	18	0
+input1.bam	FBtr0070911	R	19	0
+input1.bam	FBtr0070911	R	20	0
+input1.bam	FBtr0070911	R	21	0
+input1.bam	FBtr0078490	F	15	3
+input1.bam	FBtr0078490	F	16	3
+input1.bam	FBtr0078490	F	17	0
+input1.bam	FBtr0078490	F	18	1
+input1.bam	FBtr0078490	F	19	0
+input1.bam	FBtr0078490	F	20	0
+input1.bam	FBtr0078490	F	21	0
+input1.bam	FBtr0078490	F	22	0
+input1.bam	FBtr0078490	F	23	1
+input1.bam	FBtr0078490	R	15	0
+input1.bam	FBtr0078490	R	16	0
+input1.bam	FBtr0078490	R	17	0
+input1.bam	FBtr0078490	R	18	0
+input1.bam	FBtr0078490	R	19	0
+input1.bam	FBtr0078490	R	20	0
+input1.bam	FBtr0078490	R	21	0
+input1.bam	FBtr0078490	R	22	0
+input1.bam	FBtr0078490	R	23	0
+input1.bam	FBtr0078580	F	15	592
+input1.bam	FBtr0078580	F	16	20
+input1.bam	FBtr0078580	F	17	31
+input1.bam	FBtr0078580	F	18	9
+input1.bam	FBtr0078580	F	19	8
+input1.bam	FBtr0078580	F	20	9
+input1.bam	FBtr0078580	F	21	5
+input1.bam	FBtr0078580	F	22	13
+input1.bam	FBtr0078580	F	23	5
+input1.bam	FBtr0078580	F	24	180
+input1.bam	FBtr0078580	F	25	212
+input1.bam	FBtr0078580	F	26	1
+input1.bam	FBtr0078580	F	27	2
+input1.bam	FBtr0078580	F	28	17
+input1.bam	FBtr0078580	R	15	0
+input1.bam	FBtr0078580	R	16	0
+input1.bam	FBtr0078580	R	17	0
+input1.bam	FBtr0078580	R	18	0
+input1.bam	FBtr0078580	R	19	0
+input1.bam	FBtr0078580	R	20	0
+input1.bam	FBtr0078580	R	21	0
+input1.bam	FBtr0078580	R	22	0
+input1.bam	FBtr0078580	R	23	0
+input1.bam	FBtr0078580	R	24	0
+input1.bam	FBtr0078580	R	25	0
+input1.bam	FBtr0078580	R	26	0
+input1.bam	FBtr0078580	R	27	0
+input1.bam	FBtr0078580	R	28	0
+input1.bam	FBtr0078790	F	15	2
+input1.bam	FBtr0078790	F	16	2
+input1.bam	FBtr0078790	F	17	1
+input1.bam	FBtr0078790	F	18	1
+input1.bam	FBtr0078790	F	19	2
+input1.bam	FBtr0078790	F	20	2
+input1.bam	FBtr0078790	F	21	0
+input1.bam	FBtr0078790	F	22	2
+input1.bam	FBtr0078790	F	23	1
+input1.bam	FBtr0078790	R	15	1
+input1.bam	FBtr0078790	R	16	0
+input1.bam	FBtr0078790	R	17	0
+input1.bam	FBtr0078790	R	18	0
+input1.bam	FBtr0078790	R	19	0
+input1.bam	FBtr0078790	R	20	0
+input1.bam	FBtr0078790	R	21	0
+input1.bam	FBtr0078790	R	22	0
+input1.bam	FBtr0078790	R	23	0
+input1.bam	FBtr0079064	F	15	2
+input1.bam	FBtr0079064	F	16	0
+input1.bam	FBtr0079064	F	17	1
+input1.bam	FBtr0079064	F	18	0
+input1.bam	FBtr0079064	F	19	0
+input1.bam	FBtr0079064	F	20	0
+input1.bam	FBtr0079064	F	21	1
+input1.bam	FBtr0079064	R	15	0
+input1.bam	FBtr0079064	R	16	0
+input1.bam	FBtr0079064	R	17	0
+input1.bam	FBtr0079064	R	18	0
+input1.bam	FBtr0079064	R	19	0
+input1.bam	FBtr0079064	R	20	0
+input1.bam	FBtr0079064	R	21	0
+input1.bam	FBtr0079090	F	15	1
+input1.bam	FBtr0079090	F	16	1
+input1.bam	FBtr0079090	F	17	0
+input1.bam	FBtr0079090	F	18	1
+input1.bam	FBtr0079090	F	19	0
+input1.bam	FBtr0079090	F	20	0
+input1.bam	FBtr0079090	F	21	0
+input1.bam	FBtr0079090	F	22	0
+input1.bam	FBtr0079090	F	23	0
+input1.bam	FBtr0079090	F	24	1
+input1.bam	FBtr0079090	F	25	0
+input1.bam	FBtr0079090	F	26	0
+input1.bam	FBtr0079090	F	27	0
+input1.bam	FBtr0079090	F	28	1
+input1.bam	FBtr0079090	R	15	0
+input1.bam	FBtr0079090	R	16	0
+input1.bam	FBtr0079090	R	17	0
+input1.bam	FBtr0079090	R	18	0
+input1.bam	FBtr0079090	R	19	0
+input1.bam	FBtr0079090	R	20	0
+input1.bam	FBtr0079090	R	21	1
+input1.bam	FBtr0079090	R	22	0
+input1.bam	FBtr0079090	R	23	0
+input1.bam	FBtr0079090	R	24	0
+input1.bam	FBtr0079090	R	25	0
+input1.bam	FBtr0079090	R	26	0
+input1.bam	FBtr0079090	R	27	0
+input1.bam	FBtr0079090	R	28	0
+input1.bam	FBtr0079338	F	15	2
+input1.bam	FBtr0079338	F	16	2
+input1.bam	FBtr0079338	F	17	1
+input1.bam	FBtr0079338	F	18	1
+input1.bam	FBtr0079338	F	19	1
+input1.bam	FBtr0079338	F	20	0
+input1.bam	FBtr0079338	F	21	3
+input1.bam	FBtr0079338	F	22	6
+input1.bam	FBtr0079338	R	15	0
+input1.bam	FBtr0079338	R	16	0
+input1.bam	FBtr0079338	R	17	0
+input1.bam	FBtr0079338	R	18	0
+input1.bam	FBtr0079338	R	19	0
+input1.bam	FBtr0079338	R	20	0
+input1.bam	FBtr0079338	R	21	0
+input1.bam	FBtr0079338	R	22	0
+input1.bam	FBtr0079528	F	15	12
+input1.bam	FBtr0079528	F	16	11
+input1.bam	FBtr0079528	F	17	0
+input1.bam	FBtr0079528	F	18	5
+input1.bam	FBtr0079528	F	19	4
+input1.bam	FBtr0079528	F	20	12
+input1.bam	FBtr0079528	F	21	3
+input1.bam	FBtr0079528	F	22	2
+input1.bam	FBtr0079528	F	23	3
+input1.bam	FBtr0079528	F	24	36
+input1.bam	FBtr0079528	F	25	8
+input1.bam	FBtr0079528	F	26	5
+input1.bam	FBtr0079528	F	27	2
+input1.bam	FBtr0079528	F	28	2
+input1.bam	FBtr0079528	F	29	1
+input1.bam	FBtr0079528	R	15	0
+input1.bam	FBtr0079528	R	16	0
+input1.bam	FBtr0079528	R	17	0
+input1.bam	FBtr0079528	R	18	0
+input1.bam	FBtr0079528	R	19	0
+input1.bam	FBtr0079528	R	20	0
+input1.bam	FBtr0079528	R	21	0
+input1.bam	FBtr0079528	R	22	0
+input1.bam	FBtr0079528	R	23	0
+input1.bam	FBtr0079528	R	24	0
+input1.bam	FBtr0079528	R	25	0
+input1.bam	FBtr0079528	R	26	0
+input1.bam	FBtr0079528	R	27	0
+input1.bam	FBtr0079528	R	28	0
+input1.bam	FBtr0079528	R	29	0
+input1.bam	FBtr0079596	F	15	43
+input1.bam	FBtr0079596	F	16	34
+input1.bam	FBtr0079596	F	17	16
+input1.bam	FBtr0079596	F	18	5
+input1.bam	FBtr0079596	F	19	10
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1__single_plot_mean.pdf
Binary file test-data/input1__single_plot_mean.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_cluster5_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_cluster5_counts.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,132 @@
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+input1.bam	FBtr0078580	72	52	F	2
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	1
+input1.bam	FBtr0078790	73	17	F	2
+input1.bam	FBtr0078790	73	33	F	1
+input1.bam	FBtr0078790	73	47	F	9
+input1.bam	FBtr0078790	73	69	R	1
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	0
+input1.bam	FBtr0079064	72	2	F	2
+input1.bam	FBtr0079064	72	33	F	1
+input1.bam	FBtr0079064	72	52	F	1
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	26	F	1
+input1.bam	FBtr0079090	72	33	F	1
+input1.bam	FBtr0079090	72	53	F	1
+input1.bam	FBtr0079090	72	56	R	1
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	14	F	5
+input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	44	F	10
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	0
+input1.bam	FBtr0079528	71	9	F	97
+input1.bam	FBtr0079528	71	28	F	1
+input1.bam	FBtr0079528	71	36	F	3
+input1.bam	FBtr0079528	71	51	F	5
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	0
+input1.bam	FBtr0079596	73	10	F	148
+input1.bam	FBtr0079596	73	53	F	4
+input1.bam	FBtr0079596	73	73	F	0
+input1.bam	FBtr0079677	72	1	F	0
+input1.bam	FBtr0079677	72	3	F	2
+input1.bam	FBtr0079677	72	52	F	2
+input1.bam	FBtr0079677	72	72	F	0
+input1.bam	FBtr0079690	72	1	F	1
+input1.bam	FBtr0079690	72	24	F	2
+input1.bam	FBtr0079690	72	33	F	2
+input1.bam	FBtr0079690	72	72	F	0
+input1.bam	FBtr0079692	73	1	F	3
+input1.bam	FBtr0079692	73	18	F	1
+input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	32	F	1
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+input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	25	F	1
+input1.bam	FBtr0079693	72	72	F	0
+input1.bam	FBtr0079694	72	1	F	5
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+input1.bam	FBtr0079694	72	72	F	0
+input1.bam	FBtr0079702	72	1	F	1
+input1.bam	FBtr0079702	72	19	F	2
+input1.bam	FBtr0079702	72	56	F	1
+input1.bam	FBtr0079702	72	72	F	0
+input1.bam	FBtr0079728	72	1	F	2
+input1.bam	FBtr0079728	72	8	F	1
+input1.bam	FBtr0079728	72	19	F	1
+input1.bam	FBtr0079728	72	33	F	3
+input1.bam	FBtr0079728	72	56	F	1
+input1.bam	FBtr0079728	72	72	F	0
+input1.bam	FBtr0079729	72	1	F	1
+input1.bam	FBtr0079729	72	13	F	1
+input1.bam	FBtr0079729	72	54	F	2
+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	2
+input1.bam	FBtr0079752	72	9	F	2
+input1.bam	FBtr0079752	72	33	F	2
+input1.bam	FBtr0079752	72	52	F	2
+input1.bam	FBtr0079752	72	72	F	0
+input1.bam	FBtr0079820	74	1	F	0
+input1.bam	FBtr0079820	74	50	F	13
+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	0
+input1.bam	FBtr0080609	72	10	F	60
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+input1.bam	FBtr0080647	72	6	F	10
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+input1.bam	FBtr0080660	72	4	F	7
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	0
+input1.bam	FBtr0080663	71	9	F	102
+input1.bam	FBtr0080663	71	26	F	1
+input1.bam	FBtr0080663	71	32	F	2
+input1.bam	FBtr0080663	71	50	F	10
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	0
+input1.bam	FBtr0080664	71	11	F	108
+input1.bam	FBtr0080664	71	33	F	9
+input1.bam	FBtr0080664	71	53	F	11
+input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_cluster5_single_plot_coverage.pdf
Binary file test-data/input1_cluster5_single_plot_coverage.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_counts.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,300 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	8	F	3
+input1.bam	FBtr0070001	72	11	F	2
+input1.bam	FBtr0070001	72	16	F	1
+input1.bam	FBtr0070001	72	17	F	1
+input1.bam	FBtr0070001	72	18	F	1
+input1.bam	FBtr0070001	72	27	F	2
+input1.bam	FBtr0070001	72	30	F	1
+input1.bam	FBtr0070001	72	31	F	11
+input1.bam	FBtr0070001	72	32	F	27
+input1.bam	FBtr0070001	72	34	F	1
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	12	F	2
+input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	19	F	5
+input1.bam	FBtr0070533	72	20	F	1
+input1.bam	FBtr0070533	72	21	F	1
+input1.bam	FBtr0070533	72	22	F	1
+input1.bam	FBtr0070533	72	25	F	1
+input1.bam	FBtr0070533	72	26	F	1
+input1.bam	FBtr0070533	72	28	F	1
+input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	35	F	1
+input1.bam	FBtr0070533	72	37	F	2
+input1.bam	FBtr0070533	72	38	F	2
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
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+input1.bam	FBtr0070603	72	4	F	1
+input1.bam	FBtr0070603	72	6	F	1
+input1.bam	FBtr0070603	72	7	F	7
+input1.bam	FBtr0070603	72	8	F	4
+input1.bam	FBtr0070603	72	9	F	7
+input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	13	F	1
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+input1.bam	FBtr0070603	72	17	F	3
+input1.bam	FBtr0070603	72	18	F	1
+input1.bam	FBtr0070603	72	19	F	9
+input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	21	F	1
+input1.bam	FBtr0070603	72	22	F	3
+input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	25	F	1
+input1.bam	FBtr0070603	72	26	F	6
+input1.bam	FBtr0070603	72	27	F	3
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+input1.bam	FBtr0070603	72	34	F	3
+input1.bam	FBtr0070603	72	38	F	1
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+input1.bam	FBtr0070603	72	51	F	1
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+input1.bam	FBtr0070604	72	1	F	1
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+input1.bam	FBtr0070604	72	30	F	2
+input1.bam	FBtr0070604	72	31	F	10
+input1.bam	FBtr0070604	72	32	F	24
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	38	F	1
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	2
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+input1.bam	FBtr0078490	72	18	F	1
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+input1.bam	FBtr0078490	72	28	F	2
+input1.bam	FBtr0078490	72	38	F	1
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+input1.bam	FBtr0078580	72	1	F	1041
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+input1.bam	FBtr0078580	72	4	F	4
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+input1.bam	FBtr0079338	73	42	F	8
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+input1.bam	FBtr0079528	71	1	F	19
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+input1.bam	FBtr0079528	71	28	F	1
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+input1.bam	FBtr0079528	71	51	F	5
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+input1.bam	FBtr0079728	72	19	F	1
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+input1.bam	FBtr0080663	71	8	F	4
+input1.bam	FBtr0080663	71	12	F	2
+input1.bam	FBtr0080663	71	14	F	2
+input1.bam	FBtr0080663	71	15	F	1
+input1.bam	FBtr0080663	71	16	F	3
+input1.bam	FBtr0080663	71	17	F	7
+input1.bam	FBtr0080663	71	26	F	1
+input1.bam	FBtr0080663	71	32	F	2
+input1.bam	FBtr0080663	71	50	F	1
+input1.bam	FBtr0080663	71	51	F	9
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	3	F	56
+input1.bam	FBtr0080664	71	4	F	4
+input1.bam	FBtr0080664	71	6	F	1
+input1.bam	FBtr0080664	71	7	F	1
+input1.bam	FBtr0080664	71	8	F	4
+input1.bam	FBtr0080664	71	9	F	1
+input1.bam	FBtr0080664	71	11	F	3
+input1.bam	FBtr0080664	71	12	F	3
+input1.bam	FBtr0080664	71	13	F	2
+input1.bam	FBtr0080664	71	14	F	3
+input1.bam	FBtr0080664	71	16	F	2
+input1.bam	FBtr0080664	71	17	F	10
+input1.bam	FBtr0080664	71	18	F	1
+input1.bam	FBtr0080664	71	21	F	1
+input1.bam	FBtr0080664	71	28	F	2
+input1.bam	FBtr0080664	71	32	F	1
+input1.bam	FBtr0080664	71	33	F	1
+input1.bam	FBtr0080664	71	34	F	1
+input1.bam	FBtr0080664	71	35	F	1
+input1.bam	FBtr0080664	71	36	F	1
+input1.bam	FBtr0080664	71	37	F	1
+input1.bam	FBtr0080664	71	38	F	1
+input1.bam	FBtr0080664	71	50	F	2
+input1.bam	FBtr0080664	71	51	F	7
+input1.bam	FBtr0080664	71	52	F	1
+input1.bam	FBtr0080664	71	56	F	1
+input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_counts_yminneg5_5.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_counts_yminneg5_5.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,300 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	8	F	3
+input1.bam	FBtr0070001	72	11	F	2
+input1.bam	FBtr0070001	72	16	F	1
+input1.bam	FBtr0070001	72	17	F	1
+input1.bam	FBtr0070001	72	18	F	1
+input1.bam	FBtr0070001	72	27	F	2
+input1.bam	FBtr0070001	72	30	F	1
+input1.bam	FBtr0070001	72	31	F	11
+input1.bam	FBtr0070001	72	32	F	27
+input1.bam	FBtr0070001	72	34	F	1
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	12	F	2
+input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	19	F	5
+input1.bam	FBtr0070533	72	20	F	1
+input1.bam	FBtr0070533	72	21	F	1
+input1.bam	FBtr0070533	72	22	F	1
+input1.bam	FBtr0070533	72	25	F	1
+input1.bam	FBtr0070533	72	26	F	1
+input1.bam	FBtr0070533	72	28	F	1
+input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	35	F	1
+input1.bam	FBtr0070533	72	37	F	2
+input1.bam	FBtr0070533	72	38	F	2
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	3	F	1
+input1.bam	FBtr0070603	72	4	F	1
+input1.bam	FBtr0070603	72	6	F	1
+input1.bam	FBtr0070603	72	7	F	7
+input1.bam	FBtr0070603	72	8	F	4
+input1.bam	FBtr0070603	72	9	F	7
+input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	13	F	1
+input1.bam	FBtr0070603	72	15	F	2
+input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	17	F	3
+input1.bam	FBtr0070603	72	18	F	1
+input1.bam	FBtr0070603	72	19	F	9
+input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	21	F	1
+input1.bam	FBtr0070603	72	22	F	3
+input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	25	F	1
+input1.bam	FBtr0070603	72	26	F	6
+input1.bam	FBtr0070603	72	27	F	3
+input1.bam	FBtr0070603	72	32	F	1
+input1.bam	FBtr0070603	72	34	F	3
+input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	42	F	1
+input1.bam	FBtr0070603	72	51	F	1
+input1.bam	FBtr0070603	72	56	F	1
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	18	F	1
+input1.bam	FBtr0070604	72	22	F	1
+input1.bam	FBtr0070604	72	30	F	2
+input1.bam	FBtr0070604	72	31	F	10
+input1.bam	FBtr0070604	72	32	F	24
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	38	F	1
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	2
+input1.bam	FBtr0078490	72	17	F	1
+input1.bam	FBtr0078490	72	18	F	1
+input1.bam	FBtr0078490	72	25	F	1
+input1.bam	FBtr0078490	72	28	F	2
+input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	3	F	3
+input1.bam	FBtr0078580	72	4	F	4
+input1.bam	FBtr0078580	72	5	F	5
+input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	7	F	1
+input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	11	F	1
+input1.bam	FBtr0078580	72	12	F	13
+input1.bam	FBtr0078580	72	14	F	7
+input1.bam	FBtr0078580	72	15	F	1
+input1.bam	FBtr0078580	72	16	F	4
+input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	19	F	1
+input1.bam	FBtr0078580	72	20	F	2
+input1.bam	FBtr0078580	72	21	F	5
+input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	25	F	2
+input1.bam	FBtr0078580	72	29	F	1
+input1.bam	FBtr0078580	72	31	F	1
+input1.bam	FBtr0078580	72	52	F	2
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	1
+input1.bam	FBtr0078790	73	17	F	2
+input1.bam	FBtr0078790	73	33	F	1
+input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	44	F	2
+input1.bam	FBtr0078790	73	46	F	1
+input1.bam	FBtr0078790	73	47	F	1
+input1.bam	FBtr0078790	73	52	F	1
+input1.bam	FBtr0078790	73	69	R	1
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	3	F	1
+input1.bam	FBtr0079064	72	33	F	1
+input1.bam	FBtr0079064	72	52	F	1
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	26	F	1
+input1.bam	FBtr0079090	72	33	F	1
+input1.bam	FBtr0079090	72	53	F	1
+input1.bam	FBtr0079090	72	56	R	1
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	12	F	1
+input1.bam	FBtr0079338	73	13	F	2
+input1.bam	FBtr0079338	73	14	F	1
+input1.bam	FBtr0079338	73	17	F	1
+input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	42	F	8
+input1.bam	FBtr0079338	73	43	F	1
+input1.bam	FBtr0079338	73	46	F	1
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	3	F	55
+input1.bam	FBtr0079528	71	4	F	2
+input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	10	F	1
+input1.bam	FBtr0079528	71	11	F	2
+input1.bam	FBtr0079528	71	13	F	1
+input1.bam	FBtr0079528	71	14	F	4
+input1.bam	FBtr0079528	71	16	F	1
+input1.bam	FBtr0079528	71	17	F	4
+input1.bam	FBtr0079528	71	18	F	4
+input1.bam	FBtr0079528	71	28	F	1
+input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	36	F	1
+input1.bam	FBtr0079528	71	37	F	1
+input1.bam	FBtr0079528	71	51	F	5
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	13
+input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	4	F	31
+input1.bam	FBtr0079596	73	5	F	2
+input1.bam	FBtr0079596	73	6	F	11
+input1.bam	FBtr0079596	73	8	F	9
+input1.bam	FBtr0079596	73	9	F	12
+input1.bam	FBtr0079596	73	10	F	3
+input1.bam	FBtr0079596	73	11	F	19
+input1.bam	FBtr0079596	73	12	F	1
+input1.bam	FBtr0079596	73	13	F	20
+input1.bam	FBtr0079596	73	14	F	6
+input1.bam	FBtr0079596	73	15	F	1
+input1.bam	FBtr0079596	73	16	F	3
+input1.bam	FBtr0079596	73	17	F	2
+input1.bam	FBtr0079596	73	18	F	1
+input1.bam	FBtr0079596	73	19	F	1
+input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	54	F	2
+input1.bam	FBtr0079596	73	73	F	0
+input1.bam	FBtr0079677	72	1	F	1
+input1.bam	FBtr0079677	72	5	F	1
+input1.bam	FBtr0079677	72	52	F	1
+input1.bam	FBtr0079677	72	53	F	1
+input1.bam	FBtr0079677	72	72	F	0
+input1.bam	FBtr0079690	72	1	F	1
+input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	27	F	1
+input1.bam	FBtr0079690	72	33	F	2
+input1.bam	FBtr0079690	72	72	F	0
+input1.bam	FBtr0079692	73	1	F	3
+input1.bam	FBtr0079692	73	18	F	1
+input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	32	F	1
+input1.bam	FBtr0079692	73	73	F	0
+input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	25	F	1
+input1.bam	FBtr0079693	72	72	F	0
+input1.bam	FBtr0079694	72	1	F	5
+input1.bam	FBtr0079694	72	18	F	1
+input1.bam	FBtr0079694	72	52	F	1
+input1.bam	FBtr0079694	72	72	F	0
+input1.bam	FBtr0079702	72	1	F	1
+input1.bam	FBtr0079702	72	19	F	2
+input1.bam	FBtr0079702	72	56	F	1
+input1.bam	FBtr0079702	72	72	F	0
+input1.bam	FBtr0079728	72	1	F	2
+input1.bam	FBtr0079728	72	8	F	1
+input1.bam	FBtr0079728	72	19	F	1
+input1.bam	FBtr0079728	72	33	F	3
+input1.bam	FBtr0079728	72	56	F	1
+input1.bam	FBtr0079728	72	72	F	0
+input1.bam	FBtr0079729	72	1	F	1
+input1.bam	FBtr0079729	72	13	F	1
+input1.bam	FBtr0079729	72	52	F	1
+input1.bam	FBtr0079729	72	57	F	1
+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	2
+input1.bam	FBtr0079752	72	7	F	1
+input1.bam	FBtr0079752	72	12	F	1
+input1.bam	FBtr0079752	72	33	F	2
+input1.bam	FBtr0079752	72	52	F	2
+input1.bam	FBtr0079752	72	72	F	0
+input1.bam	FBtr0079820	74	1	F	0
+input1.bam	FBtr0079820	74	45	F	1
+input1.bam	FBtr0079820	74	46	F	2
+input1.bam	FBtr0079820	74	48	F	1
+input1.bam	FBtr0079820	74	49	F	1
+input1.bam	FBtr0079820	74	51	F	1
+input1.bam	FBtr0079820	74	54	F	4
+input1.bam	FBtr0079820	74	55	F	1
+input1.bam	FBtr0079820	74	56	F	2
+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	13
+input1.bam	FBtr0080609	72	3	F	2
+input1.bam	FBtr0080609	72	4	F	10
+input1.bam	FBtr0080609	72	5	F	2
+input1.bam	FBtr0080609	72	7	F	19
+input1.bam	FBtr0080609	72	8	F	4
+input1.bam	FBtr0080609	72	9	F	3
+input1.bam	FBtr0080609	72	12	F	1
+input1.bam	FBtr0080609	72	15	F	1
+input1.bam	FBtr0080609	72	16	F	1
+input1.bam	FBtr0080609	72	17	F	2
+input1.bam	FBtr0080609	72	19	F	1
+input1.bam	FBtr0080609	72	20	F	1
+input1.bam	FBtr0080609	72	42	F	1
+input1.bam	FBtr0080609	72	51	F	1
+input1.bam	FBtr0080609	72	52	F	1
+input1.bam	FBtr0080609	72	72	F	0
+input1.bam	FBtr0080644	72	1	F	1
+input1.bam	FBtr0080644	72	4	F	2
+input1.bam	FBtr0080644	72	7	F	1
+input1.bam	FBtr0080644	72	12	F	2
+input1.bam	FBtr0080644	72	72	F	0
+input1.bam	FBtr0080646	72	1	F	1
+input1.bam	FBtr0080646	72	6	F	1
+input1.bam	FBtr0080646	72	7	F	1
+input1.bam	FBtr0080646	72	72	F	0
+input1.bam	FBtr0080647	72	1	F	3
+input1.bam	FBtr0080647	72	3	F	1
+input1.bam	FBtr0080647	72	6	F	2
+input1.bam	FBtr0080647	72	8	F	1
+input1.bam	FBtr0080647	72	11	F	2
+input1.bam	FBtr0080647	72	12	F	1
+input1.bam	FBtr0080647	72	72	F	0
+input1.bam	FBtr0080660	72	1	F	0
+input1.bam	FBtr0080660	72	4	F	4
+input1.bam	FBtr0080660	72	7	F	3
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	22
+input1.bam	FBtr0080663	71	3	F	56
+input1.bam	FBtr0080663	71	4	F	4
+input1.bam	FBtr0080663	71	7	F	1
+input1.bam	FBtr0080663	71	8	F	4
+input1.bam	FBtr0080663	71	12	F	2
+input1.bam	FBtr0080663	71	14	F	2
+input1.bam	FBtr0080663	71	15	F	1
+input1.bam	FBtr0080663	71	16	F	3
+input1.bam	FBtr0080663	71	17	F	7
+input1.bam	FBtr0080663	71	26	F	1
+input1.bam	FBtr0080663	71	32	F	2
+input1.bam	FBtr0080663	71	50	F	1
+input1.bam	FBtr0080663	71	51	F	9
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	3	F	56
+input1.bam	FBtr0080664	71	4	F	4
+input1.bam	FBtr0080664	71	6	F	1
+input1.bam	FBtr0080664	71	7	F	1
+input1.bam	FBtr0080664	71	8	F	4
+input1.bam	FBtr0080664	71	9	F	1
+input1.bam	FBtr0080664	71	11	F	3
+input1.bam	FBtr0080664	71	12	F	3
+input1.bam	FBtr0080664	71	13	F	2
+input1.bam	FBtr0080664	71	14	F	3
+input1.bam	FBtr0080664	71	16	F	2
+input1.bam	FBtr0080664	71	17	F	10
+input1.bam	FBtr0080664	71	18	F	1
+input1.bam	FBtr0080664	71	21	F	1
+input1.bam	FBtr0080664	71	28	F	2
+input1.bam	FBtr0080664	71	32	F	1
+input1.bam	FBtr0080664	71	33	F	1
+input1.bam	FBtr0080664	71	34	F	1
+input1.bam	FBtr0080664	71	35	F	1
+input1.bam	FBtr0080664	71	36	F	1
+input1.bam	FBtr0080664	71	37	F	1
+input1.bam	FBtr0080664	71	38	F	1
+input1.bam	FBtr0080664	71	50	F	2
+input1.bam	FBtr0080664	71	51	F	7
+input1.bam	FBtr0080664	71	52	F	1
+input1.bam	FBtr0080664	71	56	F	1
+input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_coverage.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_coverage.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,1603 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	2	F	1
+input1.bam	FBtr0070001	72	3	F	1
+input1.bam	FBtr0070001	72	4	F	1
+input1.bam	FBtr0070001	72	5	F	1
+input1.bam	FBtr0070001	72	6	F	1
+input1.bam	FBtr0070001	72	7	F	7
+input1.bam	FBtr0070001	72	8	F	10
+input1.bam	FBtr0070001	72	9	F	10
+input1.bam	FBtr0070001	72	10	F	10
+input1.bam	FBtr0070001	72	11	F	12
+input1.bam	FBtr0070001	72	12	F	12
+input1.bam	FBtr0070001	72	13	F	12
+input1.bam	FBtr0070001	72	14	F	12
+input1.bam	FBtr0070001	72	15	F	12
+input1.bam	FBtr0070001	72	16	F	13
+input1.bam	FBtr0070001	72	17	F	14
+input1.bam	FBtr0070001	72	18	F	14
+input1.bam	FBtr0070001	72	19	F	14
+input1.bam	FBtr0070001	72	20	F	14
+input1.bam	FBtr0070001	72	21	F	14
+input1.bam	FBtr0070001	72	22	F	14
+input1.bam	FBtr0070001	72	23	F	13
+input1.bam	FBtr0070001	72	24	F	13
+input1.bam	FBtr0070001	72	25	F	13
+input1.bam	FBtr0070001	72	26	F	13
+input1.bam	FBtr0070001	72	27	F	14
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+input1.bam	FBtr0080663	71	67	F	1
+input1.bam	FBtr0080663	71	68	F	1
+input1.bam	FBtr0080663	71	69	F	1
+input1.bam	FBtr0080663	71	70	F	1
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	2	F	16
+input1.bam	FBtr0080664	71	3	F	72
+input1.bam	FBtr0080664	71	4	F	76
+input1.bam	FBtr0080664	71	5	F	76
+input1.bam	FBtr0080664	71	6	F	77
+input1.bam	FBtr0080664	71	7	F	78
+input1.bam	FBtr0080664	71	8	F	82
+input1.bam	FBtr0080664	71	9	F	83
+input1.bam	FBtr0080664	71	10	F	83
+input1.bam	FBtr0080664	71	11	F	86
+input1.bam	FBtr0080664	71	12	F	89
+input1.bam	FBtr0080664	71	13	F	91
+input1.bam	FBtr0080664	71	14	F	94
+input1.bam	FBtr0080664	71	15	F	94
+input1.bam	FBtr0080664	71	16	F	95
+input1.bam	FBtr0080664	71	17	F	100
+input1.bam	FBtr0080664	71	18	F	98
+input1.bam	FBtr0080664	71	19	F	97
+input1.bam	FBtr0080664	71	20	F	97
+input1.bam	FBtr0080664	71	21	F	97
+input1.bam	FBtr0080664	71	22	F	97
+input1.bam	FBtr0080664	71	23	F	93
+input1.bam	FBtr0080664	71	24	F	88
+input1.bam	FBtr0080664	71	25	F	88
+input1.bam	FBtr0080664	71	26	F	82
+input1.bam	FBtr0080664	71	27	F	47
+input1.bam	FBtr0080664	71	28	F	33
+input1.bam	FBtr0080664	71	29	F	23
+input1.bam	FBtr0080664	71	30	F	23
+input1.bam	FBtr0080664	71	31	F	20
+input1.bam	FBtr0080664	71	32	F	13
+input1.bam	FBtr0080664	71	33	F	6
+input1.bam	FBtr0080664	71	34	F	7
+input1.bam	FBtr0080664	71	35	F	8
+input1.bam	FBtr0080664	71	36	F	7
+input1.bam	FBtr0080664	71	37	F	8
+input1.bam	FBtr0080664	71	38	F	9
+input1.bam	FBtr0080664	71	39	F	9
+input1.bam	FBtr0080664	71	40	F	9
+input1.bam	FBtr0080664	71	41	F	9
+input1.bam	FBtr0080664	71	42	F	9
+input1.bam	FBtr0080664	71	43	F	9
+input1.bam	FBtr0080664	71	44	F	7
+input1.bam	FBtr0080664	71	45	F	7
+input1.bam	FBtr0080664	71	46	F	7
+input1.bam	FBtr0080664	71	47	F	6
+input1.bam	FBtr0080664	71	48	F	6
+input1.bam	FBtr0080664	71	49	F	6
+input1.bam	FBtr0080664	71	50	F	6
+input1.bam	FBtr0080664	71	51	F	13
+input1.bam	FBtr0080664	71	52	F	14
+input1.bam	FBtr0080664	71	53	F	12
+input1.bam	FBtr0080664	71	54	F	12
+input1.bam	FBtr0080664	71	55	F	11
+input1.bam	FBtr0080664	71	56	F	12
+input1.bam	FBtr0080664	71	57	F	11
+input1.bam	FBtr0080664	71	58	F	11
+input1.bam	FBtr0080664	71	59	F	11
+input1.bam	FBtr0080664	71	60	F	11
+input1.bam	FBtr0080664	71	61	F	11
+input1.bam	FBtr0080664	71	62	F	11
+input1.bam	FBtr0080664	71	63	F	11
+input1.bam	FBtr0080664	71	64	F	11
+input1.bam	FBtr0080664	71	65	F	11
+input1.bam	FBtr0080664	71	66	F	2
+input1.bam	FBtr0080664	71	67	F	1
+input1.bam	FBtr0080664	71	68	F	1
+input1.bam	FBtr0080664	71	69	F	1
+input1.bam	FBtr0080664	71	70	F	1
+input1.bam	FBtr0080664	71	71	F	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_coverage_cluster5.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_coverage_cluster5.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,1603 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	2	F	1
+input1.bam	FBtr0070001	72	3	F	1
+input1.bam	FBtr0070001	72	4	F	1
+input1.bam	FBtr0070001	72	5	F	1
+input1.bam	FBtr0070001	72	6	F	1
+input1.bam	FBtr0070001	72	7	F	7
+input1.bam	FBtr0070001	72	8	F	10
+input1.bam	FBtr0070001	72	9	F	10
+input1.bam	FBtr0070001	72	10	F	10
+input1.bam	FBtr0070001	72	11	F	12
+input1.bam	FBtr0070001	72	12	F	12
+input1.bam	FBtr0070001	72	13	F	12
+input1.bam	FBtr0070001	72	14	F	12
+input1.bam	FBtr0070001	72	15	F	12
+input1.bam	FBtr0070001	72	16	F	13
+input1.bam	FBtr0070001	72	17	F	14
+input1.bam	FBtr0070001	72	18	F	14
+input1.bam	FBtr0070001	72	19	F	14
+input1.bam	FBtr0070001	72	20	F	14
+input1.bam	FBtr0070001	72	21	F	14
+input1.bam	FBtr0070001	72	22	F	14
+input1.bam	FBtr0070001	72	23	F	13
+input1.bam	FBtr0070001	72	24	F	13
+input1.bam	FBtr0070001	72	25	F	13
+input1.bam	FBtr0070001	72	26	F	13
+input1.bam	FBtr0070001	72	27	F	14
+input1.bam	FBtr0070001	72	28	F	11
+input1.bam	FBtr0070001	72	29	F	8
+input1.bam	FBtr0070001	72	30	F	9
+input1.bam	FBtr0070001	72	31	F	18
+input1.bam	FBtr0070001	72	32	F	44
+input1.bam	FBtr0070001	72	33	F	44
+input1.bam	FBtr0070001	72	34	F	44
+input1.bam	FBtr0070001	72	35	F	43
+input1.bam	FBtr0070001	72	36	F	43
+input1.bam	FBtr0070001	72	37	F	43
+input1.bam	FBtr0070001	72	38	F	43
+input1.bam	FBtr0070001	72	39	F	43
+input1.bam	FBtr0070001	72	40	F	42
+input1.bam	FBtr0070001	72	41	F	42
+input1.bam	FBtr0070001	72	42	F	42
+input1.bam	FBtr0070001	72	43	F	42
+input1.bam	FBtr0070001	72	44	F	42
+input1.bam	FBtr0070001	72	45	F	42
+input1.bam	FBtr0070001	72	46	F	42
+input1.bam	FBtr0070001	72	47	F	42
+input1.bam	FBtr0070001	72	48	F	42
+input1.bam	FBtr0070001	72	49	F	42
+input1.bam	FBtr0070001	72	50	F	41
+input1.bam	FBtr0070001	72	51	F	40
+input1.bam	FBtr0070001	72	52	F	40
+input1.bam	FBtr0070001	72	53	F	39
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	2	F	1
+input1.bam	FBtr0070533	72	3	F	1
+input1.bam	FBtr0070533	72	4	F	1
+input1.bam	FBtr0070533	72	5	F	1
+input1.bam	FBtr0070533	72	6	F	1
+input1.bam	FBtr0070533	72	7	F	1
+input1.bam	FBtr0070533	72	8	F	1
+input1.bam	FBtr0070533	72	9	F	1
+input1.bam	FBtr0070533	72	10	F	1
+input1.bam	FBtr0070533	72	11	F	1
+input1.bam	FBtr0070533	72	12	F	3
+input1.bam	FBtr0070533	72	13	F	3
+input1.bam	FBtr0070533	72	14	F	3
+input1.bam	FBtr0070533	72	15	F	4
+input1.bam	FBtr0070533	72	16	F	3
+input1.bam	FBtr0070533	72	17	F	3
+input1.bam	FBtr0070533	72	18	F	3
+input1.bam	FBtr0070533	72	19	F	8
+input1.bam	FBtr0070533	72	20	F	9
+input1.bam	FBtr0070533	72	21	F	10
+input1.bam	FBtr0070533	72	22	F	11
+input1.bam	FBtr0070533	72	23	F	11
+input1.bam	FBtr0070533	72	24	F	11
+input1.bam	FBtr0070533	72	25	F	12
+input1.bam	FBtr0070533	72	26	F	13
+input1.bam	FBtr0070533	72	27	F	13
+input1.bam	FBtr0070533	72	28	F	14
+input1.bam	FBtr0070533	72	29	F	14
+input1.bam	FBtr0070533	72	30	F	11
+input1.bam	FBtr0070533	72	31	F	11
+input1.bam	FBtr0070533	72	32	F	15
+input1.bam	FBtr0070533	72	33	F	15
+input1.bam	FBtr0070533	72	34	F	15
+input1.bam	FBtr0070533	72	35	F	16
+input1.bam	FBtr0070533	72	36	F	16
+input1.bam	FBtr0070533	72	37	F	18
+input1.bam	FBtr0070533	72	38	F	20
+input1.bam	FBtr0070533	72	39	F	19
+input1.bam	FBtr0070533	72	40	F	17
+input1.bam	FBtr0070533	72	41	F	15
+input1.bam	FBtr0070533	72	42	F	11
+input1.bam	FBtr0070533	72	43	F	10
+input1.bam	FBtr0070533	72	44	F	10
+input1.bam	FBtr0070533	72	45	F	10
+input1.bam	FBtr0070533	72	46	F	10
+input1.bam	FBtr0070533	72	47	F	10
+input1.bam	FBtr0070533	72	48	F	10
+input1.bam	FBtr0070533	72	49	F	10
+input1.bam	FBtr0070533	72	50	F	9
+input1.bam	FBtr0070533	72	51	F	9
+input1.bam	FBtr0070533	72	52	F	8
+input1.bam	FBtr0070533	72	53	F	7
+input1.bam	FBtr0070533	72	54	F	4
+input1.bam	FBtr0070533	72	55	F	4
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	2	F	2
+input1.bam	FBtr0070603	72	3	F	3
+input1.bam	FBtr0070603	72	4	F	4
+input1.bam	FBtr0070603	72	5	F	4
+input1.bam	FBtr0070603	72	6	F	5
+input1.bam	FBtr0070603	72	7	F	12
+input1.bam	FBtr0070603	72	8	F	16
+input1.bam	FBtr0070603	72	9	F	23
+input1.bam	FBtr0070603	72	10	F	23
+input1.bam	FBtr0070603	72	11	F	23
+input1.bam	FBtr0070603	72	12	F	25
+input1.bam	FBtr0070603	72	13	F	26
+input1.bam	FBtr0070603	72	14	F	26
+input1.bam	FBtr0070603	72	15	F	28
+input1.bam	FBtr0070603	72	16	F	29
+input1.bam	FBtr0070603	72	17	F	32
+input1.bam	FBtr0070603	72	18	F	33
+input1.bam	FBtr0070603	72	19	F	41
+input1.bam	FBtr0070603	72	20	F	44
+input1.bam	FBtr0070603	72	21	F	45
+input1.bam	FBtr0070603	72	22	F	48
+input1.bam	FBtr0070603	72	23	F	48
+input1.bam	FBtr0070603	72	24	F	30
+input1.bam	FBtr0070603	72	25	F	30
+input1.bam	FBtr0070603	72	26	F	36
+input1.bam	FBtr0070603	72	27	F	39
+input1.bam	FBtr0070603	72	28	F	39
+input1.bam	FBtr0070603	72	29	F	38
+input1.bam	FBtr0070603	72	30	F	38
+input1.bam	FBtr0070603	72	31	F	38
+input1.bam	FBtr0070603	72	32	F	38
+input1.bam	FBtr0070603	72	33	F	37
+input1.bam	FBtr0070603	72	34	F	39
+input1.bam	FBtr0070603	72	35	F	35
+input1.bam	FBtr0070603	72	36	F	34
+input1.bam	FBtr0070603	72	37	F	34
+input1.bam	FBtr0070603	72	38	F	35
+input1.bam	FBtr0070603	72	39	F	34
+input1.bam	FBtr0070603	72	40	F	33
+input1.bam	FBtr0070603	72	41	F	32
+input1.bam	FBtr0070603	72	42	F	21
+input1.bam	FBtr0070603	72	43	F	21
+input1.bam	FBtr0070603	72	44	F	20
+input1.bam	FBtr0070603	72	45	F	18
+input1.bam	FBtr0070603	72	46	F	16
+input1.bam	FBtr0070603	72	47	F	16
+input1.bam	FBtr0070603	72	48	F	15
+input1.bam	FBtr0070603	72	49	F	15
+input1.bam	FBtr0070603	72	50	F	14
+input1.bam	FBtr0070603	72	51	F	14
+input1.bam	FBtr0070603	72	52	F	10
+input1.bam	FBtr0070603	72	53	F	6
+input1.bam	FBtr0070603	72	54	F	3
+input1.bam	FBtr0070603	72	55	F	3
+input1.bam	FBtr0070603	72	56	F	3
+input1.bam	FBtr0070603	72	57	F	3
+input1.bam	FBtr0070603	72	58	F	3
+input1.bam	FBtr0070603	72	59	F	3
+input1.bam	FBtr0070603	72	60	F	3
+input1.bam	FBtr0070603	72	61	F	3
+input1.bam	FBtr0070603	72	62	F	3
+input1.bam	FBtr0070603	72	63	F	2
+input1.bam	FBtr0070603	72	64	F	2
+input1.bam	FBtr0070603	72	65	F	2
+input1.bam	FBtr0070603	72	66	F	2
+input1.bam	FBtr0070603	72	67	F	2
+input1.bam	FBtr0070603	72	68	F	2
+input1.bam	FBtr0070603	72	69	F	1
+input1.bam	FBtr0070603	72	70	F	1
+input1.bam	FBtr0070603	72	71	F	1
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	2	F	1
+input1.bam	FBtr0070604	72	3	F	1
+input1.bam	FBtr0070604	72	4	F	1
+input1.bam	FBtr0070604	72	5	F	1
+input1.bam	FBtr0070604	72	6	F	1
+input1.bam	FBtr0070604	72	7	F	1
+input1.bam	FBtr0070604	72	8	F	1
+input1.bam	FBtr0070604	72	9	F	1
+input1.bam	FBtr0070604	72	10	F	1
+input1.bam	FBtr0070604	72	11	F	1
+input1.bam	FBtr0070604	72	12	F	1
+input1.bam	FBtr0070604	72	13	F	1
+input1.bam	FBtr0070604	72	14	F	1
+input1.bam	FBtr0070604	72	15	F	1
+input1.bam	FBtr0070604	72	18	F	1
+input1.bam	FBtr0070604	72	19	F	1
+input1.bam	FBtr0070604	72	20	F	1
+input1.bam	FBtr0070604	72	21	F	1
+input1.bam	FBtr0070604	72	22	F	2
+input1.bam	FBtr0070604	72	23	F	2
+input1.bam	FBtr0070604	72	24	F	2
+input1.bam	FBtr0070604	72	25	F	2
+input1.bam	FBtr0070604	72	26	F	2
+input1.bam	FBtr0070604	72	27	F	2
+input1.bam	FBtr0070604	72	28	F	2
+input1.bam	FBtr0070604	72	29	F	2
+input1.bam	FBtr0070604	72	30	F	4
+input1.bam	FBtr0070604	72	31	F	14
+input1.bam	FBtr0070604	72	32	F	38
+input1.bam	FBtr0070604	72	33	F	38
+input1.bam	FBtr0070604	72	34	F	38
+input1.bam	FBtr0070604	72	35	F	38
+input1.bam	FBtr0070604	72	36	F	38
+input1.bam	FBtr0070604	72	37	F	38
+input1.bam	FBtr0070604	72	38	F	38
+input1.bam	FBtr0070604	72	39	F	38
+input1.bam	FBtr0070604	72	40	F	38
+input1.bam	FBtr0070604	72	41	F	36
+input1.bam	FBtr0070604	72	42	F	36
+input1.bam	FBtr0070604	72	43	F	36
+input1.bam	FBtr0070604	72	44	F	36
+input1.bam	FBtr0070604	72	45	F	36
+input1.bam	FBtr0070604	72	46	F	35
+input1.bam	FBtr0070604	72	47	F	36
+input1.bam	FBtr0070604	72	48	F	34
+input1.bam	FBtr0070604	72	49	F	34
+input1.bam	FBtr0070604	72	50	F	33
+input1.bam	FBtr0070604	72	51	F	33
+input1.bam	FBtr0070604	72	52	F	33
+input1.bam	FBtr0070604	72	53	F	31
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	58	F	1
+input1.bam	FBtr0070604	72	59	F	1
+input1.bam	FBtr0070604	72	60	F	1
+input1.bam	FBtr0070604	72	61	F	1
+input1.bam	FBtr0070604	72	62	F	1
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+input1.bam	FBtr0070604	72	64	F	1
+input1.bam	FBtr0070604	72	65	F	1
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+input1.bam	FBtr0070604	72	67	F	1
+input1.bam	FBtr0070604	72	68	F	1
+input1.bam	FBtr0070604	72	69	F	1
+input1.bam	FBtr0070604	72	70	F	1
+input1.bam	FBtr0070604	72	71	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	16	F	1
+input1.bam	FBtr0070911	73	17	F	1
+input1.bam	FBtr0070911	73	18	F	1
+input1.bam	FBtr0070911	73	19	F	1
+input1.bam	FBtr0070911	73	20	F	1
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+input1.bam	FBtr0070911	73	22	F	1
+input1.bam	FBtr0070911	73	23	F	1
+input1.bam	FBtr0070911	73	24	F	1
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+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
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+input1.bam	FBtr0078490	72	17	F	3
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+input1.bam	FBtr0078490	72	19	F	4
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+input1.bam	FBtr0080647	72	5	F	4
+input1.bam	FBtr0080647	72	6	F	6
+input1.bam	FBtr0080647	72	7	F	6
+input1.bam	FBtr0080647	72	8	F	7
+input1.bam	FBtr0080647	72	9	F	7
+input1.bam	FBtr0080647	72	10	F	7
+input1.bam	FBtr0080647	72	11	F	9
+input1.bam	FBtr0080647	72	12	F	10
+input1.bam	FBtr0080647	72	13	F	10
+input1.bam	FBtr0080647	72	14	F	10
+input1.bam	FBtr0080647	72	15	F	10
+input1.bam	FBtr0080647	72	16	F	9
+input1.bam	FBtr0080647	72	17	F	8
+input1.bam	FBtr0080647	72	18	F	8
+input1.bam	FBtr0080647	72	19	F	6
+input1.bam	FBtr0080647	72	20	F	6
+input1.bam	FBtr0080647	72	21	F	6
+input1.bam	FBtr0080647	72	22	F	5
+input1.bam	FBtr0080647	72	23	F	5
+input1.bam	FBtr0080647	72	24	F	5
+input1.bam	FBtr0080647	72	25	F	5
+input1.bam	FBtr0080647	72	26	F	5
+input1.bam	FBtr0080647	72	27	F	5
+input1.bam	FBtr0080647	72	72	F	0
+input1.bam	FBtr0080660	72	1	F	0
+input1.bam	FBtr0080660	72	4	F	4
+input1.bam	FBtr0080660	72	5	F	4
+input1.bam	FBtr0080660	72	6	F	4
+input1.bam	FBtr0080660	72	7	F	7
+input1.bam	FBtr0080660	72	8	F	7
+input1.bam	FBtr0080660	72	9	F	7
+input1.bam	FBtr0080660	72	10	F	7
+input1.bam	FBtr0080660	72	11	F	7
+input1.bam	FBtr0080660	72	12	F	7
+input1.bam	FBtr0080660	72	13	F	7
+input1.bam	FBtr0080660	72	14	F	7
+input1.bam	FBtr0080660	72	15	F	7
+input1.bam	FBtr0080660	72	16	F	7
+input1.bam	FBtr0080660	72	17	F	7
+input1.bam	FBtr0080660	72	18	F	7
+input1.bam	FBtr0080660	72	19	F	7
+input1.bam	FBtr0080660	72	20	F	7
+input1.bam	FBtr0080660	72	21	F	7
+input1.bam	FBtr0080660	72	22	F	7
+input1.bam	FBtr0080660	72	23	F	6
+input1.bam	FBtr0080660	72	24	F	6
+input1.bam	FBtr0080660	72	25	F	6
+input1.bam	FBtr0080660	72	26	F	6
+input1.bam	FBtr0080660	72	27	F	6
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	22
+input1.bam	FBtr0080663	71	2	F	22
+input1.bam	FBtr0080663	71	3	F	78
+input1.bam	FBtr0080663	71	4	F	82
+input1.bam	FBtr0080663	71	5	F	82
+input1.bam	FBtr0080663	71	6	F	82
+input1.bam	FBtr0080663	71	7	F	83
+input1.bam	FBtr0080663	71	8	F	87
+input1.bam	FBtr0080663	71	9	F	87
+input1.bam	FBtr0080663	71	10	F	87
+input1.bam	FBtr0080663	71	11	F	87
+input1.bam	FBtr0080663	71	12	F	89
+input1.bam	FBtr0080663	71	13	F	89
+input1.bam	FBtr0080663	71	14	F	91
+input1.bam	FBtr0080663	71	15	F	92
+input1.bam	FBtr0080663	71	16	F	93
+input1.bam	FBtr0080663	71	17	F	89
+input1.bam	FBtr0080663	71	18	F	86
+input1.bam	FBtr0080663	71	19	F	86
+input1.bam	FBtr0080663	71	20	F	86
+input1.bam	FBtr0080663	71	21	F	86
+input1.bam	FBtr0080663	71	22	F	86
+input1.bam	FBtr0080663	71	23	F	78
+input1.bam	FBtr0080663	71	24	F	77
+input1.bam	FBtr0080663	71	25	F	77
+input1.bam	FBtr0080663	71	26	F	70
+input1.bam	FBtr0080663	71	27	F	34
+input1.bam	FBtr0080663	71	28	F	21
+input1.bam	FBtr0080663	71	29	F	14
+input1.bam	FBtr0080663	71	30	F	14
+input1.bam	FBtr0080663	71	31	F	13
+input1.bam	FBtr0080663	71	32	F	7
+input1.bam	FBtr0080663	71	33	F	4
+input1.bam	FBtr0080663	71	34	F	4
+input1.bam	FBtr0080663	71	35	F	3
+input1.bam	FBtr0080663	71	36	F	3
+input1.bam	FBtr0080663	71	37	F	3
+input1.bam	FBtr0080663	71	38	F	3
+input1.bam	FBtr0080663	71	39	F	3
+input1.bam	FBtr0080663	71	40	F	3
+input1.bam	FBtr0080663	71	41	F	3
+input1.bam	FBtr0080663	71	42	F	3
+input1.bam	FBtr0080663	71	43	F	3
+input1.bam	FBtr0080663	71	44	F	2
+input1.bam	FBtr0080663	71	45	F	2
+input1.bam	FBtr0080663	71	46	F	2
+input1.bam	FBtr0080663	71	47	F	1
+input1.bam	FBtr0080663	71	50	F	1
+input1.bam	FBtr0080663	71	51	F	10
+input1.bam	FBtr0080663	71	52	F	10
+input1.bam	FBtr0080663	71	53	F	10
+input1.bam	FBtr0080663	71	54	F	10
+input1.bam	FBtr0080663	71	55	F	10
+input1.bam	FBtr0080663	71	56	F	10
+input1.bam	FBtr0080663	71	57	F	10
+input1.bam	FBtr0080663	71	58	F	10
+input1.bam	FBtr0080663	71	59	F	10
+input1.bam	FBtr0080663	71	60	F	10
+input1.bam	FBtr0080663	71	61	F	10
+input1.bam	FBtr0080663	71	62	F	10
+input1.bam	FBtr0080663	71	63	F	10
+input1.bam	FBtr0080663	71	64	F	10
+input1.bam	FBtr0080663	71	65	F	10
+input1.bam	FBtr0080663	71	66	F	2
+input1.bam	FBtr0080663	71	67	F	1
+input1.bam	FBtr0080663	71	68	F	1
+input1.bam	FBtr0080663	71	69	F	1
+input1.bam	FBtr0080663	71	70	F	1
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	2	F	16
+input1.bam	FBtr0080664	71	3	F	72
+input1.bam	FBtr0080664	71	4	F	76
+input1.bam	FBtr0080664	71	5	F	76
+input1.bam	FBtr0080664	71	6	F	77
+input1.bam	FBtr0080664	71	7	F	78
+input1.bam	FBtr0080664	71	8	F	82
+input1.bam	FBtr0080664	71	9	F	83
+input1.bam	FBtr0080664	71	10	F	83
+input1.bam	FBtr0080664	71	11	F	86
+input1.bam	FBtr0080664	71	12	F	89
+input1.bam	FBtr0080664	71	13	F	91
+input1.bam	FBtr0080664	71	14	F	94
+input1.bam	FBtr0080664	71	15	F	94
+input1.bam	FBtr0080664	71	16	F	95
+input1.bam	FBtr0080664	71	17	F	100
+input1.bam	FBtr0080664	71	18	F	98
+input1.bam	FBtr0080664	71	19	F	97
+input1.bam	FBtr0080664	71	20	F	97
+input1.bam	FBtr0080664	71	21	F	97
+input1.bam	FBtr0080664	71	22	F	97
+input1.bam	FBtr0080664	71	23	F	93
+input1.bam	FBtr0080664	71	24	F	88
+input1.bam	FBtr0080664	71	25	F	88
+input1.bam	FBtr0080664	71	26	F	82
+input1.bam	FBtr0080664	71	27	F	47
+input1.bam	FBtr0080664	71	28	F	33
+input1.bam	FBtr0080664	71	29	F	23
+input1.bam	FBtr0080664	71	30	F	23
+input1.bam	FBtr0080664	71	31	F	20
+input1.bam	FBtr0080664	71	32	F	13
+input1.bam	FBtr0080664	71	33	F	6
+input1.bam	FBtr0080664	71	34	F	7
+input1.bam	FBtr0080664	71	35	F	8
+input1.bam	FBtr0080664	71	36	F	7
+input1.bam	FBtr0080664	71	37	F	8
+input1.bam	FBtr0080664	71	38	F	9
+input1.bam	FBtr0080664	71	39	F	9
+input1.bam	FBtr0080664	71	40	F	9
+input1.bam	FBtr0080664	71	41	F	9
+input1.bam	FBtr0080664	71	42	F	9
+input1.bam	FBtr0080664	71	43	F	9
+input1.bam	FBtr0080664	71	44	F	7
+input1.bam	FBtr0080664	71	45	F	7
+input1.bam	FBtr0080664	71	46	F	7
+input1.bam	FBtr0080664	71	47	F	6
+input1.bam	FBtr0080664	71	48	F	6
+input1.bam	FBtr0080664	71	49	F	6
+input1.bam	FBtr0080664	71	50	F	6
+input1.bam	FBtr0080664	71	51	F	13
+input1.bam	FBtr0080664	71	52	F	14
+input1.bam	FBtr0080664	71	53	F	12
+input1.bam	FBtr0080664	71	54	F	12
+input1.bam	FBtr0080664	71	55	F	11
+input1.bam	FBtr0080664	71	56	F	12
+input1.bam	FBtr0080664	71	57	F	11
+input1.bam	FBtr0080664	71	58	F	11
+input1.bam	FBtr0080664	71	59	F	11
+input1.bam	FBtr0080664	71	60	F	11
+input1.bam	FBtr0080664	71	61	F	11
+input1.bam	FBtr0080664	71	62	F	11
+input1.bam	FBtr0080664	71	63	F	11
+input1.bam	FBtr0080664	71	64	F	11
+input1.bam	FBtr0080664	71	65	F	11
+input1.bam	FBtr0080664	71	66	F	2
+input1.bam	FBtr0080664	71	67	F	1
+input1.bam	FBtr0080664	71	68	F	1
+input1.bam	FBtr0080664	71	69	F	1
+input1.bam	FBtr0080664	71	70	F	1
+input1.bam	FBtr0080664	71	71	F	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_counts.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,617 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	8	F	3
+input1.bam	FBtr0070001	72	11	F	2
+input1.bam	FBtr0070001	72	16	F	1
+input1.bam	FBtr0070001	72	17	F	1
+input1.bam	FBtr0070001	72	18	F	1
+input1.bam	FBtr0070001	72	27	F	2
+input1.bam	FBtr0070001	72	30	F	1
+input1.bam	FBtr0070001	72	31	F	11
+input1.bam	FBtr0070001	72	32	F	27
+input1.bam	FBtr0070001	72	34	F	1
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	12	F	2
+input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	19	F	5
+input1.bam	FBtr0070533	72	20	F	1
+input1.bam	FBtr0070533	72	21	F	1
+input1.bam	FBtr0070533	72	22	F	1
+input1.bam	FBtr0070533	72	25	F	1
+input1.bam	FBtr0070533	72	26	F	1
+input1.bam	FBtr0070533	72	28	F	1
+input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	35	F	1
+input1.bam	FBtr0070533	72	37	F	2
+input1.bam	FBtr0070533	72	38	F	2
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	3	F	1
+input1.bam	FBtr0070603	72	4	F	1
+input1.bam	FBtr0070603	72	6	F	1
+input1.bam	FBtr0070603	72	7	F	7
+input1.bam	FBtr0070603	72	8	F	4
+input1.bam	FBtr0070603	72	9	F	7
+input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	13	F	1
+input1.bam	FBtr0070603	72	15	F	2
+input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	17	F	3
+input1.bam	FBtr0070603	72	18	F	1
+input1.bam	FBtr0070603	72	19	F	9
+input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	21	F	1
+input1.bam	FBtr0070603	72	22	F	3
+input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	25	F	1
+input1.bam	FBtr0070603	72	26	F	6
+input1.bam	FBtr0070603	72	27	F	3
+input1.bam	FBtr0070603	72	32	F	1
+input1.bam	FBtr0070603	72	34	F	3
+input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	42	F	1
+input1.bam	FBtr0070603	72	51	F	1
+input1.bam	FBtr0070603	72	56	F	1
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	18	F	1
+input1.bam	FBtr0070604	72	22	F	1
+input1.bam	FBtr0070604	72	30	F	2
+input1.bam	FBtr0070604	72	31	F	10
+input1.bam	FBtr0070604	72	32	F	24
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	38	F	1
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	2
+input1.bam	FBtr0078490	72	17	F	1
+input1.bam	FBtr0078490	72	18	F	1
+input1.bam	FBtr0078490	72	25	F	1
+input1.bam	FBtr0078490	72	28	F	2
+input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	3	F	3
+input1.bam	FBtr0078580	72	4	F	4
+input1.bam	FBtr0078580	72	5	F	5
+input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	7	F	1
+input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	11	F	1
+input1.bam	FBtr0078580	72	12	F	13
+input1.bam	FBtr0078580	72	14	F	7
+input1.bam	FBtr0078580	72	15	F	1
+input1.bam	FBtr0078580	72	16	F	4
+input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	19	F	1
+input1.bam	FBtr0078580	72	20	F	2
+input1.bam	FBtr0078580	72	21	F	5
+input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	25	F	2
+input1.bam	FBtr0078580	72	29	F	1
+input1.bam	FBtr0078580	72	31	F	1
+input1.bam	FBtr0078580	72	52	F	2
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	1
+input1.bam	FBtr0078790	73	17	F	2
+input1.bam	FBtr0078790	73	33	F	1
+input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	44	F	2
+input1.bam	FBtr0078790	73	46	F	1
+input1.bam	FBtr0078790	73	47	F	1
+input1.bam	FBtr0078790	73	52	F	1
+input1.bam	FBtr0078790	73	69	R	1
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	3	F	1
+input1.bam	FBtr0079064	72	33	F	1
+input1.bam	FBtr0079064	72	52	F	1
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	26	F	1
+input1.bam	FBtr0079090	72	33	F	1
+input1.bam	FBtr0079090	72	53	F	1
+input1.bam	FBtr0079090	72	56	R	1
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	12	F	1
+input1.bam	FBtr0079338	73	13	F	2
+input1.bam	FBtr0079338	73	14	F	1
+input1.bam	FBtr0079338	73	17	F	1
+input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	42	F	8
+input1.bam	FBtr0079338	73	43	F	1
+input1.bam	FBtr0079338	73	46	F	1
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	3	F	55
+input1.bam	FBtr0079528	71	4	F	2
+input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	10	F	1
+input1.bam	FBtr0079528	71	11	F	2
+input1.bam	FBtr0079528	71	13	F	1
+input1.bam	FBtr0079528	71	14	F	4
+input1.bam	FBtr0079528	71	16	F	1
+input1.bam	FBtr0079528	71	17	F	4
+input1.bam	FBtr0079528	71	18	F	4
+input1.bam	FBtr0079528	71	28	F	1
+input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	36	F	1
+input1.bam	FBtr0079528	71	37	F	1
+input1.bam	FBtr0079528	71	51	F	5
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	13
+input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	4	F	31
+input1.bam	FBtr0079596	73	5	F	2
+input1.bam	FBtr0079596	73	6	F	11
+input1.bam	FBtr0079596	73	8	F	9
+input1.bam	FBtr0079596	73	9	F	12
+input1.bam	FBtr0079596	73	10	F	3
+input1.bam	FBtr0079596	73	11	F	19
+input1.bam	FBtr0079596	73	12	F	1
+input1.bam	FBtr0079596	73	13	F	20
+input1.bam	FBtr0079596	73	14	F	6
+input1.bam	FBtr0079596	73	15	F	1
+input1.bam	FBtr0079596	73	16	F	3
+input1.bam	FBtr0079596	73	17	F	2
+input1.bam	FBtr0079596	73	18	F	1
+input1.bam	FBtr0079596	73	19	F	1
+input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	54	F	2
+input1.bam	FBtr0079596	73	73	F	0
+input1.bam	FBtr0079677	72	1	F	1
+input1.bam	FBtr0079677	72	5	F	1
+input1.bam	FBtr0079677	72	52	F	1
+input1.bam	FBtr0079677	72	53	F	1
+input1.bam	FBtr0079677	72	72	F	0
+input1.bam	FBtr0079690	72	1	F	1
+input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	27	F	1
+input1.bam	FBtr0079690	72	33	F	2
+input1.bam	FBtr0079690	72	72	F	0
+input1.bam	FBtr0079692	73	1	F	3
+input1.bam	FBtr0079692	73	18	F	1
+input1.bam	FBtr0079692	73	25	F	1
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+input2.bam	FBtr0080647	72	58	F	7
+input2.bam	FBtr0080647	72	72	F	0
+input2.bam	FBtr0080660	72	1	F	0
+input2.bam	FBtr0080660	72	58	F	11
+input2.bam	FBtr0080660	72	72	F	0
+input2.bam	FBtr0080663	71	1	F	2
+input2.bam	FBtr0080663	71	11	F	1
+input2.bam	FBtr0080663	71	12	F	4
+input2.bam	FBtr0080663	71	13	F	4
+input2.bam	FBtr0080663	71	14	F	22
+input2.bam	FBtr0080663	71	15	F	14
+input2.bam	FBtr0080663	71	16	F	5
+input2.bam	FBtr0080663	71	17	F	12
+input2.bam	FBtr0080663	71	18	F	5
+input2.bam	FBtr0080663	71	19	F	6
+input2.bam	FBtr0080663	71	20	F	6
+input2.bam	FBtr0080663	71	21	F	13
+input2.bam	FBtr0080663	71	22	F	3
+input2.bam	FBtr0080663	71	31	F	1
+input2.bam	FBtr0080663	71	50	F	2
+input2.bam	FBtr0080663	71	51	F	1
+input2.bam	FBtr0080663	71	52	F	2
+input2.bam	FBtr0080663	71	57	F	3
+input2.bam	FBtr0080663	71	71	F	0
+input2.bam	FBtr0080664	71	1	F	1
+input2.bam	FBtr0080664	71	3	F	2
+input2.bam	FBtr0080664	71	10	F	1
+input2.bam	FBtr0080664	71	11	F	2
+input2.bam	FBtr0080664	71	12	F	3
+input2.bam	FBtr0080664	71	13	F	11
+input2.bam	FBtr0080664	71	14	F	11
+input2.bam	FBtr0080664	71	15	F	17
+input2.bam	FBtr0080664	71	16	F	15
+input2.bam	FBtr0080664	71	17	F	13
+input2.bam	FBtr0080664	71	18	F	10
+input2.bam	FBtr0080664	71	19	F	8
+input2.bam	FBtr0080664	71	20	F	1
+input2.bam	FBtr0080664	71	21	F	15
+input2.bam	FBtr0080664	71	22	F	6
+input2.bam	FBtr0080664	71	24	F	1
+input2.bam	FBtr0080664	71	30	F	1
+input2.bam	FBtr0080664	71	31	F	3
+input2.bam	FBtr0080664	71	32	F	39
+input2.bam	FBtr0080664	71	33	F	4
+input2.bam	FBtr0080664	71	34	F	37
+input2.bam	FBtr0080664	71	35	F	135
+input2.bam	FBtr0080664	71	36	F	8
+input2.bam	FBtr0080664	71	37	F	25
+input2.bam	FBtr0080664	71	38	F	8
+input2.bam	FBtr0080664	71	39	F	1
+input2.bam	FBtr0080664	71	42	F	1
+input2.bam	FBtr0080664	71	47	F	1
+input2.bam	FBtr0080664	71	50	F	2
+input2.bam	FBtr0080664	71	52	F	1
+input2.bam	FBtr0080664	71	53	F	1
+input2.bam	FBtr0080664	71	56	F	1
+input2.bam	FBtr0080664	71	57	F	2
+input2.bam	FBtr0080664	71	62	R	1
+input2.bam	FBtr0080664	71	71	F	0
+input2.bam	FBtr0080664	71	71	R	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_coverage.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_coverage.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,3109 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	2	F	1
+input1.bam	FBtr0070001	72	3	F	1
+input1.bam	FBtr0070001	72	4	F	1
+input1.bam	FBtr0070001	72	5	F	1
+input1.bam	FBtr0070001	72	6	F	1
+input1.bam	FBtr0070001	72	7	F	7
+input1.bam	FBtr0070001	72	8	F	10
+input1.bam	FBtr0070001	72	9	F	10
+input1.bam	FBtr0070001	72	10	F	10
+input1.bam	FBtr0070001	72	11	F	12
+input1.bam	FBtr0070001	72	12	F	12
+input1.bam	FBtr0070001	72	13	F	12
+input1.bam	FBtr0070001	72	14	F	12
+input1.bam	FBtr0070001	72	15	F	12
+input1.bam	FBtr0070001	72	16	F	13
+input1.bam	FBtr0070001	72	17	F	14
+input1.bam	FBtr0070001	72	18	F	14
+input1.bam	FBtr0070001	72	19	F	14
+input1.bam	FBtr0070001	72	20	F	14
+input1.bam	FBtr0070001	72	21	F	14
+input1.bam	FBtr0070001	72	22	F	14
+input1.bam	FBtr0070001	72	23	F	13
+input1.bam	FBtr0070001	72	24	F	13
+input1.bam	FBtr0070001	72	25	F	13
+input1.bam	FBtr0070001	72	26	F	13
+input1.bam	FBtr0070001	72	27	F	14
+input1.bam	FBtr0070001	72	28	F	11
+input1.bam	FBtr0070001	72	29	F	8
+input1.bam	FBtr0070001	72	30	F	9
+input1.bam	FBtr0070001	72	31	F	18
+input1.bam	FBtr0070001	72	32	F	44
+input1.bam	FBtr0070001	72	33	F	44
+input1.bam	FBtr0070001	72	34	F	44
+input1.bam	FBtr0070001	72	35	F	43
+input1.bam	FBtr0070001	72	36	F	43
+input1.bam	FBtr0070001	72	37	F	43
+input1.bam	FBtr0070001	72	38	F	43
+input1.bam	FBtr0070001	72	39	F	43
+input1.bam	FBtr0070001	72	40	F	42
+input1.bam	FBtr0070001	72	41	F	42
+input1.bam	FBtr0070001	72	42	F	42
+input1.bam	FBtr0070001	72	43	F	42
+input1.bam	FBtr0070001	72	44	F	42
+input1.bam	FBtr0070001	72	45	F	42
+input1.bam	FBtr0070001	72	46	F	42
+input1.bam	FBtr0070001	72	47	F	42
+input1.bam	FBtr0070001	72	48	F	42
+input1.bam	FBtr0070001	72	49	F	42
+input1.bam	FBtr0070001	72	50	F	41
+input1.bam	FBtr0070001	72	51	F	40
+input1.bam	FBtr0070001	72	52	F	40
+input1.bam	FBtr0070001	72	53	F	39
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	2	F	1
+input1.bam	FBtr0070533	72	3	F	1
+input1.bam	FBtr0070533	72	4	F	1
+input1.bam	FBtr0070533	72	5	F	1
+input1.bam	FBtr0070533	72	6	F	1
+input1.bam	FBtr0070533	72	7	F	1
+input1.bam	FBtr0070533	72	8	F	1
+input1.bam	FBtr0070533	72	9	F	1
+input1.bam	FBtr0070533	72	10	F	1
+input1.bam	FBtr0070533	72	11	F	1
+input1.bam	FBtr0070533	72	12	F	3
+input1.bam	FBtr0070533	72	13	F	3
+input1.bam	FBtr0070533	72	14	F	3
+input1.bam	FBtr0070533	72	15	F	4
+input1.bam	FBtr0070533	72	16	F	3
+input1.bam	FBtr0070533	72	17	F	3
+input1.bam	FBtr0070533	72	18	F	3
+input1.bam	FBtr0070533	72	19	F	8
+input1.bam	FBtr0070533	72	20	F	9
+input1.bam	FBtr0070533	72	21	F	10
+input1.bam	FBtr0070533	72	22	F	11
+input1.bam	FBtr0070533	72	23	F	11
+input1.bam	FBtr0070533	72	24	F	11
+input1.bam	FBtr0070533	72	25	F	12
+input1.bam	FBtr0070533	72	26	F	13
+input1.bam	FBtr0070533	72	27	F	13
+input1.bam	FBtr0070533	72	28	F	14
+input1.bam	FBtr0070533	72	29	F	14
+input1.bam	FBtr0070533	72	30	F	11
+input1.bam	FBtr0070533	72	31	F	11
+input1.bam	FBtr0070533	72	32	F	15
+input1.bam	FBtr0070533	72	33	F	15
+input1.bam	FBtr0070533	72	34	F	15
+input1.bam	FBtr0070533	72	35	F	16
+input1.bam	FBtr0070533	72	36	F	16
+input1.bam	FBtr0070533	72	37	F	18
+input1.bam	FBtr0070533	72	38	F	20
+input1.bam	FBtr0070533	72	39	F	19
+input1.bam	FBtr0070533	72	40	F	17
+input1.bam	FBtr0070533	72	41	F	15
+input1.bam	FBtr0070533	72	42	F	11
+input1.bam	FBtr0070533	72	43	F	10
+input1.bam	FBtr0070533	72	44	F	10
+input1.bam	FBtr0070533	72	45	F	10
+input1.bam	FBtr0070533	72	46	F	10
+input1.bam	FBtr0070533	72	47	F	10
+input1.bam	FBtr0070533	72	48	F	10
+input1.bam	FBtr0070533	72	49	F	10
+input1.bam	FBtr0070533	72	50	F	9
+input1.bam	FBtr0070533	72	51	F	9
+input1.bam	FBtr0070533	72	52	F	8
+input1.bam	FBtr0070533	72	53	F	7
+input1.bam	FBtr0070533	72	54	F	4
+input1.bam	FBtr0070533	72	55	F	4
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	2	F	2
+input1.bam	FBtr0070603	72	3	F	3
+input1.bam	FBtr0070603	72	4	F	4
+input1.bam	FBtr0070603	72	5	F	4
+input1.bam	FBtr0070603	72	6	F	5
+input1.bam	FBtr0070603	72	7	F	12
+input1.bam	FBtr0070603	72	8	F	16
+input1.bam	FBtr0070603	72	9	F	23
+input1.bam	FBtr0070603	72	10	F	23
+input1.bam	FBtr0070603	72	11	F	23
+input1.bam	FBtr0070603	72	12	F	25
+input1.bam	FBtr0070603	72	13	F	26
+input1.bam	FBtr0070603	72	14	F	26
+input1.bam	FBtr0070603	72	15	F	28
+input1.bam	FBtr0070603	72	16	F	29
+input1.bam	FBtr0070603	72	17	F	32
+input1.bam	FBtr0070603	72	18	F	33
+input1.bam	FBtr0070603	72	19	F	41
+input1.bam	FBtr0070603	72	20	F	44
+input1.bam	FBtr0070603	72	21	F	45
+input1.bam	FBtr0070603	72	22	F	48
+input1.bam	FBtr0070603	72	23	F	48
+input1.bam	FBtr0070603	72	24	F	30
+input1.bam	FBtr0070603	72	25	F	30
+input1.bam	FBtr0070603	72	26	F	36
+input1.bam	FBtr0070603	72	27	F	39
+input1.bam	FBtr0070603	72	28	F	39
+input1.bam	FBtr0070603	72	29	F	38
+input1.bam	FBtr0070603	72	30	F	38
+input1.bam	FBtr0070603	72	31	F	38
+input1.bam	FBtr0070603	72	32	F	38
+input1.bam	FBtr0070603	72	33	F	37
+input1.bam	FBtr0070603	72	34	F	39
+input1.bam	FBtr0070603	72	35	F	35
+input1.bam	FBtr0070603	72	36	F	34
+input1.bam	FBtr0070603	72	37	F	34
+input1.bam	FBtr0070603	72	38	F	35
+input1.bam	FBtr0070603	72	39	F	34
+input1.bam	FBtr0070603	72	40	F	33
+input1.bam	FBtr0070603	72	41	F	32
+input1.bam	FBtr0070603	72	42	F	21
+input1.bam	FBtr0070603	72	43	F	21
+input1.bam	FBtr0070603	72	44	F	20
+input1.bam	FBtr0070603	72	45	F	18
+input1.bam	FBtr0070603	72	46	F	16
+input1.bam	FBtr0070603	72	47	F	16
+input1.bam	FBtr0070603	72	48	F	15
+input1.bam	FBtr0070603	72	49	F	15
+input1.bam	FBtr0070603	72	50	F	14
+input1.bam	FBtr0070603	72	51	F	14
+input1.bam	FBtr0070603	72	52	F	10
+input1.bam	FBtr0070603	72	53	F	6
+input1.bam	FBtr0070603	72	54	F	3
+input1.bam	FBtr0070603	72	55	F	3
+input1.bam	FBtr0070603	72	56	F	3
+input1.bam	FBtr0070603	72	57	F	3
+input1.bam	FBtr0070603	72	58	F	3
+input1.bam	FBtr0070603	72	59	F	3
+input1.bam	FBtr0070603	72	60	F	3
+input1.bam	FBtr0070603	72	61	F	3
+input1.bam	FBtr0070603	72	62	F	3
+input1.bam	FBtr0070603	72	63	F	2
+input1.bam	FBtr0070603	72	64	F	2
+input1.bam	FBtr0070603	72	65	F	2
+input1.bam	FBtr0070603	72	66	F	2
+input1.bam	FBtr0070603	72	67	F	2
+input1.bam	FBtr0070603	72	68	F	2
+input1.bam	FBtr0070603	72	69	F	1
+input1.bam	FBtr0070603	72	70	F	1
+input1.bam	FBtr0070603	72	71	F	1
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	2	F	1
+input1.bam	FBtr0070604	72	3	F	1
+input1.bam	FBtr0070604	72	4	F	1
+input1.bam	FBtr0070604	72	5	F	1
+input1.bam	FBtr0070604	72	6	F	1
+input1.bam	FBtr0070604	72	7	F	1
+input1.bam	FBtr0070604	72	8	F	1
+input1.bam	FBtr0070604	72	9	F	1
+input1.bam	FBtr0070604	72	10	F	1
+input1.bam	FBtr0070604	72	11	F	1
+input1.bam	FBtr0070604	72	12	F	1
+input1.bam	FBtr0070604	72	13	F	1
+input1.bam	FBtr0070604	72	14	F	1
+input1.bam	FBtr0070604	72	15	F	1
+input1.bam	FBtr0070604	72	18	F	1
+input1.bam	FBtr0070604	72	19	F	1
+input1.bam	FBtr0070604	72	20	F	1
+input1.bam	FBtr0070604	72	21	F	1
+input1.bam	FBtr0070604	72	22	F	2
+input1.bam	FBtr0070604	72	23	F	2
+input1.bam	FBtr0070604	72	24	F	2
+input1.bam	FBtr0070604	72	25	F	2
+input1.bam	FBtr0070604	72	26	F	2
+input1.bam	FBtr0070604	72	27	F	2
+input1.bam	FBtr0070604	72	28	F	2
+input1.bam	FBtr0070604	72	29	F	2
+input1.bam	FBtr0070604	72	30	F	4
+input1.bam	FBtr0070604	72	31	F	14
+input1.bam	FBtr0070604	72	32	F	38
+input1.bam	FBtr0070604	72	33	F	38
+input1.bam	FBtr0070604	72	34	F	38
+input1.bam	FBtr0070604	72	35	F	38
+input1.bam	FBtr0070604	72	36	F	38
+input1.bam	FBtr0070604	72	37	F	38
+input1.bam	FBtr0070604	72	38	F	38
+input1.bam	FBtr0070604	72	39	F	38
+input1.bam	FBtr0070604	72	40	F	38
+input1.bam	FBtr0070604	72	41	F	36
+input1.bam	FBtr0070604	72	42	F	36
+input1.bam	FBtr0070604	72	43	F	36
+input1.bam	FBtr0070604	72	44	F	36
+input1.bam	FBtr0070604	72	45	F	36
+input1.bam	FBtr0070604	72	46	F	35
+input1.bam	FBtr0070604	72	47	F	36
+input1.bam	FBtr0070604	72	48	F	34
+input1.bam	FBtr0070604	72	49	F	34
+input1.bam	FBtr0070604	72	50	F	33
+input1.bam	FBtr0070604	72	51	F	33
+input1.bam	FBtr0070604	72	52	F	33
+input1.bam	FBtr0070604	72	53	F	31
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	58	F	1
+input1.bam	FBtr0070604	72	59	F	1
+input1.bam	FBtr0070604	72	60	F	1
+input1.bam	FBtr0070604	72	61	F	1
+input1.bam	FBtr0070604	72	62	F	1
+input1.bam	FBtr0070604	72	63	F	1
+input1.bam	FBtr0070604	72	64	F	1
+input1.bam	FBtr0070604	72	65	F	1
+input1.bam	FBtr0070604	72	66	F	1
+input1.bam	FBtr0070604	72	67	F	1
+input1.bam	FBtr0070604	72	68	F	1
+input1.bam	FBtr0070604	72	69	F	1
+input1.bam	FBtr0070604	72	70	F	1
+input1.bam	FBtr0070604	72	71	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	16	F	1
+input1.bam	FBtr0070911	73	17	F	1
+input1.bam	FBtr0070911	73	18	F	1
+input1.bam	FBtr0070911	73	19	F	1
+input1.bam	FBtr0070911	73	20	F	1
+input1.bam	FBtr0070911	73	21	F	1
+input1.bam	FBtr0070911	73	22	F	1
+input1.bam	FBtr0070911	73	23	F	1
+input1.bam	FBtr0070911	73	24	F	1
+input1.bam	FBtr0070911	73	25	F	1
+input1.bam	FBtr0070911	73	26	F	1
+input1.bam	FBtr0070911	73	27	F	1
+input1.bam	FBtr0070911	73	28	F	1
+input1.bam	FBtr0070911	73	29	F	1
+input1.bam	FBtr0070911	73	30	F	1
+input1.bam	FBtr0070911	73	31	F	1
+input1.bam	FBtr0070911	73	32	F	1
+input1.bam	FBtr0070911	73	33	F	1
+input1.bam	FBtr0070911	73	34	F	1
+input1.bam	FBtr0070911	73	35	F	1
+input1.bam	FBtr0070911	73	38	F	1
+input1.bam	FBtr0070911	73	39	F	1
+input1.bam	FBtr0070911	73	40	F	1
+input1.bam	FBtr0070911	73	41	F	1
+input1.bam	FBtr0070911	73	42	F	1
+input1.bam	FBtr0070911	73	43	F	1
+input1.bam	FBtr0070911	73	44	F	1
+input1.bam	FBtr0070911	73	45	F	1
+input1.bam	FBtr0070911	73	46	F	1
+input1.bam	FBtr0070911	73	47	F	1
+input1.bam	FBtr0070911	73	48	F	1
+input1.bam	FBtr0070911	73	49	F	1
+input1.bam	FBtr0070911	73	50	F	1
+input1.bam	FBtr0070911	73	51	F	1
+input1.bam	FBtr0070911	73	52	F	1
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	2
+input1.bam	FBtr0078490	72	14	F	2
+input1.bam	FBtr0078490	72	15	F	2
+input1.bam	FBtr0078490	72	16	F	2
+input1.bam	FBtr0078490	72	17	F	3
+input1.bam	FBtr0078490	72	18	F	4
+input1.bam	FBtr0078490	72	19	F	4
+input1.bam	FBtr0078490	72	20	F	4
+input1.bam	FBtr0078490	72	21	F	4
+input1.bam	FBtr0078490	72	22	F	4
+input1.bam	FBtr0078490	72	23	F	4
+input1.bam	FBtr0078490	72	24	F	4
+input1.bam	FBtr0078490	72	25	F	5
+input1.bam	FBtr0078490	72	26	F	5
+input1.bam	FBtr0078490	72	27	F	5
+input1.bam	FBtr0078490	72	28	F	7
+input1.bam	FBtr0078490	72	29	F	5
+input1.bam	FBtr0078490	72	30	F	5
+input1.bam	FBtr0078490	72	31	F	5
+input1.bam	FBtr0078490	72	32	F	5
+input1.bam	FBtr0078490	72	33	F	3
+input1.bam	FBtr0078490	72	34	F	3
+input1.bam	FBtr0078490	72	35	F	3
+input1.bam	FBtr0078490	72	36	F	3
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+input2.bam	FBtr0080647	72	11	F	1
+input2.bam	FBtr0080647	72	12	F	1
+input2.bam	FBtr0080647	72	13	F	1
+input2.bam	FBtr0080647	72	14	F	1
+input2.bam	FBtr0080647	72	15	F	1
+input2.bam	FBtr0080647	72	16	F	1
+input2.bam	FBtr0080647	72	17	F	1
+input2.bam	FBtr0080647	72	18	F	1
+input2.bam	FBtr0080647	72	57	F	4
+input2.bam	FBtr0080647	72	58	F	11
+input2.bam	FBtr0080647	72	59	F	11
+input2.bam	FBtr0080647	72	60	F	11
+input2.bam	FBtr0080647	72	61	F	11
+input2.bam	FBtr0080647	72	62	F	11
+input2.bam	FBtr0080647	72	63	F	11
+input2.bam	FBtr0080647	72	64	F	11
+input2.bam	FBtr0080647	72	65	F	11
+input2.bam	FBtr0080647	72	66	F	11
+input2.bam	FBtr0080647	72	67	F	11
+input2.bam	FBtr0080647	72	68	F	11
+input2.bam	FBtr0080647	72	69	F	11
+input2.bam	FBtr0080647	72	70	F	11
+input2.bam	FBtr0080647	72	71	F	11
+input2.bam	FBtr0080647	72	72	F	9
+input2.bam	FBtr0080660	72	1	F	0
+input2.bam	FBtr0080660	72	58	F	11
+input2.bam	FBtr0080660	72	59	F	11
+input2.bam	FBtr0080660	72	60	F	11
+input2.bam	FBtr0080660	72	61	F	11
+input2.bam	FBtr0080660	72	62	F	11
+input2.bam	FBtr0080660	72	63	F	11
+input2.bam	FBtr0080660	72	64	F	11
+input2.bam	FBtr0080660	72	65	F	11
+input2.bam	FBtr0080660	72	66	F	11
+input2.bam	FBtr0080660	72	67	F	11
+input2.bam	FBtr0080660	72	68	F	11
+input2.bam	FBtr0080660	72	69	F	11
+input2.bam	FBtr0080660	72	70	F	11
+input2.bam	FBtr0080660	72	71	F	11
+input2.bam	FBtr0080660	72	72	F	11
+input2.bam	FBtr0080663	71	1	F	2
+input2.bam	FBtr0080663	71	2	F	2
+input2.bam	FBtr0080663	71	3	F	2
+input2.bam	FBtr0080663	71	4	F	2
+input2.bam	FBtr0080663	71	5	F	2
+input2.bam	FBtr0080663	71	6	F	2
+input2.bam	FBtr0080663	71	7	F	2
+input2.bam	FBtr0080663	71	8	F	2
+input2.bam	FBtr0080663	71	9	F	2
+input2.bam	FBtr0080663	71	10	F	2
+input2.bam	FBtr0080663	71	11	F	3
+input2.bam	FBtr0080663	71	12	F	7
+input2.bam	FBtr0080663	71	13	F	11
+input2.bam	FBtr0080663	71	14	F	33
+input2.bam	FBtr0080663	71	15	F	47
+input2.bam	FBtr0080663	71	16	F	52
+input2.bam	FBtr0080663	71	17	F	64
+input2.bam	FBtr0080663	71	18	F	69
+input2.bam	FBtr0080663	71	19	F	75
+input2.bam	FBtr0080663	71	20	F	81
+input2.bam	FBtr0080663	71	21	F	94
+input2.bam	FBtr0080663	71	22	F	97
+input2.bam	FBtr0080663	71	23	F	95
+input2.bam	FBtr0080663	71	24	F	95
+input2.bam	FBtr0080663	71	25	F	95
+input2.bam	FBtr0080663	71	26	F	95
+input2.bam	FBtr0080663	71	27	F	95
+input2.bam	FBtr0080663	71	28	F	95
+input2.bam	FBtr0080663	71	29	F	95
+input2.bam	FBtr0080663	71	30	F	95
+input2.bam	FBtr0080663	71	31	F	96
+input2.bam	FBtr0080663	71	32	F	62
+input2.bam	FBtr0080663	71	33	F	41
+input2.bam	FBtr0080663	71	34	F	40
+input2.bam	FBtr0080663	71	35	F	34
+input2.bam	FBtr0080663	71	36	F	12
+input2.bam	FBtr0080663	71	37	F	6
+input2.bam	FBtr0080663	71	38	F	5
+input2.bam	FBtr0080663	71	39	F	4
+input2.bam	FBtr0080663	71	40	F	3
+input2.bam	FBtr0080663	71	41	F	2
+input2.bam	FBtr0080663	71	42	F	1
+input2.bam	FBtr0080663	71	43	F	1
+input2.bam	FBtr0080663	71	44	F	1
+input2.bam	FBtr0080663	71	45	F	1
+input2.bam	FBtr0080663	71	46	F	1
+input2.bam	FBtr0080663	71	47	F	1
+input2.bam	FBtr0080663	71	50	F	2
+input2.bam	FBtr0080663	71	51	F	3
+input2.bam	FBtr0080663	71	52	F	5
+input2.bam	FBtr0080663	71	53	F	5
+input2.bam	FBtr0080663	71	54	F	5
+input2.bam	FBtr0080663	71	55	F	5
+input2.bam	FBtr0080663	71	56	F	5
+input2.bam	FBtr0080663	71	57	F	8
+input2.bam	FBtr0080663	71	58	F	8
+input2.bam	FBtr0080663	71	59	F	8
+input2.bam	FBtr0080663	71	60	F	8
+input2.bam	FBtr0080663	71	61	F	8
+input2.bam	FBtr0080663	71	62	F	8
+input2.bam	FBtr0080663	71	63	F	8
+input2.bam	FBtr0080663	71	64	F	8
+input2.bam	FBtr0080663	71	65	F	7
+input2.bam	FBtr0080663	71	66	F	6
+input2.bam	FBtr0080663	71	67	F	4
+input2.bam	FBtr0080663	71	68	F	4
+input2.bam	FBtr0080663	71	69	F	4
+input2.bam	FBtr0080663	71	70	F	3
+input2.bam	FBtr0080663	71	71	F	3
+input2.bam	FBtr0080664	71	1	F	1
+input2.bam	FBtr0080664	71	2	F	1
+input2.bam	FBtr0080664	71	3	F	3
+input2.bam	FBtr0080664	71	4	F	3
+input2.bam	FBtr0080664	71	5	F	3
+input2.bam	FBtr0080664	71	6	F	3
+input2.bam	FBtr0080664	71	7	F	3
+input2.bam	FBtr0080664	71	8	F	3
+input2.bam	FBtr0080664	71	9	F	3
+input2.bam	FBtr0080664	71	10	F	4
+input2.bam	FBtr0080664	71	11	F	6
+input2.bam	FBtr0080664	71	12	F	9
+input2.bam	FBtr0080664	71	13	F	20
+input2.bam	FBtr0080664	71	14	F	31
+input2.bam	FBtr0080664	71	15	F	48
+input2.bam	FBtr0080664	71	16	F	63
+input2.bam	FBtr0080664	71	17	F	76
+input2.bam	FBtr0080664	71	18	F	86
+input2.bam	FBtr0080664	71	19	F	94
+input2.bam	FBtr0080664	71	20	F	95
+input2.bam	FBtr0080664	71	21	F	110
+input2.bam	FBtr0080664	71	22	F	116
+input2.bam	FBtr0080664	71	23	F	114
+input2.bam	FBtr0080664	71	24	F	115
+input2.bam	FBtr0080664	71	25	F	115
+input2.bam	FBtr0080664	71	26	F	115
+input2.bam	FBtr0080664	71	27	F	115
+input2.bam	FBtr0080664	71	28	F	115
+input2.bam	FBtr0080664	71	29	F	113
+input2.bam	FBtr0080664	71	30	F	113
+input2.bam	FBtr0080664	71	31	F	117
+input2.bam	FBtr0080664	71	32	F	127
+input2.bam	FBtr0080664	71	33	F	97
+input2.bam	FBtr0080664	71	34	F	134
+input2.bam	FBtr0080664	71	35	F	265
+input2.bam	FBtr0080664	71	36	F	249
+input2.bam	FBtr0080664	71	37	F	266
+input2.bam	FBtr0080664	71	38	F	268
+input2.bam	FBtr0080664	71	39	F	263
+input2.bam	FBtr0080664	71	40	F	263
+input2.bam	FBtr0080664	71	41	F	262
+input2.bam	FBtr0080664	71	42	F	262
+input2.bam	FBtr0080664	71	43	F	260
+input2.bam	FBtr0080664	71	44	F	263
+input2.bam	FBtr0080664	71	45	F	263
+input2.bam	FBtr0080664	71	46	F	263
+input2.bam	FBtr0080664	71	47	F	264
+input2.bam	FBtr0080664	71	48	F	264
+input2.bam	FBtr0080664	71	49	F	254
+input2.bam	FBtr0080664	71	50	F	72
+input2.bam	FBtr0080664	71	51	F	63
+input2.bam	FBtr0080664	71	52	F	61
+input2.bam	FBtr0080664	71	53	F	31
+input2.bam	FBtr0080664	71	54	F	30
+input2.bam	FBtr0080664	71	55	F	21
+input2.bam	FBtr0080664	71	56	F	16
+input2.bam	FBtr0080664	71	57	F	18
+input2.bam	FBtr0080664	71	58	F	18
+input2.bam	FBtr0080664	71	59	F	18
+input2.bam	FBtr0080664	71	60	F	17
+input2.bam	FBtr0080664	71	61	F	16
+input2.bam	FBtr0080664	71	62	F	12
+input2.bam	FBtr0080664	71	62	R	12
+input2.bam	FBtr0080664	71	63	F	8
+input2.bam	FBtr0080664	71	64	F	8
+input2.bam	FBtr0080664	71	65	F	7
+input2.bam	FBtr0080664	71	66	F	6
+input2.bam	FBtr0080664	71	67	F	6
+input2.bam	FBtr0080664	71	68	F	5
+input2.bam	FBtr0080664	71	69	F	5
+input2.bam	FBtr0080664	71	70	F	5
+input2.bam	FBtr0080664	71	71	F	5
+input2.bam	FBtr0080664	71	71	R	5
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf
Binary file test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_double_plot_coverage_mean_ylim20_25.pdf
Binary file test-data/input1_input2_double_plot_coverage_mean_ylim20_25.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_mean.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_mean.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,617 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
+input1.bam	FBtr0070001	72	1	F	17.0
+input1.bam	FBtr0070001	72	7	F	20.3
+input1.bam	FBtr0070001	72	8	F	21.3
+input1.bam	FBtr0070001	72	11	F	20.5
+input1.bam	FBtr0070001	72	16	F	19.0
+input1.bam	FBtr0070001	72	17	F	23.0
+input1.bam	FBtr0070001	72	18	F	16.0
+input1.bam	FBtr0070001	72	27	F	23.5
+input1.bam	FBtr0070001	72	30	F	23.0
+input1.bam	FBtr0070001	72	31	F	23.0
+input1.bam	FBtr0070001	72	32	F	22.0
+input1.bam	FBtr0070001	72	34	F	20.0
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	15.0
+input1.bam	FBtr0070533	72	12	F	18.0
+input1.bam	FBtr0070533	72	15	F	15.0
+input1.bam	FBtr0070533	72	19	F	21.8
+input1.bam	FBtr0070533	72	20	F	23.0
+input1.bam	FBtr0070533	72	21	F	18.0
+input1.bam	FBtr0070533	72	22	F	20.0
+input1.bam	FBtr0070533	72	25	F	17.0
+input1.bam	FBtr0070533	72	26	F	16.0
+input1.bam	FBtr0070533	72	28	F	25.0
+input1.bam	FBtr0070533	72	32	F	20.5
+input1.bam	FBtr0070533	72	35	F	19.0
+input1.bam	FBtr0070533	72	37	F	19.0
+input1.bam	FBtr0070533	72	38	F	18.0
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	16.5
+input1.bam	FBtr0070603	72	3	F	21.0
+input1.bam	FBtr0070603	72	4	F	20.0
+input1.bam	FBtr0070603	72	6	F	18.0
+input1.bam	FBtr0070603	72	7	F	17.1
+input1.bam	FBtr0070603	72	8	F	16.0
+input1.bam	FBtr0070603	72	9	F	15.0
+input1.bam	FBtr0070603	72	12	F	20.0
+input1.bam	FBtr0070603	72	13	F	22.0
+input1.bam	FBtr0070603	72	15	F	18.5
+input1.bam	FBtr0070603	72	16	F	20.5
+input1.bam	FBtr0070603	72	17	F	24.0
+input1.bam	FBtr0070603	72	18	F	16.0
+input1.bam	FBtr0070603	72	19	F	22.6
+input1.bam	FBtr0070603	72	20	F	21.0
+input1.bam	FBtr0070603	72	21	F	25.0
+input1.bam	FBtr0070603	72	22	F	20.7
+input1.bam	FBtr0070603	72	24	F	19.5
+input1.bam	FBtr0070603	72	25	F	23.0
+input1.bam	FBtr0070603	72	26	F	25.8
+input1.bam	FBtr0070603	72	27	F	26.3
+input1.bam	FBtr0070603	72	32	F	20.0
+input1.bam	FBtr0070603	72	34	F	19.3
+input1.bam	FBtr0070603	72	38	F	18.0
+input1.bam	FBtr0070603	72	42	F	21.0
+input1.bam	FBtr0070603	72	51	F	18.0
+input1.bam	FBtr0070603	72	56	F	16.0
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	15.0
+input1.bam	FBtr0070604	72	18	F	23.0
+input1.bam	FBtr0070604	72	22	F	19.0
+input1.bam	FBtr0070604	72	30	F	18.0
+input1.bam	FBtr0070604	72	31	F	22.6
+input1.bam	FBtr0070604	72	32	F	22.0
+input1.bam	FBtr0070604	72	57	F	15.0
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	21.0
+input1.bam	FBtr0070911	73	38	F	15.0
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	16.0
+input1.bam	FBtr0078490	72	17	F	16.0
+input1.bam	FBtr0078490	72	18	F	15.0
+input1.bam	FBtr0078490	72	25	F	15.0
+input1.bam	FBtr0078490	72	28	F	19.0
+input1.bam	FBtr0078490	72	38	F	18.0
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	18.9
+input1.bam	FBtr0078580	72	3	F	22.0
+input1.bam	FBtr0078580	72	4	F	25.3
+input1.bam	FBtr0078580	72	5	F	21.0
+input1.bam	FBtr0078580	72	6	F	19.0
+input1.bam	FBtr0078580	72	7	F	22.0
+input1.bam	FBtr0078580	72	8	F	18.0
+input1.bam	FBtr0078580	72	11	F	23.0
+input1.bam	FBtr0078580	72	12	F	18.0
+input1.bam	FBtr0078580	72	14	F	15.3
+input1.bam	FBtr0078580	72	15	F	16.0
+input1.bam	FBtr0078580	72	16	F	19.0
+input1.bam	FBtr0078580	72	17	F	17.0
+input1.bam	FBtr0078580	72	19	F	24.0
+input1.bam	FBtr0078580	72	20	F	21.0
+input1.bam	FBtr0078580	72	21	F	19.4
+input1.bam	FBtr0078580	72	24	F	17.0
+input1.bam	FBtr0078580	72	25	F	27.5
+input1.bam	FBtr0078580	72	29	F	17.0
+input1.bam	FBtr0078580	72	31	F	17.0
+input1.bam	FBtr0078580	72	52	F	16.0
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	19.0
+input1.bam	FBtr0078790	73	17	F	16.0
+input1.bam	FBtr0078790	73	33	F	23.0
+input1.bam	FBtr0078790	73	42	F	18.5
+input1.bam	FBtr0078790	73	44	F	19.5
+input1.bam	FBtr0078790	73	46	F	17.0
+input1.bam	FBtr0078790	73	47	F	18.0
+input1.bam	FBtr0078790	73	52	F	20.0
+input1.bam	FBtr0078790	73	69	R	15.0
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	15.0
+input1.bam	FBtr0079064	72	3	F	21.0
+input1.bam	FBtr0079064	72	33	F	15.0
+input1.bam	FBtr0079064	72	52	F	17.0
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	21.5
+input1.bam	FBtr0079090	72	26	F	24.0
+input1.bam	FBtr0079090	72	33	F	16.0
+input1.bam	FBtr0079090	72	53	F	18.0
+input1.bam	FBtr0079090	72	56	R	21.0
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	12	F	17.0
+input1.bam	FBtr0079338	73	13	F	17.5
+input1.bam	FBtr0079338	73	14	F	15.0
+input1.bam	FBtr0079338	73	17	F	15.0
+input1.bam	FBtr0079338	73	25	F	16.0
+input1.bam	FBtr0079338	73	42	F	21.8
+input1.bam	FBtr0079338	73	43	F	21.0
+input1.bam	FBtr0079338	73	46	F	18.0
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	20.8
+input1.bam	FBtr0079528	71	3	F	23.6
+input1.bam	FBtr0079528	71	4	F	24.0
+input1.bam	FBtr0079528	71	8	F	20.3
+input1.bam	FBtr0079528	71	10	F	21.0
+input1.bam	FBtr0079528	71	11	F	19.0
+input1.bam	FBtr0079528	71	13	F	16.0
+input1.bam	FBtr0079528	71	14	F	18.5
+input1.bam	FBtr0079528	71	16	F	15.0
+input1.bam	FBtr0079528	71	17	F	15.3
+input1.bam	FBtr0079528	71	18	F	19.8
+input1.bam	FBtr0079528	71	28	F	16.0
+input1.bam	FBtr0079528	71	35	F	15.0
+input1.bam	FBtr0079528	71	36	F	20.0
+input1.bam	FBtr0079528	71	37	F	18.0
+input1.bam	FBtr0079528	71	51	F	15.0
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	16.2
+input1.bam	FBtr0079596	73	3	F	21.8
+input1.bam	FBtr0079596	73	4	F	21.5
+input1.bam	FBtr0079596	73	5	F	18.5
+input1.bam	FBtr0079596	73	6	F	17.5
+input1.bam	FBtr0079596	73	8	F	16.6
+input1.bam	FBtr0079596	73	9	F	16.1
+input1.bam	FBtr0079596	73	10	F	15.3
+input1.bam	FBtr0079596	73	11	F	15.2
+input1.bam	FBtr0079596	73	12	F	17.0
+input1.bam	FBtr0079596	73	13	F	16.1
+input1.bam	FBtr0079596	73	14	F	15.0
+input1.bam	FBtr0079596	73	15	F	18.0
+input1.bam	FBtr0079596	73	16	F	16.7
+input1.bam	FBtr0079596	73	17	F	16.0
+input1.bam	FBtr0079596	73	18	F	15.0
+input1.bam	FBtr0079596	73	19	F	15.0
+input1.bam	FBtr0079596	73	53	F	18.5
+input1.bam	FBtr0079596	73	54	F	19.5
+input1.bam	FBtr0079596	73	73	F	0
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+input2.bam	FBtr0079728	72	72	F	0
+input2.bam	FBtr0079729	72	1	F	15.0
+input2.bam	FBtr0079729	72	19	F	16.0
+input2.bam	FBtr0079729	72	33	F	17.0
+input2.bam	FBtr0079729	72	53	F	16.0
+input2.bam	FBtr0079729	72	72	F	0
+input2.bam	FBtr0079752	72	1	F	0
+input2.bam	FBtr0079752	72	49	F	24.0
+input2.bam	FBtr0079752	72	52	F	17.0
+input2.bam	FBtr0079752	72	72	F	0
+input2.bam	FBtr0079820	74	1	F	0
+input2.bam	FBtr0079820	74	39	F	16.0
+input2.bam	FBtr0079820	74	52	F	21.0
+input2.bam	FBtr0079820	74	53	F	20.0
+input2.bam	FBtr0079820	74	54	F	19.3
+input2.bam	FBtr0079820	74	55	F	18.6
+input2.bam	FBtr0079820	74	56	F	16.5
+input2.bam	FBtr0079820	74	57	F	16.8
+input2.bam	FBtr0079820	74	58	F	16.0
+input2.bam	FBtr0079820	74	59	F	15.5
+input2.bam	FBtr0079820	74	60	F	15.0
+input2.bam	FBtr0079820	74	74	F	0
+input2.bam	FBtr0080609	72	1	F	0
+input2.bam	FBtr0080609	72	20	F	19.0
+input2.bam	FBtr0080609	72	21	F	21.0
+input2.bam	FBtr0080609	72	22	F	23.0
+input2.bam	FBtr0080609	72	33	F	22.0
+input2.bam	FBtr0080609	72	39	F	17.0
+input2.bam	FBtr0080609	72	52	F	18.0
+input2.bam	FBtr0080609	72	53	F	19.0
+input2.bam	FBtr0080609	72	72	F	0
+input2.bam	FBtr0080644	72	1	F	0
+input2.bam	FBtr0080644	72	57	F	15.0
+input2.bam	FBtr0080644	72	58	F	15.0
+input2.bam	FBtr0080644	72	72	F	0
+input2.bam	FBtr0080646	72	1	F	0
+input2.bam	FBtr0080646	72	51	F	21.0
+input2.bam	FBtr0080646	72	57	F	15.5
+input2.bam	FBtr0080646	72	58	F	15.0
+input2.bam	FBtr0080646	72	72	F	0
+input2.bam	FBtr0080647	72	1	F	18.0
+input2.bam	FBtr0080647	72	57	F	15.5
+input2.bam	FBtr0080647	72	58	F	15.0
+input2.bam	FBtr0080647	72	72	F	0
+input2.bam	FBtr0080660	72	1	F	0
+input2.bam	FBtr0080660	72	58	F	15.0
+input2.bam	FBtr0080660	72	72	F	0
+input2.bam	FBtr0080663	71	1	F	22.0
+input2.bam	FBtr0080663	71	11	F	21.0
+input2.bam	FBtr0080663	71	12	F	20.5
+input2.bam	FBtr0080663	71	13	F	19.8
+input2.bam	FBtr0080663	71	14	F	18.6
+input2.bam	FBtr0080663	71	15	F	17.9
+input2.bam	FBtr0080663	71	16	F	17.0
+input2.bam	FBtr0080663	71	17	F	16.0
+input2.bam	FBtr0080663	71	18	F	18.2
+input2.bam	FBtr0080663	71	19	F	17.7
+input2.bam	FBtr0080663	71	20	F	16.7
+input2.bam	FBtr0080663	71	21	F	15.5
+input2.bam	FBtr0080663	71	22	F	15.3
+input2.bam	FBtr0080663	71	31	F	17.0
+input2.bam	FBtr0080663	71	50	F	15.5
+input2.bam	FBtr0080663	71	51	F	19.0
+input2.bam	FBtr0080663	71	52	F	15.0
+input2.bam	FBtr0080663	71	57	F	15.0
+input2.bam	FBtr0080663	71	71	F	0
+input2.bam	FBtr0080664	71	1	F	22.0
+input2.bam	FBtr0080664	71	3	F	23.0
+input2.bam	FBtr0080664	71	10	F	23.0
+input2.bam	FBtr0080664	71	11	F	22.0
+input2.bam	FBtr0080664	71	12	F	21.0
+input2.bam	FBtr0080664	71	13	F	19.7
+input2.bam	FBtr0080664	71	14	F	18.3
+input2.bam	FBtr0080664	71	15	F	18.1
+input2.bam	FBtr0080664	71	16	F	17.3
+input2.bam	FBtr0080664	71	17	F	15.8
+input2.bam	FBtr0080664	71	18	F	18.9
+input2.bam	FBtr0080664	71	19	F	19.0
+input2.bam	FBtr0080664	71	20	F	16.0
+input2.bam	FBtr0080664	71	21	F	15.3
+input2.bam	FBtr0080664	71	22	F	16.2
+input2.bam	FBtr0080664	71	24	F	15.0
+input2.bam	FBtr0080664	71	30	F	21.0
+input2.bam	FBtr0080664	71	31	F	18.7
+input2.bam	FBtr0080664	71	32	F	18.3
+input2.bam	FBtr0080664	71	33	F	17.5
+input2.bam	FBtr0080664	71	34	F	16.1
+input2.bam	FBtr0080664	71	35	F	15.2
+input2.bam	FBtr0080664	71	36	F	19.9
+input2.bam	FBtr0080664	71	37	F	17.7
+input2.bam	FBtr0080664	71	38	F	18.1
+input2.bam	FBtr0080664	71	39	F	17.0
+input2.bam	FBtr0080664	71	42	F	20.0
+input2.bam	FBtr0080664	71	47	F	15.0
+input2.bam	FBtr0080664	71	50	F	15.5
+input2.bam	FBtr0080664	71	52	F	16.0
+input2.bam	FBtr0080664	71	53	F	19.0
+input2.bam	FBtr0080664	71	56	F	16.0
+input2.bam	FBtr0080664	71	57	F	15.0
+input2.bam	FBtr0080664	71	62	R	23.0
+input2.bam	FBtr0080664	71	71	F	0
+input2.bam	FBtr0080664	71	71	R	22.0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_norm_1_2_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_norm_1_2_counts.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,617 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	7	F	6
+input1.bam	FBtr0070001	72	8	F	3
+input1.bam	FBtr0070001	72	11	F	2
+input1.bam	FBtr0070001	72	16	F	1
+input1.bam	FBtr0070001	72	17	F	1
+input1.bam	FBtr0070001	72	18	F	1
+input1.bam	FBtr0070001	72	27	F	2
+input1.bam	FBtr0070001	72	30	F	1
+input1.bam	FBtr0070001	72	31	F	11
+input1.bam	FBtr0070001	72	32	F	27
+input1.bam	FBtr0070001	72	34	F	1
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	12	F	2
+input1.bam	FBtr0070533	72	15	F	1
+input1.bam	FBtr0070533	72	19	F	5
+input1.bam	FBtr0070533	72	20	F	1
+input1.bam	FBtr0070533	72	21	F	1
+input1.bam	FBtr0070533	72	22	F	1
+input1.bam	FBtr0070533	72	25	F	1
+input1.bam	FBtr0070533	72	26	F	1
+input1.bam	FBtr0070533	72	28	F	1
+input1.bam	FBtr0070533	72	32	F	4
+input1.bam	FBtr0070533	72	35	F	1
+input1.bam	FBtr0070533	72	37	F	2
+input1.bam	FBtr0070533	72	38	F	2
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	2
+input1.bam	FBtr0070603	72	3	F	1
+input1.bam	FBtr0070603	72	4	F	1
+input1.bam	FBtr0070603	72	6	F	1
+input1.bam	FBtr0070603	72	7	F	7
+input1.bam	FBtr0070603	72	8	F	4
+input1.bam	FBtr0070603	72	9	F	7
+input1.bam	FBtr0070603	72	12	F	2
+input1.bam	FBtr0070603	72	13	F	1
+input1.bam	FBtr0070603	72	15	F	2
+input1.bam	FBtr0070603	72	16	F	2
+input1.bam	FBtr0070603	72	17	F	3
+input1.bam	FBtr0070603	72	18	F	1
+input1.bam	FBtr0070603	72	19	F	9
+input1.bam	FBtr0070603	72	20	F	3
+input1.bam	FBtr0070603	72	21	F	1
+input1.bam	FBtr0070603	72	22	F	3
+input1.bam	FBtr0070603	72	24	F	2
+input1.bam	FBtr0070603	72	25	F	1
+input1.bam	FBtr0070603	72	26	F	6
+input1.bam	FBtr0070603	72	27	F	3
+input1.bam	FBtr0070603	72	32	F	1
+input1.bam	FBtr0070603	72	34	F	3
+input1.bam	FBtr0070603	72	38	F	1
+input1.bam	FBtr0070603	72	42	F	1
+input1.bam	FBtr0070603	72	51	F	1
+input1.bam	FBtr0070603	72	56	F	1
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
+input1.bam	FBtr0070604	72	18	F	1
+input1.bam	FBtr0070604	72	22	F	1
+input1.bam	FBtr0070604	72	30	F	2
+input1.bam	FBtr0070604	72	31	F	10
+input1.bam	FBtr0070604	72	32	F	24
+input1.bam	FBtr0070604	72	57	F	1
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	1
+input1.bam	FBtr0070911	73	38	F	1
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	2
+input1.bam	FBtr0078490	72	17	F	1
+input1.bam	FBtr0078490	72	18	F	1
+input1.bam	FBtr0078490	72	25	F	1
+input1.bam	FBtr0078490	72	28	F	2
+input1.bam	FBtr0078490	72	38	F	1
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	1041
+input1.bam	FBtr0078580	72	3	F	3
+input1.bam	FBtr0078580	72	4	F	4
+input1.bam	FBtr0078580	72	5	F	5
+input1.bam	FBtr0078580	72	6	F	4
+input1.bam	FBtr0078580	72	7	F	1
+input1.bam	FBtr0078580	72	8	F	2
+input1.bam	FBtr0078580	72	11	F	1
+input1.bam	FBtr0078580	72	12	F	13
+input1.bam	FBtr0078580	72	14	F	7
+input1.bam	FBtr0078580	72	15	F	1
+input1.bam	FBtr0078580	72	16	F	4
+input1.bam	FBtr0078580	72	17	F	1
+input1.bam	FBtr0078580	72	19	F	1
+input1.bam	FBtr0078580	72	20	F	2
+input1.bam	FBtr0078580	72	21	F	5
+input1.bam	FBtr0078580	72	24	F	3
+input1.bam	FBtr0078580	72	25	F	2
+input1.bam	FBtr0078580	72	29	F	1
+input1.bam	FBtr0078580	72	31	F	1
+input1.bam	FBtr0078580	72	52	F	2
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	1
+input1.bam	FBtr0078790	73	17	F	2
+input1.bam	FBtr0078790	73	33	F	1
+input1.bam	FBtr0078790	73	42	F	4
+input1.bam	FBtr0078790	73	44	F	2
+input1.bam	FBtr0078790	73	46	F	1
+input1.bam	FBtr0078790	73	47	F	1
+input1.bam	FBtr0078790	73	52	F	1
+input1.bam	FBtr0078790	73	69	R	1
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	1
+input1.bam	FBtr0079064	72	3	F	1
+input1.bam	FBtr0079064	72	33	F	1
+input1.bam	FBtr0079064	72	52	F	1
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	2
+input1.bam	FBtr0079090	72	26	F	1
+input1.bam	FBtr0079090	72	33	F	1
+input1.bam	FBtr0079090	72	53	F	1
+input1.bam	FBtr0079090	72	56	R	1
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	12	F	1
+input1.bam	FBtr0079338	73	13	F	2
+input1.bam	FBtr0079338	73	14	F	1
+input1.bam	FBtr0079338	73	17	F	1
+input1.bam	FBtr0079338	73	25	F	1
+input1.bam	FBtr0079338	73	42	F	8
+input1.bam	FBtr0079338	73	43	F	1
+input1.bam	FBtr0079338	73	46	F	1
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	19
+input1.bam	FBtr0079528	71	3	F	55
+input1.bam	FBtr0079528	71	4	F	2
+input1.bam	FBtr0079528	71	8	F	4
+input1.bam	FBtr0079528	71	10	F	1
+input1.bam	FBtr0079528	71	11	F	2
+input1.bam	FBtr0079528	71	13	F	1
+input1.bam	FBtr0079528	71	14	F	4
+input1.bam	FBtr0079528	71	16	F	1
+input1.bam	FBtr0079528	71	17	F	4
+input1.bam	FBtr0079528	71	18	F	4
+input1.bam	FBtr0079528	71	28	F	1
+input1.bam	FBtr0079528	71	35	F	1
+input1.bam	FBtr0079528	71	36	F	1
+input1.bam	FBtr0079528	71	37	F	1
+input1.bam	FBtr0079528	71	51	F	5
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	13
+input1.bam	FBtr0079596	73	3	F	13
+input1.bam	FBtr0079596	73	4	F	31
+input1.bam	FBtr0079596	73	5	F	2
+input1.bam	FBtr0079596	73	6	F	11
+input1.bam	FBtr0079596	73	8	F	9
+input1.bam	FBtr0079596	73	9	F	12
+input1.bam	FBtr0079596	73	10	F	3
+input1.bam	FBtr0079596	73	11	F	19
+input1.bam	FBtr0079596	73	12	F	1
+input1.bam	FBtr0079596	73	13	F	20
+input1.bam	FBtr0079596	73	14	F	6
+input1.bam	FBtr0079596	73	15	F	1
+input1.bam	FBtr0079596	73	16	F	3
+input1.bam	FBtr0079596	73	17	F	2
+input1.bam	FBtr0079596	73	18	F	1
+input1.bam	FBtr0079596	73	19	F	1
+input1.bam	FBtr0079596	73	53	F	2
+input1.bam	FBtr0079596	73	54	F	2
+input1.bam	FBtr0079596	73	73	F	0
+input1.bam	FBtr0079677	72	1	F	1
+input1.bam	FBtr0079677	72	5	F	1
+input1.bam	FBtr0079677	72	52	F	1
+input1.bam	FBtr0079677	72	53	F	1
+input1.bam	FBtr0079677	72	72	F	0
+input1.bam	FBtr0079690	72	1	F	1
+input1.bam	FBtr0079690	72	22	F	1
+input1.bam	FBtr0079690	72	27	F	1
+input1.bam	FBtr0079690	72	33	F	2
+input1.bam	FBtr0079690	72	72	F	0
+input1.bam	FBtr0079692	73	1	F	3
+input1.bam	FBtr0079692	73	18	F	1
+input1.bam	FBtr0079692	73	25	F	1
+input1.bam	FBtr0079692	73	32	F	1
+input1.bam	FBtr0079692	73	73	F	0
+input1.bam	FBtr0079693	72	1	F	5
+input1.bam	FBtr0079693	72	25	F	1
+input1.bam	FBtr0079693	72	72	F	0
+input1.bam	FBtr0079694	72	1	F	5
+input1.bam	FBtr0079694	72	18	F	1
+input1.bam	FBtr0079694	72	52	F	1
+input1.bam	FBtr0079694	72	72	F	0
+input1.bam	FBtr0079702	72	1	F	1
+input1.bam	FBtr0079702	72	19	F	2
+input1.bam	FBtr0079702	72	56	F	1
+input1.bam	FBtr0079702	72	72	F	0
+input1.bam	FBtr0079728	72	1	F	2
+input1.bam	FBtr0079728	72	8	F	1
+input1.bam	FBtr0079728	72	19	F	1
+input1.bam	FBtr0079728	72	33	F	3
+input1.bam	FBtr0079728	72	56	F	1
+input1.bam	FBtr0079728	72	72	F	0
+input1.bam	FBtr0079729	72	1	F	1
+input1.bam	FBtr0079729	72	13	F	1
+input1.bam	FBtr0079729	72	52	F	1
+input1.bam	FBtr0079729	72	57	F	1
+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	2
+input1.bam	FBtr0079752	72	7	F	1
+input1.bam	FBtr0079752	72	12	F	1
+input1.bam	FBtr0079752	72	33	F	2
+input1.bam	FBtr0079752	72	52	F	2
+input1.bam	FBtr0079752	72	72	F	0
+input1.bam	FBtr0079820	74	1	F	0
+input1.bam	FBtr0079820	74	45	F	1
+input1.bam	FBtr0079820	74	46	F	2
+input1.bam	FBtr0079820	74	48	F	1
+input1.bam	FBtr0079820	74	49	F	1
+input1.bam	FBtr0079820	74	51	F	1
+input1.bam	FBtr0079820	74	54	F	4
+input1.bam	FBtr0079820	74	55	F	1
+input1.bam	FBtr0079820	74	56	F	2
+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	13
+input1.bam	FBtr0080609	72	3	F	2
+input1.bam	FBtr0080609	72	4	F	10
+input1.bam	FBtr0080609	72	5	F	2
+input1.bam	FBtr0080609	72	7	F	19
+input1.bam	FBtr0080609	72	8	F	4
+input1.bam	FBtr0080609	72	9	F	3
+input1.bam	FBtr0080609	72	12	F	1
+input1.bam	FBtr0080609	72	15	F	1
+input1.bam	FBtr0080609	72	16	F	1
+input1.bam	FBtr0080609	72	17	F	2
+input1.bam	FBtr0080609	72	19	F	1
+input1.bam	FBtr0080609	72	20	F	1
+input1.bam	FBtr0080609	72	42	F	1
+input1.bam	FBtr0080609	72	51	F	1
+input1.bam	FBtr0080609	72	52	F	1
+input1.bam	FBtr0080609	72	72	F	0
+input1.bam	FBtr0080644	72	1	F	1
+input1.bam	FBtr0080644	72	4	F	2
+input1.bam	FBtr0080644	72	7	F	1
+input1.bam	FBtr0080644	72	12	F	2
+input1.bam	FBtr0080644	72	72	F	0
+input1.bam	FBtr0080646	72	1	F	1
+input1.bam	FBtr0080646	72	6	F	1
+input1.bam	FBtr0080646	72	7	F	1
+input1.bam	FBtr0080646	72	72	F	0
+input1.bam	FBtr0080647	72	1	F	3
+input1.bam	FBtr0080647	72	3	F	1
+input1.bam	FBtr0080647	72	6	F	2
+input1.bam	FBtr0080647	72	8	F	1
+input1.bam	FBtr0080647	72	11	F	2
+input1.bam	FBtr0080647	72	12	F	1
+input1.bam	FBtr0080647	72	72	F	0
+input1.bam	FBtr0080660	72	1	F	0
+input1.bam	FBtr0080660	72	4	F	4
+input1.bam	FBtr0080660	72	7	F	3
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	22
+input1.bam	FBtr0080663	71	3	F	56
+input1.bam	FBtr0080663	71	4	F	4
+input1.bam	FBtr0080663	71	7	F	1
+input1.bam	FBtr0080663	71	8	F	4
+input1.bam	FBtr0080663	71	12	F	2
+input1.bam	FBtr0080663	71	14	F	2
+input1.bam	FBtr0080663	71	15	F	1
+input1.bam	FBtr0080663	71	16	F	3
+input1.bam	FBtr0080663	71	17	F	7
+input1.bam	FBtr0080663	71	26	F	1
+input1.bam	FBtr0080663	71	32	F	2
+input1.bam	FBtr0080663	71	50	F	1
+input1.bam	FBtr0080663	71	51	F	9
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	16
+input1.bam	FBtr0080664	71	3	F	56
+input1.bam	FBtr0080664	71	4	F	4
+input1.bam	FBtr0080664	71	6	F	1
+input1.bam	FBtr0080664	71	7	F	1
+input1.bam	FBtr0080664	71	8	F	4
+input1.bam	FBtr0080664	71	9	F	1
+input1.bam	FBtr0080664	71	11	F	3
+input1.bam	FBtr0080664	71	12	F	3
+input1.bam	FBtr0080664	71	13	F	2
+input1.bam	FBtr0080664	71	14	F	3
+input1.bam	FBtr0080664	71	16	F	2
+input1.bam	FBtr0080664	71	17	F	10
+input1.bam	FBtr0080664	71	18	F	1
+input1.bam	FBtr0080664	71	21	F	1
+input1.bam	FBtr0080664	71	28	F	2
+input1.bam	FBtr0080664	71	32	F	1
+input1.bam	FBtr0080664	71	33	F	1
+input1.bam	FBtr0080664	71	34	F	1
+input1.bam	FBtr0080664	71	35	F	1
+input1.bam	FBtr0080664	71	36	F	1
+input1.bam	FBtr0080664	71	37	F	1
+input1.bam	FBtr0080664	71	38	F	1
+input1.bam	FBtr0080664	71	50	F	2
+input1.bam	FBtr0080664	71	51	F	7
+input1.bam	FBtr0080664	71	52	F	1
+input1.bam	FBtr0080664	71	56	F	1
+input1.bam	FBtr0080664	71	71	F	0
+input2.bam	FBtr0070001	72	1	F	1
+input2.bam	FBtr0070001	72	12	F	1
+input2.bam	FBtr0070001	72	13	F	1
+input2.bam	FBtr0070001	72	18	F	1
+input2.bam	FBtr0070001	72	19	F	1
+input2.bam	FBtr0070001	72	28	F	1
+input2.bam	FBtr0070001	72	32	F	3
+input2.bam	FBtr0070001	72	53	F	2
+input2.bam	FBtr0070001	72	56	F	2
+input2.bam	FBtr0070001	72	57	F	1
+input2.bam	FBtr0070001	72	58	F	10
+input2.bam	FBtr0070001	72	72	F	0
+input2.bam	FBtr0070533	72	1	F	0
+input2.bam	FBtr0070533	72	15	F	1
+input2.bam	FBtr0070533	72	16	F	2
+input2.bam	FBtr0070533	72	17	F	2
+input2.bam	FBtr0070533	72	19	F	1
+input2.bam	FBtr0070533	72	20	F	1
+input2.bam	FBtr0070533	72	21	F	4
+input2.bam	FBtr0070533	72	22	F	20
+input2.bam	FBtr0070533	72	23	F	1
+input2.bam	FBtr0070533	72	24	F	6
+input2.bam	FBtr0070533	72	25	F	5
+input2.bam	FBtr0070533	72	27	F	1
+input2.bam	FBtr0070533	72	39	F	1
+input2.bam	FBtr0070533	72	72	F	0
+input2.bam	FBtr0070603	72	1	F	0
+input2.bam	FBtr0070603	72	12	F	2
+input2.bam	FBtr0070603	72	17	F	6
+input2.bam	FBtr0070603	72	19	F	3
+input2.bam	FBtr0070603	72	20	F	2
+input2.bam	FBtr0070603	72	21	F	1
+input2.bam	FBtr0070603	72	22	F	21
+input2.bam	FBtr0070603	72	25	F	1
+input2.bam	FBtr0070603	72	27	F	2
+input2.bam	FBtr0070603	72	28	F	2
+input2.bam	FBtr0070603	72	30	F	2
+input2.bam	FBtr0070603	72	31	F	2
+input2.bam	FBtr0070603	72	34	F	4
+input2.bam	FBtr0070603	72	35	F	2
+input2.bam	FBtr0070603	72	37	F	2
+input2.bam	FBtr0070603	72	38	F	2
+input2.bam	FBtr0070603	72	41	F	3
+input2.bam	FBtr0070603	72	51	F	2
+input2.bam	FBtr0070603	72	53	F	2
+input2.bam	FBtr0070603	72	72	F	0
+input2.bam	FBtr0070604	72	1	F	0
+input2.bam	FBtr0070604	72	3	F	1
+input2.bam	FBtr0070604	72	31	F	1
+input2.bam	FBtr0070604	72	32	F	5
+input2.bam	FBtr0070604	72	40	F	1
+input2.bam	FBtr0070604	72	53	F	3
+input2.bam	FBtr0070604	72	56	F	4
+input2.bam	FBtr0070604	72	57	F	18
+input2.bam	FBtr0070604	72	58	F	22
+input2.bam	FBtr0070604	72	72	F	0
+input2.bam	FBtr0070911	73	1	F	0
+input2.bam	FBtr0070911	73	11	F	1
+input2.bam	FBtr0070911	73	32	F	1
+input2.bam	FBtr0070911	73	48	F	1
+input2.bam	FBtr0070911	73	73	F	0
+input2.bam	FBtr0078490	72	1	F	3
+input2.bam	FBtr0078490	72	13	F	2
+input2.bam	FBtr0078490	72	14	F	4
+input2.bam	FBtr0078490	72	20	F	1
+input2.bam	FBtr0078490	72	30	F	1
+input2.bam	FBtr0078490	72	38	F	2
+input2.bam	FBtr0078490	72	41	F	1
+input2.bam	FBtr0078490	72	72	F	0
+input2.bam	FBtr0078580	72	1	F	146
+input2.bam	FBtr0078580	72	11	F	1
+input2.bam	FBtr0078580	72	13	F	1
+input2.bam	FBtr0078580	72	15	F	3
+input2.bam	FBtr0078580	72	16	F	5
+input2.bam	FBtr0078580	72	17	F	2
+input2.bam	FBtr0078580	72	18	F	9
+input2.bam	FBtr0078580	72	19	F	20
+input2.bam	FBtr0078580	72	20	F	21
+input2.bam	FBtr0078580	72	21	F	55
+input2.bam	FBtr0078580	72	22	F	1
+input2.bam	FBtr0078580	72	23	F	11
+input2.bam	FBtr0078580	72	24	F	24
+input2.bam	FBtr0078580	72	25	F	20
+input2.bam	FBtr0078580	72	26	F	19
+input2.bam	FBtr0078580	72	27	F	9
+input2.bam	FBtr0078580	72	28	F	2
+input2.bam	FBtr0078580	72	29	F	9
+input2.bam	FBtr0078580	72	30	F	2
+input2.bam	FBtr0078580	72	31	F	1
+input2.bam	FBtr0078580	72	40	F	5
+input2.bam	FBtr0078580	72	43	F	1
+input2.bam	FBtr0078580	72	52	F	3
+input2.bam	FBtr0078580	72	72	F	0
+input2.bam	FBtr0078790	73	1	F	0
+input2.bam	FBtr0078790	73	17	F	1
+input2.bam	FBtr0078790	73	41	F	2
+input2.bam	FBtr0078790	73	42	F	1
+input2.bam	FBtr0078790	73	46	F	1
+input2.bam	FBtr0078790	73	51	F	1
+input2.bam	FBtr0078790	73	52	F	2
+input2.bam	FBtr0078790	73	54	F	2
+input2.bam	FBtr0078790	73	73	F	0
+input2.bam	FBtr0079064	72	1	F	3
+input2.bam	FBtr0079064	72	52	F	2
+input2.bam	FBtr0079064	72	72	F	0
+input2.bam	FBtr0079090	72	1	F	1
+input2.bam	FBtr0079090	72	16	F	1
+input2.bam	FBtr0079090	72	20	F	1
+input2.bam	FBtr0079090	72	33	F	1
+input2.bam	FBtr0079090	72	35	F	1
+input2.bam	FBtr0079090	72	52	F	2
+input2.bam	FBtr0079090	72	72	F	0
+input2.bam	FBtr0079338	73	1	F	0
+input2.bam	FBtr0079338	73	12	F	2
+input2.bam	FBtr0079338	73	13	F	4
+input2.bam	FBtr0079338	73	14	F	6
+input2.bam	FBtr0079338	73	16	F	4
+input2.bam	FBtr0079338	73	17	F	2
+input2.bam	FBtr0079338	73	18	F	1
+input2.bam	FBtr0079338	73	39	F	1
+input2.bam	FBtr0079338	73	41	F	2
+input2.bam	FBtr0079338	73	42	F	1
+input2.bam	FBtr0079338	73	73	F	0
+input2.bam	FBtr0079528	71	1	F	2
+input2.bam	FBtr0079528	71	3	F	1
+input2.bam	FBtr0079528	71	10	F	4
+input2.bam	FBtr0079528	71	11	F	3
+input2.bam	FBtr0079528	71	13	F	4
+input2.bam	FBtr0079528	71	14	F	17
+input2.bam	FBtr0079528	71	15	F	19
+input2.bam	FBtr0079528	71	16	F	10
+input2.bam	FBtr0079528	71	17	F	12
+input2.bam	FBtr0079528	71	18	F	13
+input2.bam	FBtr0079528	71	19	F	6
+input2.bam	FBtr0079528	71	20	F	7
+input2.bam	FBtr0079528	71	21	F	13
+input2.bam	FBtr0079528	71	22	F	5
+input2.bam	FBtr0079528	71	23	F	1
+input2.bam	FBtr0079528	71	30	F	1
+input2.bam	FBtr0079528	71	31	F	2
+input2.bam	FBtr0079528	71	32	F	39
+input2.bam	FBtr0079528	71	33	F	4
+input2.bam	FBtr0079528	71	34	F	27
+input2.bam	FBtr0079528	71	35	F	122
+input2.bam	FBtr0079528	71	36	F	6
+input2.bam	FBtr0079528	71	37	F	21
+input2.bam	FBtr0079528	71	38	F	12
+input2.bam	FBtr0079528	71	43	F	1
+input2.bam	FBtr0079528	71	46	F	1
+input2.bam	FBtr0079528	71	50	F	2
+input2.bam	FBtr0079528	71	51	F	4
+input2.bam	FBtr0079528	71	53	F	1
+input2.bam	FBtr0079528	71	56	F	2
+input2.bam	FBtr0079528	71	57	F	3
+input2.bam	FBtr0079528	71	71	F	0
+input2.bam	FBtr0079596	73	1	F	22
+input2.bam	FBtr0079596	73	2	F	1
+input2.bam	FBtr0079596	73	3	F	8
+input2.bam	FBtr0079596	73	4	F	5
+input2.bam	FBtr0079596	73	5	F	9
+input2.bam	FBtr0079596	73	6	F	1
+input2.bam	FBtr0079596	73	8	F	2
+input2.bam	FBtr0079596	73	9	F	2
+input2.bam	FBtr0079596	73	11	F	18
+input2.bam	FBtr0079596	73	12	F	44
+input2.bam	FBtr0079596	73	13	F	40
+input2.bam	FBtr0079596	73	14	F	36
+input2.bam	FBtr0079596	73	15	F	81
+input2.bam	FBtr0079596	73	16	F	13
+input2.bam	FBtr0079596	73	17	F	11
+input2.bam	FBtr0079596	73	18	F	12
+input2.bam	FBtr0079596	73	19	F	4
+input2.bam	FBtr0079596	73	22	F	2
+input2.bam	FBtr0079596	73	42	F	1
+input2.bam	FBtr0079596	73	53	F	3
+input2.bam	FBtr0079596	73	59	R	1
+input2.bam	FBtr0079596	73	73	F	0
+input2.bam	FBtr0079677	72	1	F	2
+input2.bam	FBtr0079677	72	15	F	1
+input2.bam	FBtr0079677	72	24	F	1
+input2.bam	FBtr0079677	72	43	F	1
+input2.bam	FBtr0079677	72	52	F	1
+input2.bam	FBtr0079677	72	54	F	1
+input2.bam	FBtr0079677	72	72	F	0
+input2.bam	FBtr0079690	72	1	F	1
+input2.bam	FBtr0079690	72	15	F	1
+input2.bam	FBtr0079690	72	17	F	1
+input2.bam	FBtr0079690	72	19	F	1
+input2.bam	FBtr0079690	72	21	F	1
+input2.bam	FBtr0079690	72	72	F	0
+input2.bam	FBtr0079692	73	1	F	0
+input2.bam	FBtr0079692	73	4	F	1
+input2.bam	FBtr0079692	73	7	F	1
+input2.bam	FBtr0079692	73	12	F	1
+input2.bam	FBtr0079692	73	15	F	1
+input2.bam	FBtr0079692	73	73	F	0
+input2.bam	FBtr0079693	72	1	F	3
+input2.bam	FBtr0079693	72	17	F	2
+input2.bam	FBtr0079693	72	20	F	1
+input2.bam	FBtr0079693	72	45	F	1
+input2.bam	FBtr0079693	72	52	F	1
+input2.bam	FBtr0079693	72	54	F	1
+input2.bam	FBtr0079693	72	72	F	0
+input2.bam	FBtr0079694	72	1	F	2
+input2.bam	FBtr0079694	72	16	F	1
+input2.bam	FBtr0079694	72	17	F	1
+input2.bam	FBtr0079694	72	18	F	1
+input2.bam	FBtr0079694	72	52	F	1
+input2.bam	FBtr0079694	72	72	F	0
+input2.bam	FBtr0079702	72	1	F	2
+input2.bam	FBtr0079702	72	52	F	2
+input2.bam	FBtr0079702	72	72	F	0
+input2.bam	FBtr0079728	72	1	F	3
+input2.bam	FBtr0079728	72	20	F	1
+input2.bam	FBtr0079728	72	52	F	2
+input2.bam	FBtr0079728	72	72	F	0
+input2.bam	FBtr0079729	72	1	F	1
+input2.bam	FBtr0079729	72	19	F	1
+input2.bam	FBtr0079729	72	33	F	1
+input2.bam	FBtr0079729	72	53	F	1
+input2.bam	FBtr0079729	72	72	F	0
+input2.bam	FBtr0079752	72	1	F	0
+input2.bam	FBtr0079752	72	49	F	1
+input2.bam	FBtr0079752	72	52	F	1
+input2.bam	FBtr0079752	72	72	F	0
+input2.bam	FBtr0079820	74	1	F	0
+input2.bam	FBtr0079820	74	39	F	1
+input2.bam	FBtr0079820	74	52	F	1
+input2.bam	FBtr0079820	74	53	F	28
+input2.bam	FBtr0079820	74	54	F	26
+input2.bam	FBtr0079820	74	55	F	10
+input2.bam	FBtr0079820	74	56	F	2
+input2.bam	FBtr0079820	74	57	F	6
+input2.bam	FBtr0079820	74	58	F	5
+input2.bam	FBtr0079820	74	59	F	11
+input2.bam	FBtr0079820	74	60	F	19
+input2.bam	FBtr0079820	74	74	F	0
+input2.bam	FBtr0080609	72	1	F	0
+input2.bam	FBtr0080609	72	20	F	1
+input2.bam	FBtr0080609	72	21	F	2
+input2.bam	FBtr0080609	72	22	F	1
+input2.bam	FBtr0080609	72	33	F	1
+input2.bam	FBtr0080609	72	39	F	1
+input2.bam	FBtr0080609	72	52	F	1
+input2.bam	FBtr0080609	72	53	F	1
+input2.bam	FBtr0080609	72	72	F	0
+input2.bam	FBtr0080644	72	1	F	0
+input2.bam	FBtr0080644	72	57	F	1
+input2.bam	FBtr0080644	72	58	F	7
+input2.bam	FBtr0080644	72	72	F	0
+input2.bam	FBtr0080646	72	1	F	0
+input2.bam	FBtr0080646	72	51	F	1
+input2.bam	FBtr0080646	72	57	F	2
+input2.bam	FBtr0080646	72	58	F	9
+input2.bam	FBtr0080646	72	72	F	0
+input2.bam	FBtr0080647	72	1	F	1
+input2.bam	FBtr0080647	72	57	F	4
+input2.bam	FBtr0080647	72	58	F	7
+input2.bam	FBtr0080647	72	72	F	0
+input2.bam	FBtr0080660	72	1	F	0
+input2.bam	FBtr0080660	72	58	F	11
+input2.bam	FBtr0080660	72	72	F	0
+input2.bam	FBtr0080663	71	1	F	2
+input2.bam	FBtr0080663	71	11	F	1
+input2.bam	FBtr0080663	71	12	F	4
+input2.bam	FBtr0080663	71	13	F	4
+input2.bam	FBtr0080663	71	14	F	22
+input2.bam	FBtr0080663	71	15	F	14
+input2.bam	FBtr0080663	71	16	F	5
+input2.bam	FBtr0080663	71	17	F	12
+input2.bam	FBtr0080663	71	18	F	5
+input2.bam	FBtr0080663	71	19	F	6
+input2.bam	FBtr0080663	71	20	F	6
+input2.bam	FBtr0080663	71	21	F	13
+input2.bam	FBtr0080663	71	22	F	3
+input2.bam	FBtr0080663	71	31	F	1
+input2.bam	FBtr0080663	71	50	F	2
+input2.bam	FBtr0080663	71	51	F	1
+input2.bam	FBtr0080663	71	52	F	2
+input2.bam	FBtr0080663	71	57	F	3
+input2.bam	FBtr0080663	71	71	F	0
+input2.bam	FBtr0080664	71	1	F	1
+input2.bam	FBtr0080664	71	3	F	2
+input2.bam	FBtr0080664	71	10	F	1
+input2.bam	FBtr0080664	71	11	F	2
+input2.bam	FBtr0080664	71	12	F	3
+input2.bam	FBtr0080664	71	13	F	11
+input2.bam	FBtr0080664	71	14	F	11
+input2.bam	FBtr0080664	71	15	F	17
+input2.bam	FBtr0080664	71	16	F	15
+input2.bam	FBtr0080664	71	17	F	13
+input2.bam	FBtr0080664	71	18	F	10
+input2.bam	FBtr0080664	71	19	F	8
+input2.bam	FBtr0080664	71	20	F	1
+input2.bam	FBtr0080664	71	21	F	15
+input2.bam	FBtr0080664	71	22	F	6
+input2.bam	FBtr0080664	71	24	F	1
+input2.bam	FBtr0080664	71	30	F	1
+input2.bam	FBtr0080664	71	31	F	3
+input2.bam	FBtr0080664	71	32	F	39
+input2.bam	FBtr0080664	71	33	F	4
+input2.bam	FBtr0080664	71	34	F	37
+input2.bam	FBtr0080664	71	35	F	135
+input2.bam	FBtr0080664	71	36	F	8
+input2.bam	FBtr0080664	71	37	F	25
+input2.bam	FBtr0080664	71	38	F	8
+input2.bam	FBtr0080664	71	39	F	1
+input2.bam	FBtr0080664	71	42	F	1
+input2.bam	FBtr0080664	71	47	F	1
+input2.bam	FBtr0080664	71	50	F	2
+input2.bam	FBtr0080664	71	52	F	1
+input2.bam	FBtr0080664	71	53	F	1
+input2.bam	FBtr0080664	71	56	F	1
+input2.bam	FBtr0080664	71	57	F	2
+input2.bam	FBtr0080664	71	62	R	1
+input2.bam	FBtr0080664	71	71	F	0
+input2.bam	FBtr0080664	71	71	R	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_norm_1_2_coverage.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_norm_1_2_coverage.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,3109 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	2	F	1
+input1.bam	FBtr0070001	72	3	F	1
+input1.bam	FBtr0070001	72	4	F	1
+input1.bam	FBtr0070001	72	5	F	1
+input1.bam	FBtr0070001	72	6	F	1
+input1.bam	FBtr0070001	72	7	F	7
+input1.bam	FBtr0070001	72	8	F	10
+input1.bam	FBtr0070001	72	9	F	10
+input1.bam	FBtr0070001	72	10	F	10
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+input2.bam	FBtr0080663	71	40	F	3
+input2.bam	FBtr0080663	71	41	F	2
+input2.bam	FBtr0080663	71	42	F	1
+input2.bam	FBtr0080663	71	43	F	1
+input2.bam	FBtr0080663	71	44	F	1
+input2.bam	FBtr0080663	71	45	F	1
+input2.bam	FBtr0080663	71	46	F	1
+input2.bam	FBtr0080663	71	47	F	1
+input2.bam	FBtr0080663	71	50	F	2
+input2.bam	FBtr0080663	71	51	F	3
+input2.bam	FBtr0080663	71	52	F	5
+input2.bam	FBtr0080663	71	53	F	5
+input2.bam	FBtr0080663	71	54	F	5
+input2.bam	FBtr0080663	71	55	F	5
+input2.bam	FBtr0080663	71	56	F	5
+input2.bam	FBtr0080663	71	57	F	8
+input2.bam	FBtr0080663	71	58	F	8
+input2.bam	FBtr0080663	71	59	F	8
+input2.bam	FBtr0080663	71	60	F	8
+input2.bam	FBtr0080663	71	61	F	8
+input2.bam	FBtr0080663	71	62	F	8
+input2.bam	FBtr0080663	71	63	F	8
+input2.bam	FBtr0080663	71	64	F	8
+input2.bam	FBtr0080663	71	65	F	7
+input2.bam	FBtr0080663	71	66	F	6
+input2.bam	FBtr0080663	71	67	F	4
+input2.bam	FBtr0080663	71	68	F	4
+input2.bam	FBtr0080663	71	69	F	4
+input2.bam	FBtr0080663	71	70	F	3
+input2.bam	FBtr0080663	71	71	F	3
+input2.bam	FBtr0080664	71	1	F	1
+input2.bam	FBtr0080664	71	2	F	1
+input2.bam	FBtr0080664	71	3	F	3
+input2.bam	FBtr0080664	71	4	F	3
+input2.bam	FBtr0080664	71	5	F	3
+input2.bam	FBtr0080664	71	6	F	3
+input2.bam	FBtr0080664	71	7	F	3
+input2.bam	FBtr0080664	71	8	F	3
+input2.bam	FBtr0080664	71	9	F	3
+input2.bam	FBtr0080664	71	10	F	4
+input2.bam	FBtr0080664	71	11	F	6
+input2.bam	FBtr0080664	71	12	F	9
+input2.bam	FBtr0080664	71	13	F	20
+input2.bam	FBtr0080664	71	14	F	31
+input2.bam	FBtr0080664	71	15	F	48
+input2.bam	FBtr0080664	71	16	F	63
+input2.bam	FBtr0080664	71	17	F	76
+input2.bam	FBtr0080664	71	18	F	86
+input2.bam	FBtr0080664	71	19	F	94
+input2.bam	FBtr0080664	71	20	F	95
+input2.bam	FBtr0080664	71	21	F	110
+input2.bam	FBtr0080664	71	22	F	116
+input2.bam	FBtr0080664	71	23	F	114
+input2.bam	FBtr0080664	71	24	F	115
+input2.bam	FBtr0080664	71	25	F	115
+input2.bam	FBtr0080664	71	26	F	115
+input2.bam	FBtr0080664	71	27	F	115
+input2.bam	FBtr0080664	71	28	F	115
+input2.bam	FBtr0080664	71	29	F	113
+input2.bam	FBtr0080664	71	30	F	113
+input2.bam	FBtr0080664	71	31	F	117
+input2.bam	FBtr0080664	71	32	F	127
+input2.bam	FBtr0080664	71	33	F	97
+input2.bam	FBtr0080664	71	34	F	134
+input2.bam	FBtr0080664	71	35	F	265
+input2.bam	FBtr0080664	71	36	F	249
+input2.bam	FBtr0080664	71	37	F	266
+input2.bam	FBtr0080664	71	38	F	268
+input2.bam	FBtr0080664	71	39	F	263
+input2.bam	FBtr0080664	71	40	F	263
+input2.bam	FBtr0080664	71	41	F	262
+input2.bam	FBtr0080664	71	42	F	262
+input2.bam	FBtr0080664	71	43	F	260
+input2.bam	FBtr0080664	71	44	F	263
+input2.bam	FBtr0080664	71	45	F	263
+input2.bam	FBtr0080664	71	46	F	263
+input2.bam	FBtr0080664	71	47	F	264
+input2.bam	FBtr0080664	71	48	F	264
+input2.bam	FBtr0080664	71	49	F	254
+input2.bam	FBtr0080664	71	50	F	72
+input2.bam	FBtr0080664	71	51	F	63
+input2.bam	FBtr0080664	71	52	F	61
+input2.bam	FBtr0080664	71	53	F	31
+input2.bam	FBtr0080664	71	54	F	30
+input2.bam	FBtr0080664	71	55	F	21
+input2.bam	FBtr0080664	71	56	F	16
+input2.bam	FBtr0080664	71	57	F	18
+input2.bam	FBtr0080664	71	58	F	18
+input2.bam	FBtr0080664	71	59	F	18
+input2.bam	FBtr0080664	71	60	F	17
+input2.bam	FBtr0080664	71	61	F	16
+input2.bam	FBtr0080664	71	62	F	12
+input2.bam	FBtr0080664	71	62	R	12
+input2.bam	FBtr0080664	71	63	F	8
+input2.bam	FBtr0080664	71	64	F	8
+input2.bam	FBtr0080664	71	65	F	7
+input2.bam	FBtr0080664	71	66	F	6
+input2.bam	FBtr0080664	71	67	F	6
+input2.bam	FBtr0080664	71	68	F	5
+input2.bam	FBtr0080664	71	69	F	5
+input2.bam	FBtr0080664	71	70	F	5
+input2.bam	FBtr0080664	71	71	F	5
+input2.bam	FBtr0080664	71	71	R	5
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_norm_1_2_single_plot_counts.pdf
Binary file test-data/input1_input2_norm_1_2_single_plot_counts.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_norm_1_2_single_plot_coverage.pdf
Binary file test-data/input1_input2_norm_1_2_single_plot_coverage.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_input2_size.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_input2_size.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,1045 @@
+Dataset	Chromosome	Polarity	Size	Counts
+input1.bam	FBtr0070001	F	16	2
+input1.bam	FBtr0070001	F	17	1
+input1.bam	FBtr0070001	F	18	0
+input1.bam	FBtr0070001	F	19	1
+input1.bam	FBtr0070001	F	20	4
+input1.bam	FBtr0070001	F	21	4
+input1.bam	FBtr0070001	F	22	29
+input1.bam	FBtr0070001	F	23	15
+input1.bam	FBtr0070001	F	24	1
+input1.bam	FBtr0070001	R	16	0
+input1.bam	FBtr0070001	R	17	0
+input1.bam	FBtr0070001	R	18	0
+input1.bam	FBtr0070001	R	19	0
+input1.bam	FBtr0070001	R	20	0
+input1.bam	FBtr0070001	R	21	0
+input1.bam	FBtr0070001	R	22	0
+input1.bam	FBtr0070001	R	23	0
+input1.bam	FBtr0070001	R	24	0
+input1.bam	FBtr0070533	F	15	2
+input1.bam	FBtr0070533	F	16	1
+input1.bam	FBtr0070533	F	17	1
+input1.bam	FBtr0070533	F	18	6
+input1.bam	FBtr0070533	F	19	3
+input1.bam	FBtr0070533	F	20	2
+input1.bam	FBtr0070533	F	21	2
+input1.bam	FBtr0070533	F	22	4
+input1.bam	FBtr0070533	F	23	2
+input1.bam	FBtr0070533	F	24	0
+input1.bam	FBtr0070533	F	25	1
+input1.bam	FBtr0070533	R	15	0
+input1.bam	FBtr0070533	R	16	0
+input1.bam	FBtr0070533	R	17	0
+input1.bam	FBtr0070533	R	18	0
+input1.bam	FBtr0070533	R	19	0
+input1.bam	FBtr0070533	R	20	0
+input1.bam	FBtr0070533	R	21	0
+input1.bam	FBtr0070533	R	22	0
+input1.bam	FBtr0070533	R	23	0
+input1.bam	FBtr0070533	R	24	0
+input1.bam	FBtr0070533	R	25	0
+input1.bam	FBtr0070603	F	15	9
+input1.bam	FBtr0070603	F	16	6
+input1.bam	FBtr0070603	F	17	10
+input1.bam	FBtr0070603	F	18	7
+input1.bam	FBtr0070603	F	19	1
+input1.bam	FBtr0070603	F	20	6
+input1.bam	FBtr0070603	F	21	3
+input1.bam	FBtr0070603	F	22	3
+input1.bam	FBtr0070603	F	23	10
+input1.bam	FBtr0070603	F	24	2
+input1.bam	FBtr0070603	F	25	5
+input1.bam	FBtr0070603	F	26	5
+input1.bam	FBtr0070603	F	27	3
+input1.bam	FBtr0070603	R	15	0
+input1.bam	FBtr0070603	R	16	0
+input1.bam	FBtr0070603	R	17	0
+input1.bam	FBtr0070603	R	18	0
+input1.bam	FBtr0070603	R	19	0
+input1.bam	FBtr0070603	R	20	0
+input1.bam	FBtr0070603	R	21	0
+input1.bam	FBtr0070603	R	22	0
+input1.bam	FBtr0070603	R	23	0
+input1.bam	FBtr0070603	R	24	0
+input1.bam	FBtr0070603	R	25	0
+input1.bam	FBtr0070603	R	26	0
+input1.bam	FBtr0070603	R	27	0
+input1.bam	FBtr0070604	F	15	2
+input1.bam	FBtr0070604	F	16	0
+input1.bam	FBtr0070604	F	17	0
+input1.bam	FBtr0070604	F	18	2
+input1.bam	FBtr0070604	F	19	2
+input1.bam	FBtr0070604	F	20	0
+input1.bam	FBtr0070604	F	21	1
+input1.bam	FBtr0070604	F	22	23
+input1.bam	FBtr0070604	F	23	10
+input1.bam	FBtr0070604	R	15	0
+input1.bam	FBtr0070604	R	16	0
+input1.bam	FBtr0070604	R	17	0
+input1.bam	FBtr0070604	R	18	0
+input1.bam	FBtr0070604	R	19	0
+input1.bam	FBtr0070604	R	20	0
+input1.bam	FBtr0070604	R	21	0
+input1.bam	FBtr0070604	R	22	0
+input1.bam	FBtr0070604	R	23	0
+input1.bam	FBtr0070911	F	15	1
+input1.bam	FBtr0070911	F	16	0
+input1.bam	FBtr0070911	F	17	0
+input1.bam	FBtr0070911	F	18	0
+input1.bam	FBtr0070911	F	19	0
+input1.bam	FBtr0070911	F	20	0
+input1.bam	FBtr0070911	F	21	1
+input1.bam	FBtr0070911	R	15	0
+input1.bam	FBtr0070911	R	16	0
+input1.bam	FBtr0070911	R	17	0
+input1.bam	FBtr0070911	R	18	0
+input1.bam	FBtr0070911	R	19	0
+input1.bam	FBtr0070911	R	20	0
+input1.bam	FBtr0070911	R	21	0
+input1.bam	FBtr0078490	F	15	3
+input1.bam	FBtr0078490	F	16	3
+input1.bam	FBtr0078490	F	17	0
+input1.bam	FBtr0078490	F	18	1
+input1.bam	FBtr0078490	F	19	0
+input1.bam	FBtr0078490	F	20	0
+input1.bam	FBtr0078490	F	21	0
+input1.bam	FBtr0078490	F	22	0
+input1.bam	FBtr0078490	F	23	1
+input1.bam	FBtr0078490	R	15	0
+input1.bam	FBtr0078490	R	16	0
+input1.bam	FBtr0078490	R	17	0
+input1.bam	FBtr0078490	R	18	0
+input1.bam	FBtr0078490	R	19	0
+input1.bam	FBtr0078490	R	20	0
+input1.bam	FBtr0078490	R	21	0
+input1.bam	FBtr0078490	R	22	0
+input1.bam	FBtr0078490	R	23	0
+input1.bam	FBtr0078580	F	15	592
+input1.bam	FBtr0078580	F	16	20
+input1.bam	FBtr0078580	F	17	31
+input1.bam	FBtr0078580	F	18	9
+input1.bam	FBtr0078580	F	19	8
+input1.bam	FBtr0078580	F	20	9
+input1.bam	FBtr0078580	F	21	5
+input1.bam	FBtr0078580	F	22	13
+input1.bam	FBtr0078580	F	23	5
+input1.bam	FBtr0078580	F	24	180
+input1.bam	FBtr0078580	F	25	212
+input1.bam	FBtr0078580	F	26	1
+input1.bam	FBtr0078580	F	27	2
+input1.bam	FBtr0078580	F	28	17
+input1.bam	FBtr0078580	R	15	0
+input1.bam	FBtr0078580	R	16	0
+input1.bam	FBtr0078580	R	17	0
+input1.bam	FBtr0078580	R	18	0
+input1.bam	FBtr0078580	R	19	0
+input1.bam	FBtr0078580	R	20	0
+input1.bam	FBtr0078580	R	21	0
+input1.bam	FBtr0078580	R	22	0
+input1.bam	FBtr0078580	R	23	0
+input1.bam	FBtr0078580	R	24	0
+input1.bam	FBtr0078580	R	25	0
+input1.bam	FBtr0078580	R	26	0
+input1.bam	FBtr0078580	R	27	0
+input1.bam	FBtr0078580	R	28	0
+input1.bam	FBtr0078790	F	15	2
+input1.bam	FBtr0078790	F	16	2
+input1.bam	FBtr0078790	F	17	1
+input1.bam	FBtr0078790	F	18	1
+input1.bam	FBtr0078790	F	19	2
+input1.bam	FBtr0078790	F	20	2
+input1.bam	FBtr0078790	F	21	0
+input1.bam	FBtr0078790	F	22	2
+input1.bam	FBtr0078790	F	23	1
+input1.bam	FBtr0078790	R	15	1
+input1.bam	FBtr0078790	R	16	0
+input1.bam	FBtr0078790	R	17	0
+input1.bam	FBtr0078790	R	18	0
+input1.bam	FBtr0078790	R	19	0
+input1.bam	FBtr0078790	R	20	0
+input1.bam	FBtr0078790	R	21	0
+input1.bam	FBtr0078790	R	22	0
+input1.bam	FBtr0078790	R	23	0
+input1.bam	FBtr0079064	F	15	2
+input1.bam	FBtr0079064	F	16	0
+input1.bam	FBtr0079064	F	17	1
+input1.bam	FBtr0079064	F	18	0
+input1.bam	FBtr0079064	F	19	0
+input1.bam	FBtr0079064	F	20	0
+input1.bam	FBtr0079064	F	21	1
+input1.bam	FBtr0079064	R	15	0
+input1.bam	FBtr0079064	R	16	0
+input1.bam	FBtr0079064	R	17	0
+input1.bam	FBtr0079064	R	18	0
+input1.bam	FBtr0079064	R	19	0
+input1.bam	FBtr0079064	R	20	0
+input1.bam	FBtr0079064	R	21	0
+input1.bam	FBtr0079090	F	15	1
+input1.bam	FBtr0079090	F	16	1
+input1.bam	FBtr0079090	F	17	0
+input1.bam	FBtr0079090	F	18	1
+input1.bam	FBtr0079090	F	19	0
+input1.bam	FBtr0079090	F	20	0
+input1.bam	FBtr0079090	F	21	0
+input1.bam	FBtr0079090	F	22	0
+input1.bam	FBtr0079090	F	23	0
+input1.bam	FBtr0079090	F	24	1
+input1.bam	FBtr0079090	F	25	0
+input1.bam	FBtr0079090	F	26	0
+input1.bam	FBtr0079090	F	27	0
+input1.bam	FBtr0079090	F	28	1
+input1.bam	FBtr0079090	R	15	0
+input1.bam	FBtr0079090	R	16	0
+input1.bam	FBtr0079090	R	17	0
+input1.bam	FBtr0079090	R	18	0
+input1.bam	FBtr0079090	R	19	0
+input1.bam	FBtr0079090	R	20	0
+input1.bam	FBtr0079090	R	21	1
+input1.bam	FBtr0079090	R	22	0
+input1.bam	FBtr0079090	R	23	0
+input1.bam	FBtr0079090	R	24	0
+input1.bam	FBtr0079090	R	25	0
+input1.bam	FBtr0079090	R	26	0
+input1.bam	FBtr0079090	R	27	0
+input1.bam	FBtr0079090	R	28	0
+input1.bam	FBtr0079338	F	15	2
+input1.bam	FBtr0079338	F	16	2
+input1.bam	FBtr0079338	F	17	1
+input1.bam	FBtr0079338	F	18	1
+input1.bam	FBtr0079338	F	19	1
+input1.bam	FBtr0079338	F	20	0
+input1.bam	FBtr0079338	F	21	3
+input1.bam	FBtr0079338	F	22	6
+input1.bam	FBtr0079338	R	15	0
+input1.bam	FBtr0079338	R	16	0
+input1.bam	FBtr0079338	R	17	0
+input1.bam	FBtr0079338	R	18	0
+input1.bam	FBtr0079338	R	19	0
+input1.bam	FBtr0079338	R	20	0
+input1.bam	FBtr0079338	R	21	0
+input1.bam	FBtr0079338	R	22	0
+input1.bam	FBtr0079528	F	15	12
+input1.bam	FBtr0079528	F	16	11
+input1.bam	FBtr0079528	F	17	0
+input1.bam	FBtr0079528	F	18	5
+input1.bam	FBtr0079528	F	19	4
+input1.bam	FBtr0079528	F	20	12
+input1.bam	FBtr0079528	F	21	3
+input1.bam	FBtr0079528	F	22	2
+input1.bam	FBtr0079528	F	23	3
+input1.bam	FBtr0079528	F	24	36
+input1.bam	FBtr0079528	F	25	8
+input1.bam	FBtr0079528	F	26	5
+input1.bam	FBtr0079528	F	27	2
+input1.bam	FBtr0079528	F	28	2
+input1.bam	FBtr0079528	F	29	1
+input1.bam	FBtr0079528	R	15	0
+input1.bam	FBtr0079528	R	16	0
+input1.bam	FBtr0079528	R	17	0
+input1.bam	FBtr0079528	R	18	0
+input1.bam	FBtr0079528	R	19	0
+input1.bam	FBtr0079528	R	20	0
+input1.bam	FBtr0079528	R	21	0
+input1.bam	FBtr0079528	R	22	0
+input1.bam	FBtr0079528	R	23	0
+input1.bam	FBtr0079528	R	24	0
+input1.bam	FBtr0079528	R	25	0
+input1.bam	FBtr0079528	R	26	0
+input1.bam	FBtr0079528	R	27	0
+input1.bam	FBtr0079528	R	28	0
+input1.bam	FBtr0079528	R	29	0
+input1.bam	FBtr0079596	F	15	43
+input1.bam	FBtr0079596	F	16	34
+input1.bam	FBtr0079596	F	17	16
+input1.bam	FBtr0079596	F	18	5
+input1.bam	FBtr0079596	F	19	10
+input1.bam	FBtr0079596	F	20	13
+input1.bam	FBtr0079596	F	21	3
+input1.bam	FBtr0079596	F	22	16
+input1.bam	FBtr0079596	F	23	8
+input1.bam	FBtr0079596	F	24	0
+input1.bam	FBtr0079596	F	25	0
+input1.bam	FBtr0079596	F	26	3
+input1.bam	FBtr0079596	F	27	1
+input1.bam	FBtr0079596	R	15	0
+input1.bam	FBtr0079596	R	16	0
+input1.bam	FBtr0079596	R	17	0
+input1.bam	FBtr0079596	R	18	0
+input1.bam	FBtr0079596	R	19	0
+input1.bam	FBtr0079596	R	20	0
+input1.bam	FBtr0079596	R	21	0
+input1.bam	FBtr0079596	R	22	0
+input1.bam	FBtr0079596	R	23	0
+input1.bam	FBtr0079596	R	24	0
+input1.bam	FBtr0079596	R	25	0
+input1.bam	FBtr0079596	R	26	0
+input1.bam	FBtr0079596	R	27	0
+input1.bam	FBtr0079677	F	18	1
+input1.bam	FBtr0079677	F	19	2
+input1.bam	FBtr0079677	F	20	0
+input1.bam	FBtr0079677	F	21	0
+input1.bam	FBtr0079677	F	22	0
+input1.bam	FBtr0079677	F	23	1
+input1.bam	FBtr0079677	R	18	0
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+input2.bam	FBtr0078490	F	21	1
+input2.bam	FBtr0078490	F	22	0
+input2.bam	FBtr0078490	F	23	0
+input2.bam	FBtr0078490	F	24	2
+input2.bam	FBtr0078490	R	15	0
+input2.bam	FBtr0078490	R	16	0
+input2.bam	FBtr0078490	R	17	0
+input2.bam	FBtr0078490	R	18	0
+input2.bam	FBtr0078490	R	19	0
+input2.bam	FBtr0078490	R	20	0
+input2.bam	FBtr0078490	R	21	0
+input2.bam	FBtr0078490	R	22	0
+input2.bam	FBtr0078490	R	23	0
+input2.bam	FBtr0078490	R	24	0
+input2.bam	FBtr0078580	F	15	166
+input2.bam	FBtr0078580	F	16	26
+input2.bam	FBtr0078580	F	17	35
+input2.bam	FBtr0078580	F	18	16
+input2.bam	FBtr0078580	F	19	23
+input2.bam	FBtr0078580	F	20	35
+input2.bam	FBtr0078580	F	21	24
+input2.bam	FBtr0078580	F	22	16
+input2.bam	FBtr0078580	F	23	21
+input2.bam	FBtr0078580	F	24	4
+input2.bam	FBtr0078580	F	25	3
+input2.bam	FBtr0078580	F	26	1
+input2.bam	FBtr0078580	R	15	0
+input2.bam	FBtr0078580	R	16	0
+input2.bam	FBtr0078580	R	17	0
+input2.bam	FBtr0078580	R	18	0
+input2.bam	FBtr0078580	R	19	0
+input2.bam	FBtr0078580	R	20	0
+input2.bam	FBtr0078580	R	21	0
+input2.bam	FBtr0078580	R	22	0
+input2.bam	FBtr0078580	R	23	0
+input2.bam	FBtr0078580	R	24	0
+input2.bam	FBtr0078580	R	25	0
+input2.bam	FBtr0078580	R	26	0
+input2.bam	FBtr0078790	F	15	1
+input2.bam	FBtr0078790	F	16	3
+input2.bam	FBtr0078790	F	17	1
+input2.bam	FBtr0078790	F	18	1
+input2.bam	FBtr0078790	F	19	0
+input2.bam	FBtr0078790	F	20	1
+input2.bam	FBtr0078790	F	21	2
+input2.bam	FBtr0078790	F	22	1
+input2.bam	FBtr0078790	R	15	0
+input2.bam	FBtr0078790	R	16	0
+input2.bam	FBtr0078790	R	17	0
+input2.bam	FBtr0078790	R	18	0
+input2.bam	FBtr0078790	R	19	0
+input2.bam	FBtr0078790	R	20	0
+input2.bam	FBtr0078790	R	21	0
+input2.bam	FBtr0078790	R	22	0
+input2.bam	FBtr0079064	F	15	3
+input2.bam	FBtr0079064	F	16	0
+input2.bam	FBtr0079064	F	17	1
+input2.bam	FBtr0079064	F	18	1
+input2.bam	FBtr0079064	R	15	0
+input2.bam	FBtr0079064	R	16	0
+input2.bam	FBtr0079064	R	17	0
+input2.bam	FBtr0079064	R	18	0
+input2.bam	FBtr0079090	F	15	3
+input2.bam	FBtr0079090	F	16	0
+input2.bam	FBtr0079090	F	17	3
+input2.bam	FBtr0079090	F	18	0
+input2.bam	FBtr0079090	F	19	0
+input2.bam	FBtr0079090	F	20	0
+input2.bam	FBtr0079090	F	21	1
+input2.bam	FBtr0079090	R	15	0
+input2.bam	FBtr0079090	R	16	0
+input2.bam	FBtr0079090	R	17	0
+input2.bam	FBtr0079090	R	18	0
+input2.bam	FBtr0079090	R	19	0
+input2.bam	FBtr0079090	R	20	0
+input2.bam	FBtr0079090	R	21	0
+input2.bam	FBtr0079338	F	15	4
+input2.bam	FBtr0079338	F	16	6
+input2.bam	FBtr0079338	F	17	2
+input2.bam	FBtr0079338	F	18	6
+input2.bam	FBtr0079338	F	19	2
+input2.bam	FBtr0079338	F	20	1
+input2.bam	FBtr0079338	F	21	0
+input2.bam	FBtr0079338	F	22	1
+input2.bam	FBtr0079338	F	23	1
+input2.bam	FBtr0079338	R	15	0
+input2.bam	FBtr0079338	R	16	0
+input2.bam	FBtr0079338	R	17	0
+input2.bam	FBtr0079338	R	18	0
+input2.bam	FBtr0079338	R	19	0
+input2.bam	FBtr0079338	R	20	0
+input2.bam	FBtr0079338	R	21	0
+input2.bam	FBtr0079338	R	22	0
+input2.bam	FBtr0079338	R	23	0
+input2.bam	FBtr0079528	F	15	164
+input2.bam	FBtr0079528	F	16	46
+input2.bam	FBtr0079528	F	17	31
+input2.bam	FBtr0079528	F	18	56
+input2.bam	FBtr0079528	F	19	34
+input2.bam	FBtr0079528	F	20	8
+input2.bam	FBtr0079528	F	21	8
+input2.bam	FBtr0079528	F	22	8
+input2.bam	FBtr0079528	F	23	4
+input2.bam	FBtr0079528	F	24	1
+input2.bam	FBtr0079528	F	25	1
+input2.bam	FBtr0079528	F	26	4
+input2.bam	FBtr0079528	R	15	0
+input2.bam	FBtr0079528	R	16	0
+input2.bam	FBtr0079528	R	17	0
+input2.bam	FBtr0079528	R	18	0
+input2.bam	FBtr0079528	R	19	0
+input2.bam	FBtr0079528	R	20	0
+input2.bam	FBtr0079528	R	21	0
+input2.bam	FBtr0079528	R	22	0
+input2.bam	FBtr0079528	R	23	0
+input2.bam	FBtr0079528	R	24	0
+input2.bam	FBtr0079528	R	25	0
+input2.bam	FBtr0079528	R	26	0
+input2.bam	FBtr0079596	F	15	31
+input2.bam	FBtr0079596	F	16	21
+input2.bam	FBtr0079596	F	17	18
+input2.bam	FBtr0079596	F	18	79
+input2.bam	FBtr0079596	F	19	48
+input2.bam	FBtr0079596	F	20	49
+input2.bam	FBtr0079596	F	21	40
+input2.bam	FBtr0079596	F	22	26
+input2.bam	FBtr0079596	F	23	2
+input2.bam	FBtr0079596	F	24	1
+input2.bam	FBtr0079596	R	15	0
+input2.bam	FBtr0079596	R	16	0
+input2.bam	FBtr0079596	R	17	0
+input2.bam	FBtr0079596	R	18	0
+input2.bam	FBtr0079596	R	19	0
+input2.bam	FBtr0079596	R	20	0
+input2.bam	FBtr0079596	R	21	1
+input2.bam	FBtr0079596	R	22	0
+input2.bam	FBtr0079596	R	23	0
+input2.bam	FBtr0079596	R	24	0
+input2.bam	FBtr0079677	F	15	2
+input2.bam	FBtr0079677	F	16	1
+input2.bam	FBtr0079677	F	17	2
+input2.bam	FBtr0079677	F	18	0
+input2.bam	FBtr0079677	F	19	1
+input2.bam	FBtr0079677	F	20	1
+input2.bam	FBtr0079677	R	15	0
+input2.bam	FBtr0079677	R	16	0
+input2.bam	FBtr0079677	R	17	0
+input2.bam	FBtr0079677	R	18	0
+input2.bam	FBtr0079677	R	19	0
+input2.bam	FBtr0079677	R	20	0
+input2.bam	FBtr0079690	F	15	1
+input2.bam	FBtr0079690	F	16	1
+input2.bam	FBtr0079690	F	17	0
+input2.bam	FBtr0079690	F	18	0
+input2.bam	FBtr0079690	F	19	0
+input2.bam	FBtr0079690	F	20	2
+input2.bam	FBtr0079690	F	21	1
+input2.bam	FBtr0079690	R	15	0
+input2.bam	FBtr0079690	R	16	0
+input2.bam	FBtr0079690	R	17	0
+input2.bam	FBtr0079690	R	18	0
+input2.bam	FBtr0079690	R	19	0
+input2.bam	FBtr0079690	R	20	0
+input2.bam	FBtr0079690	R	21	0
+input2.bam	FBtr0079692	F	15	1
+input2.bam	FBtr0079692	F	16	0
+input2.bam	FBtr0079692	F	17	0
+input2.bam	FBtr0079692	F	18	1
+input2.bam	FBtr0079692	F	19	0
+input2.bam	FBtr0079692	F	20	0
+input2.bam	FBtr0079692	F	21	1
+input2.bam	FBtr0079692	F	22	1
+input2.bam	FBtr0079692	R	15	0
+input2.bam	FBtr0079692	R	16	0
+input2.bam	FBtr0079692	R	17	0
+input2.bam	FBtr0079692	R	18	0
+input2.bam	FBtr0079692	R	19	0
+input2.bam	FBtr0079692	R	20	0
+input2.bam	FBtr0079692	R	21	0
+input2.bam	FBtr0079692	R	22	0
+input2.bam	FBtr0079693	F	15	4
+input2.bam	FBtr0079693	F	16	2
+input2.bam	FBtr0079693	F	17	0
+input2.bam	FBtr0079693	F	18	1
+input2.bam	FBtr0079693	F	19	0
+input2.bam	FBtr0079693	F	20	2
+input2.bam	FBtr0079693	R	15	0
+input2.bam	FBtr0079693	R	16	0
+input2.bam	FBtr0079693	R	17	0
+input2.bam	FBtr0079693	R	18	0
+input2.bam	FBtr0079693	R	19	0
+input2.bam	FBtr0079693	R	20	0
+input2.bam	FBtr0079694	F	15	2
+input2.bam	FBtr0079694	F	16	0
+input2.bam	FBtr0079694	F	17	1
+input2.bam	FBtr0079694	F	18	2
+input2.bam	FBtr0079694	F	19	1
+input2.bam	FBtr0079694	R	15	0
+input2.bam	FBtr0079694	R	16	0
+input2.bam	FBtr0079694	R	17	0
+input2.bam	FBtr0079694	R	18	0
+input2.bam	FBtr0079694	R	19	0
+input2.bam	FBtr0079702	F	15	2
+input2.bam	FBtr0079702	F	16	0
+input2.bam	FBtr0079702	F	17	1
+input2.bam	FBtr0079702	F	18	1
+input2.bam	FBtr0079702	R	15	0
+input2.bam	FBtr0079702	R	16	0
+input2.bam	FBtr0079702	R	17	0
+input2.bam	FBtr0079702	R	18	0
+input2.bam	FBtr0079728	F	15	3
+input2.bam	FBtr0079728	F	16	1
+input2.bam	FBtr0079728	F	17	1
+input2.bam	FBtr0079728	F	18	1
+input2.bam	FBtr0079728	R	15	0
+input2.bam	FBtr0079728	R	16	0
+input2.bam	FBtr0079728	R	17	0
+input2.bam	FBtr0079728	R	18	0
+input2.bam	FBtr0079729	F	15	1
+input2.bam	FBtr0079729	F	16	2
+input2.bam	FBtr0079729	F	17	1
+input2.bam	FBtr0079729	R	15	0
+input2.bam	FBtr0079729	R	16	0
+input2.bam	FBtr0079729	R	17	0
+input2.bam	FBtr0079752	F	17	1
+input2.bam	FBtr0079752	F	18	0
+input2.bam	FBtr0079752	F	19	0
+input2.bam	FBtr0079752	F	20	0
+input2.bam	FBtr0079752	F	21	0
+input2.bam	FBtr0079752	F	22	0
+input2.bam	FBtr0079752	F	23	0
+input2.bam	FBtr0079752	F	24	1
+input2.bam	FBtr0079752	R	17	0
+input2.bam	FBtr0079752	R	18	0
+input2.bam	FBtr0079752	R	19	0
+input2.bam	FBtr0079752	R	20	0
+input2.bam	FBtr0079752	R	21	0
+input2.bam	FBtr0079752	R	22	0
+input2.bam	FBtr0079752	R	23	0
+input2.bam	FBtr0079752	R	24	0
+input2.bam	FBtr0079820	F	15	27
+input2.bam	FBtr0079820	F	16	10
+input2.bam	FBtr0079820	F	17	7
+input2.bam	FBtr0079820	F	18	8
+input2.bam	FBtr0079820	F	19	25
+input2.bam	FBtr0079820	F	20	24
+input2.bam	FBtr0079820	F	21	7
+input2.bam	FBtr0079820	F	22	1
+input2.bam	FBtr0079820	R	15	0
+input2.bam	FBtr0079820	R	16	0
+input2.bam	FBtr0079820	R	17	0
+input2.bam	FBtr0079820	R	18	0
+input2.bam	FBtr0079820	R	19	0
+input2.bam	FBtr0079820	R	20	0
+input2.bam	FBtr0079820	R	21	0
+input2.bam	FBtr0079820	R	22	0
+input2.bam	FBtr0080609	F	17	2
+input2.bam	FBtr0080609	F	18	1
+input2.bam	FBtr0080609	F	19	2
+input2.bam	FBtr0080609	F	20	0
+input2.bam	FBtr0080609	F	21	0
+input2.bam	FBtr0080609	F	22	1
+input2.bam	FBtr0080609	F	23	1
+input2.bam	FBtr0080609	F	24	0
+input2.bam	FBtr0080609	F	25	1
+input2.bam	FBtr0080609	R	17	0
+input2.bam	FBtr0080609	R	18	0
+input2.bam	FBtr0080609	R	19	0
+input2.bam	FBtr0080609	R	20	0
+input2.bam	FBtr0080609	R	21	0
+input2.bam	FBtr0080609	R	22	0
+input2.bam	FBtr0080609	R	23	0
+input2.bam	FBtr0080609	R	24	0
+input2.bam	FBtr0080609	R	25	0
+input2.bam	FBtr0080644	F	15	8
+input2.bam	FBtr0080644	R	15	0
+input2.bam	FBtr0080646	F	15	10
+input2.bam	FBtr0080646	F	16	1
+input2.bam	FBtr0080646	F	17	0
+input2.bam	FBtr0080646	F	18	0
+input2.bam	FBtr0080646	F	19	0
+input2.bam	FBtr0080646	F	20	0
+input2.bam	FBtr0080646	F	21	1
+input2.bam	FBtr0080646	R	15	0
+input2.bam	FBtr0080646	R	16	0
+input2.bam	FBtr0080646	R	17	0
+input2.bam	FBtr0080646	R	18	0
+input2.bam	FBtr0080646	R	19	0
+input2.bam	FBtr0080646	R	20	0
+input2.bam	FBtr0080646	R	21	0
+input2.bam	FBtr0080647	F	15	9
+input2.bam	FBtr0080647	F	16	2
+input2.bam	FBtr0080647	F	17	0
+input2.bam	FBtr0080647	F	18	1
+input2.bam	FBtr0080647	R	15	0
+input2.bam	FBtr0080647	R	16	0
+input2.bam	FBtr0080647	R	17	0
+input2.bam	FBtr0080647	R	18	0
+input2.bam	FBtr0080660	F	15	11
+input2.bam	FBtr0080660	R	15	0
+input2.bam	FBtr0080663	F	15	26
+input2.bam	FBtr0080663	F	16	14
+input2.bam	FBtr0080663	F	17	14
+input2.bam	FBtr0080663	F	18	26
+input2.bam	FBtr0080663	F	19	9
+input2.bam	FBtr0080663	F	20	7
+input2.bam	FBtr0080663	F	21	4
+input2.bam	FBtr0080663	F	22	5
+input2.bam	FBtr0080663	F	23	0
+input2.bam	FBtr0080663	F	24	1
+input2.bam	FBtr0080663	R	15	0
+input2.bam	FBtr0080663	R	16	0
+input2.bam	FBtr0080663	R	17	0
+input2.bam	FBtr0080663	R	18	0
+input2.bam	FBtr0080663	R	19	0
+input2.bam	FBtr0080663	R	20	0
+input2.bam	FBtr0080663	R	21	0
+input2.bam	FBtr0080663	R	22	0
+input2.bam	FBtr0080663	R	23	0
+input2.bam	FBtr0080663	R	24	0
+input2.bam	FBtr0080664	F	15	165
+input2.bam	FBtr0080664	F	16	59
+input2.bam	FBtr0080664	F	17	20
+input2.bam	FBtr0080664	F	18	75
+input2.bam	FBtr0080664	F	19	24
+input2.bam	FBtr0080664	F	20	21
+input2.bam	FBtr0080664	F	21	8
+input2.bam	FBtr0080664	F	22	4
+input2.bam	FBtr0080664	F	23	4
+input2.bam	FBtr0080664	F	24	0
+input2.bam	FBtr0080664	F	25	3
+input2.bam	FBtr0080664	F	26	4
+input2.bam	FBtr0080664	R	15	0
+input2.bam	FBtr0080664	R	16	0
+input2.bam	FBtr0080664	R	17	0
+input2.bam	FBtr0080664	R	18	0
+input2.bam	FBtr0080664	R	19	0
+input2.bam	FBtr0080664	R	20	0
+input2.bam	FBtr0080664	R	21	0
+input2.bam	FBtr0080664	R	22	1
+input2.bam	FBtr0080664	R	23	1
+input2.bam	FBtr0080664	R	24	0
+input2.bam	FBtr0080664	R	25	0
+input2.bam	FBtr0080664	R	26	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_mean.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_mean.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,300 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
+input1.bam	FBtr0070001	72	1	F	17.0
+input1.bam	FBtr0070001	72	7	F	20.3
+input1.bam	FBtr0070001	72	8	F	21.3
+input1.bam	FBtr0070001	72	11	F	20.5
+input1.bam	FBtr0070001	72	16	F	19.0
+input1.bam	FBtr0070001	72	17	F	23.0
+input1.bam	FBtr0070001	72	18	F	16.0
+input1.bam	FBtr0070001	72	27	F	23.5
+input1.bam	FBtr0070001	72	30	F	23.0
+input1.bam	FBtr0070001	72	31	F	23.0
+input1.bam	FBtr0070001	72	32	F	22.0
+input1.bam	FBtr0070001	72	34	F	20.0
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	15.0
+input1.bam	FBtr0070533	72	12	F	18.0
+input1.bam	FBtr0070533	72	15	F	15.0
+input1.bam	FBtr0070533	72	19	F	21.8
+input1.bam	FBtr0070533	72	20	F	23.0
+input1.bam	FBtr0070533	72	21	F	18.0
+input1.bam	FBtr0070533	72	22	F	20.0
+input1.bam	FBtr0070533	72	25	F	17.0
+input1.bam	FBtr0070533	72	26	F	16.0
+input1.bam	FBtr0070533	72	28	F	25.0
+input1.bam	FBtr0070533	72	32	F	20.5
+input1.bam	FBtr0070533	72	35	F	19.0
+input1.bam	FBtr0070533	72	37	F	19.0
+input1.bam	FBtr0070533	72	38	F	18.0
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	16.5
+input1.bam	FBtr0070603	72	3	F	21.0
+input1.bam	FBtr0070603	72	4	F	20.0
+input1.bam	FBtr0070603	72	6	F	18.0
+input1.bam	FBtr0070603	72	7	F	17.1
+input1.bam	FBtr0070603	72	8	F	16.0
+input1.bam	FBtr0070603	72	9	F	15.0
+input1.bam	FBtr0070603	72	12	F	20.0
+input1.bam	FBtr0070603	72	13	F	22.0
+input1.bam	FBtr0070603	72	15	F	18.5
+input1.bam	FBtr0070603	72	16	F	20.5
+input1.bam	FBtr0070603	72	17	F	24.0
+input1.bam	FBtr0070603	72	18	F	16.0
+input1.bam	FBtr0070603	72	19	F	22.6
+input1.bam	FBtr0070603	72	20	F	21.0
+input1.bam	FBtr0070603	72	21	F	25.0
+input1.bam	FBtr0070603	72	22	F	20.7
+input1.bam	FBtr0070603	72	24	F	19.5
+input1.bam	FBtr0070603	72	25	F	23.0
+input1.bam	FBtr0070603	72	26	F	25.8
+input1.bam	FBtr0070603	72	27	F	26.3
+input1.bam	FBtr0070603	72	32	F	20.0
+input1.bam	FBtr0070603	72	34	F	19.3
+input1.bam	FBtr0070603	72	38	F	18.0
+input1.bam	FBtr0070603	72	42	F	21.0
+input1.bam	FBtr0070603	72	51	F	18.0
+input1.bam	FBtr0070603	72	56	F	16.0
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	15.0
+input1.bam	FBtr0070604	72	18	F	23.0
+input1.bam	FBtr0070604	72	22	F	19.0
+input1.bam	FBtr0070604	72	30	F	18.0
+input1.bam	FBtr0070604	72	31	F	22.6
+input1.bam	FBtr0070604	72	32	F	22.0
+input1.bam	FBtr0070604	72	57	F	15.0
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	21.0
+input1.bam	FBtr0070911	73	38	F	15.0
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	16.0
+input1.bam	FBtr0078490	72	17	F	16.0
+input1.bam	FBtr0078490	72	18	F	15.0
+input1.bam	FBtr0078490	72	25	F	15.0
+input1.bam	FBtr0078490	72	28	F	19.0
+input1.bam	FBtr0078490	72	38	F	18.0
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	18.9
+input1.bam	FBtr0078580	72	3	F	22.0
+input1.bam	FBtr0078580	72	4	F	25.3
+input1.bam	FBtr0078580	72	5	F	21.0
+input1.bam	FBtr0078580	72	6	F	19.0
+input1.bam	FBtr0078580	72	7	F	22.0
+input1.bam	FBtr0078580	72	8	F	18.0
+input1.bam	FBtr0078580	72	11	F	23.0
+input1.bam	FBtr0078580	72	12	F	18.0
+input1.bam	FBtr0078580	72	14	F	15.3
+input1.bam	FBtr0078580	72	15	F	16.0
+input1.bam	FBtr0078580	72	16	F	19.0
+input1.bam	FBtr0078580	72	17	F	17.0
+input1.bam	FBtr0078580	72	19	F	24.0
+input1.bam	FBtr0078580	72	20	F	21.0
+input1.bam	FBtr0078580	72	21	F	19.4
+input1.bam	FBtr0078580	72	24	F	17.0
+input1.bam	FBtr0078580	72	25	F	27.5
+input1.bam	FBtr0078580	72	29	F	17.0
+input1.bam	FBtr0078580	72	31	F	17.0
+input1.bam	FBtr0078580	72	52	F	16.0
+input1.bam	FBtr0078580	72	72	F	0
+input1.bam	FBtr0078790	73	1	F	19.0
+input1.bam	FBtr0078790	73	17	F	16.0
+input1.bam	FBtr0078790	73	33	F	23.0
+input1.bam	FBtr0078790	73	42	F	18.5
+input1.bam	FBtr0078790	73	44	F	19.5
+input1.bam	FBtr0078790	73	46	F	17.0
+input1.bam	FBtr0078790	73	47	F	18.0
+input1.bam	FBtr0078790	73	52	F	20.0
+input1.bam	FBtr0078790	73	69	R	15.0
+input1.bam	FBtr0078790	73	73	F	0
+input1.bam	FBtr0079064	72	1	F	15.0
+input1.bam	FBtr0079064	72	3	F	21.0
+input1.bam	FBtr0079064	72	33	F	15.0
+input1.bam	FBtr0079064	72	52	F	17.0
+input1.bam	FBtr0079064	72	72	F	0
+input1.bam	FBtr0079090	72	1	F	21.5
+input1.bam	FBtr0079090	72	26	F	24.0
+input1.bam	FBtr0079090	72	33	F	16.0
+input1.bam	FBtr0079090	72	53	F	18.0
+input1.bam	FBtr0079090	72	56	R	21.0
+input1.bam	FBtr0079090	72	72	F	0
+input1.bam	FBtr0079338	73	1	F	0
+input1.bam	FBtr0079338	73	12	F	17.0
+input1.bam	FBtr0079338	73	13	F	17.5
+input1.bam	FBtr0079338	73	14	F	15.0
+input1.bam	FBtr0079338	73	17	F	15.0
+input1.bam	FBtr0079338	73	25	F	16.0
+input1.bam	FBtr0079338	73	42	F	21.8
+input1.bam	FBtr0079338	73	43	F	21.0
+input1.bam	FBtr0079338	73	46	F	18.0
+input1.bam	FBtr0079338	73	73	F	0
+input1.bam	FBtr0079528	71	1	F	20.8
+input1.bam	FBtr0079528	71	3	F	23.6
+input1.bam	FBtr0079528	71	4	F	24.0
+input1.bam	FBtr0079528	71	8	F	20.3
+input1.bam	FBtr0079528	71	10	F	21.0
+input1.bam	FBtr0079528	71	11	F	19.0
+input1.bam	FBtr0079528	71	13	F	16.0
+input1.bam	FBtr0079528	71	14	F	18.5
+input1.bam	FBtr0079528	71	16	F	15.0
+input1.bam	FBtr0079528	71	17	F	15.3
+input1.bam	FBtr0079528	71	18	F	19.8
+input1.bam	FBtr0079528	71	28	F	16.0
+input1.bam	FBtr0079528	71	35	F	15.0
+input1.bam	FBtr0079528	71	36	F	20.0
+input1.bam	FBtr0079528	71	37	F	18.0
+input1.bam	FBtr0079528	71	51	F	15.0
+input1.bam	FBtr0079528	71	71	F	0
+input1.bam	FBtr0079596	73	1	F	16.2
+input1.bam	FBtr0079596	73	3	F	21.8
+input1.bam	FBtr0079596	73	4	F	21.5
+input1.bam	FBtr0079596	73	5	F	18.5
+input1.bam	FBtr0079596	73	6	F	17.5
+input1.bam	FBtr0079596	73	8	F	16.6
+input1.bam	FBtr0079596	73	9	F	16.1
+input1.bam	FBtr0079596	73	10	F	15.3
+input1.bam	FBtr0079596	73	11	F	15.2
+input1.bam	FBtr0079596	73	12	F	17.0
+input1.bam	FBtr0079596	73	13	F	16.1
+input1.bam	FBtr0079596	73	14	F	15.0
+input1.bam	FBtr0079596	73	15	F	18.0
+input1.bam	FBtr0079596	73	16	F	16.7
+input1.bam	FBtr0079596	73	17	F	16.0
+input1.bam	FBtr0079596	73	18	F	15.0
+input1.bam	FBtr0079596	73	19	F	15.0
+input1.bam	FBtr0079596	73	53	F	18.5
+input1.bam	FBtr0079596	73	54	F	19.5
+input1.bam	FBtr0079596	73	73	F	0
+input1.bam	FBtr0079677	72	1	F	23.0
+input1.bam	FBtr0079677	72	5	F	19.0
+input1.bam	FBtr0079677	72	52	F	19.0
+input1.bam	FBtr0079677	72	53	F	18.0
+input1.bam	FBtr0079677	72	72	F	0
+input1.bam	FBtr0079690	72	1	F	15.0
+input1.bam	FBtr0079690	72	22	F	15.0
+input1.bam	FBtr0079690	72	27	F	25.0
+input1.bam	FBtr0079690	72	33	F	16.0
+input1.bam	FBtr0079690	72	72	F	0
+input1.bam	FBtr0079692	73	1	F	19.3
+input1.bam	FBtr0079692	73	18	F	18.0
+input1.bam	FBtr0079692	73	25	F	17.0
+input1.bam	FBtr0079692	73	32	F	20.0
+input1.bam	FBtr0079692	73	73	F	0
+input1.bam	FBtr0079693	72	1	F	17.2
+input1.bam	FBtr0079693	72	25	F	23.0
+input1.bam	FBtr0079693	72	72	F	0
+input1.bam	FBtr0079694	72	1	F	20.4
+input1.bam	FBtr0079694	72	18	F	19.0
+input1.bam	FBtr0079694	72	52	F	17.0
+input1.bam	FBtr0079694	72	72	F	0
+input1.bam	FBtr0079702	72	1	F	15.0
+input1.bam	FBtr0079702	72	19	F	18.0
+input1.bam	FBtr0079702	72	56	F	15.0
+input1.bam	FBtr0079702	72	72	F	0
+input1.bam	FBtr0079728	72	1	F	16.0
+input1.bam	FBtr0079728	72	8	F	20.0
+input1.bam	FBtr0079728	72	19	F	24.0
+input1.bam	FBtr0079728	72	33	F	15.7
+input1.bam	FBtr0079728	72	56	F	15.0
+input1.bam	FBtr0079728	72	72	F	0
+input1.bam	FBtr0079729	72	1	F	15.0
+input1.bam	FBtr0079729	72	13	F	22.0
+input1.bam	FBtr0079729	72	52	F	18.0
+input1.bam	FBtr0079729	72	57	F	16.0
+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	19.5
+input1.bam	FBtr0079752	72	7	F	20.0
+input1.bam	FBtr0079752	72	12	F	16.0
+input1.bam	FBtr0079752	72	33	F	16.0
+input1.bam	FBtr0079752	72	52	F	19.5
+input1.bam	FBtr0079752	72	72	F	0
+input1.bam	FBtr0079820	74	1	F	0
+input1.bam	FBtr0079820	74	45	F	20.0
+input1.bam	FBtr0079820	74	46	F	17.0
+input1.bam	FBtr0079820	74	48	F	18.0
+input1.bam	FBtr0079820	74	49	F	24.0
+input1.bam	FBtr0079820	74	51	F	20.0
+input1.bam	FBtr0079820	74	54	F	17.0
+input1.bam	FBtr0079820	74	55	F	18.0
+input1.bam	FBtr0079820	74	56	F	18.5
+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	18.8
+input1.bam	FBtr0080609	72	3	F	21.0
+input1.bam	FBtr0080609	72	4	F	20.0
+input1.bam	FBtr0080609	72	5	F	19.0
+input1.bam	FBtr0080609	72	7	F	17.1
+input1.bam	FBtr0080609	72	8	F	16.0
+input1.bam	FBtr0080609	72	9	F	15.0
+input1.bam	FBtr0080609	72	12	F	23.0
+input1.bam	FBtr0080609	72	15	F	19.0
+input1.bam	FBtr0080609	72	16	F	23.0
+input1.bam	FBtr0080609	72	17	F	20.5
+input1.bam	FBtr0080609	72	19	F	26.0
+input1.bam	FBtr0080609	72	20	F	25.0
+input1.bam	FBtr0080609	72	42	F	21.0
+input1.bam	FBtr0080609	72	51	F	18.0
+input1.bam	FBtr0080609	72	52	F	15.0
+input1.bam	FBtr0080609	72	72	F	0
+input1.bam	FBtr0080644	72	1	F	27.0
+input1.bam	FBtr0080644	72	4	F	20.5
+input1.bam	FBtr0080644	72	7	F	16.0
+input1.bam	FBtr0080644	72	12	F	16.0
+input1.bam	FBtr0080644	72	72	F	0
+input1.bam	FBtr0080646	72	1	F	16.0
+input1.bam	FBtr0080646	72	6	F	22.0
+input1.bam	FBtr0080646	72	7	F	21.0
+input1.bam	FBtr0080646	72	72	F	0
+input1.bam	FBtr0080647	72	1	F	16.3
+input1.bam	FBtr0080647	72	3	F	16.0
+input1.bam	FBtr0080647	72	6	F	19.0
+input1.bam	FBtr0080647	72	8	F	20.0
+input1.bam	FBtr0080647	72	11	F	17.0
+input1.bam	FBtr0080647	72	12	F	16.0
+input1.bam	FBtr0080647	72	72	F	0
+input1.bam	FBtr0080660	72	1	F	0
+input1.bam	FBtr0080660	72	4	F	24.0
+input1.bam	FBtr0080660	72	7	F	19.3
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	18.8
+input1.bam	FBtr0080663	71	3	F	23.7
+input1.bam	FBtr0080663	71	4	F	23.3
+input1.bam	FBtr0080663	71	7	F	16.0
+input1.bam	FBtr0080663	71	8	F	19.3
+input1.bam	FBtr0080663	71	12	F	16.0
+input1.bam	FBtr0080663	71	14	F	19.0
+input1.bam	FBtr0080663	71	15	F	17.0
+input1.bam	FBtr0080663	71	16	F	15.7
+input1.bam	FBtr0080663	71	17	F	15.6
+input1.bam	FBtr0080663	71	26	F	18.0
+input1.bam	FBtr0080663	71	32	F	15.5
+input1.bam	FBtr0080663	71	50	F	17.0
+input1.bam	FBtr0080663	71	51	F	15.6
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	19.5
+input1.bam	FBtr0080664	71	3	F	23.8
+input1.bam	FBtr0080664	71	4	F	23.5
+input1.bam	FBtr0080664	71	6	F	23.0
+input1.bam	FBtr0080664	71	7	F	21.0
+input1.bam	FBtr0080664	71	8	F	20.5
+input1.bam	FBtr0080664	71	9	F	20.0
+input1.bam	FBtr0080664	71	11	F	16.7
+input1.bam	FBtr0080664	71	12	F	18.0
+input1.bam	FBtr0080664	71	13	F	20.0
+input1.bam	FBtr0080664	71	14	F	18.3
+input1.bam	FBtr0080664	71	16	F	15.0
+input1.bam	FBtr0080664	71	17	F	15.8
+input1.bam	FBtr0080664	71	18	F	15.0
+input1.bam	FBtr0080664	71	21	F	15.0
+input1.bam	FBtr0080664	71	28	F	16.0
+input1.bam	FBtr0080664	71	32	F	15.0
+input1.bam	FBtr0080664	71	33	F	20.0
+input1.bam	FBtr0080664	71	34	F	16.0
+input1.bam	FBtr0080664	71	35	F	15.0
+input1.bam	FBtr0080664	71	36	F	21.0
+input1.bam	FBtr0080664	71	37	F	18.0
+input1.bam	FBtr0080664	71	38	F	15.0
+input1.bam	FBtr0080664	71	50	F	16.0
+input1.bam	FBtr0080664	71	51	F	15.0
+input1.bam	FBtr0080664	71	52	F	15.0
+input1.bam	FBtr0080664	71	56	F	16.0
+input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_median.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_median.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,300 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
+input1.bam	FBtr0070001	72	1	F	17.0
+input1.bam	FBtr0070001	72	7	F	21.0
+input1.bam	FBtr0070001	72	8	F	21.0
+input1.bam	FBtr0070001	72	11	F	20.5
+input1.bam	FBtr0070001	72	16	F	19.0
+input1.bam	FBtr0070001	72	17	F	23.0
+input1.bam	FBtr0070001	72	18	F	16.0
+input1.bam	FBtr0070001	72	27	F	23.5
+input1.bam	FBtr0070001	72	30	F	23.0
+input1.bam	FBtr0070001	72	31	F	23.0
+input1.bam	FBtr0070001	72	32	F	22.0
+input1.bam	FBtr0070001	72	34	F	20.0
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	15.0
+input1.bam	FBtr0070533	72	12	F	18.0
+input1.bam	FBtr0070533	72	15	F	15.0
+input1.bam	FBtr0070533	72	19	F	22.0
+input1.bam	FBtr0070533	72	20	F	23.0
+input1.bam	FBtr0070533	72	21	F	18.0
+input1.bam	FBtr0070533	72	22	F	20.0
+input1.bam	FBtr0070533	72	25	F	17.0
+input1.bam	FBtr0070533	72	26	F	16.0
+input1.bam	FBtr0070533	72	28	F	25.0
+input1.bam	FBtr0070533	72	32	F	21.0
+input1.bam	FBtr0070533	72	35	F	19.0
+input1.bam	FBtr0070533	72	37	F	19.0
+input1.bam	FBtr0070533	72	38	F	18.0
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	16.5
+input1.bam	FBtr0070603	72	3	F	21.0
+input1.bam	FBtr0070603	72	4	F	20.0
+input1.bam	FBtr0070603	72	6	F	18.0
+input1.bam	FBtr0070603	72	7	F	17.0
+input1.bam	FBtr0070603	72	8	F	16.0
+input1.bam	FBtr0070603	72	9	F	15.0
+input1.bam	FBtr0070603	72	12	F	20.0
+input1.bam	FBtr0070603	72	13	F	22.0
+input1.bam	FBtr0070603	72	15	F	18.5
+input1.bam	FBtr0070603	72	16	F	20.5
+input1.bam	FBtr0070603	72	17	F	25.0
+input1.bam	FBtr0070603	72	18	F	16.0
+input1.bam	FBtr0070603	72	19	F	23.0
+input1.bam	FBtr0070603	72	20	F	22.0
+input1.bam	FBtr0070603	72	21	F	25.0
+input1.bam	FBtr0070603	72	22	F	20.0
+input1.bam	FBtr0070603	72	24	F	19.5
+input1.bam	FBtr0070603	72	25	F	23.0
+input1.bam	FBtr0070603	72	26	F	26.0
+input1.bam	FBtr0070603	72	27	F	26.0
+input1.bam	FBtr0070603	72	32	F	20.0
+input1.bam	FBtr0070603	72	34	F	20.0
+input1.bam	FBtr0070603	72	38	F	18.0
+input1.bam	FBtr0070603	72	42	F	21.0
+input1.bam	FBtr0070603	72	51	F	18.0
+input1.bam	FBtr0070603	72	56	F	16.0
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	15.0
+input1.bam	FBtr0070604	72	18	F	23.0
+input1.bam	FBtr0070604	72	22	F	19.0
+input1.bam	FBtr0070604	72	30	F	18.0
+input1.bam	FBtr0070604	72	31	F	23.0
+input1.bam	FBtr0070604	72	32	F	22.0
+input1.bam	FBtr0070604	72	57	F	15.0
+input1.bam	FBtr0070604	72	72	F	0
+input1.bam	FBtr0070911	73	1	F	0
+input1.bam	FBtr0070911	73	15	F	21.0
+input1.bam	FBtr0070911	73	38	F	15.0
+input1.bam	FBtr0070911	73	73	F	0
+input1.bam	FBtr0078490	72	1	F	0
+input1.bam	FBtr0078490	72	13	F	16.0
+input1.bam	FBtr0078490	72	17	F	16.0
+input1.bam	FBtr0078490	72	18	F	15.0
+input1.bam	FBtr0078490	72	25	F	15.0
+input1.bam	FBtr0078490	72	28	F	19.0
+input1.bam	FBtr0078490	72	38	F	18.0
+input1.bam	FBtr0078490	72	72	F	0
+input1.bam	FBtr0078580	72	1	F	15.0
+input1.bam	FBtr0078580	72	3	F	22.0
+input1.bam	FBtr0078580	72	4	F	25.0
+input1.bam	FBtr0078580	72	5	F	20.0
+input1.bam	FBtr0078580	72	6	F	19.0
+input1.bam	FBtr0078580	72	7	F	22.0
+input1.bam	FBtr0078580	72	8	F	18.0
+input1.bam	FBtr0078580	72	11	F	23.0
+input1.bam	FBtr0078580	72	12	F	17.0
+input1.bam	FBtr0078580	72	14	F	15.0
+input1.bam	FBtr0078580	72	15	F	16.0
+input1.bam	FBtr0078580	72	16	F	19.0
+input1.bam	FBtr0078580	72	17	F	17.0
+input1.bam	FBtr0078580	72	19	F	24.0
+input1.bam	FBtr0078580	72	20	F	21.0
+input1.bam	FBtr0078580	72	21	F	20.0
+input1.bam	FBtr0078580	72	24	F	17.0
+input1.bam	FBtr0078580	72	25	F	27.5
+input1.bam	FBtr0078580	72	29	F	17.0
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+input1.bam	FBtr0078580	72	52	F	16.0
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+input1.bam	FBtr0078790	73	1	F	19.0
+input1.bam	FBtr0078790	73	17	F	16.0
+input1.bam	FBtr0078790	73	33	F	23.0
+input1.bam	FBtr0078790	73	42	F	18.5
+input1.bam	FBtr0078790	73	44	F	19.5
+input1.bam	FBtr0078790	73	46	F	17.0
+input1.bam	FBtr0078790	73	47	F	18.0
+input1.bam	FBtr0078790	73	52	F	20.0
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+input1.bam	FBtr0079064	72	1	F	15.0
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+input1.bam	FBtr0079528	71	1	F	20.0
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min0_max10000_cluster0_single_plot_counts.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min0_max10000_cluster0_ylimneg5_pos5_single_plot_counts.pdf
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diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min0_max10000_cluster5_single_plot_counts.pdf
Binary file test-data/input1_min0_max10000_cluster5_single_plot_counts.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min20_max30_cluster0_single_plot_counts.pdf
Binary file test-data/input1_min20_max30_cluster0_single_plot_counts.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min20_max30_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_min20_max30_counts.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,171 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
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+input1.bam	FBtr0070533	72	1	F	0
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+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	1
+input1.bam	FBtr0079752	72	7	F	1
+input1.bam	FBtr0079752	72	52	F	1
+input1.bam	FBtr0079752	72	72	F	0
+input1.bam	FBtr0079820	74	1	F	0
+input1.bam	FBtr0079820	74	45	F	1
+input1.bam	FBtr0079820	74	49	F	1
+input1.bam	FBtr0079820	74	51	F	1
+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	3
+input1.bam	FBtr0080609	72	3	F	2
+input1.bam	FBtr0080609	72	4	F	10
+input1.bam	FBtr0080609	72	12	F	1
+input1.bam	FBtr0080609	72	16	F	1
+input1.bam	FBtr0080609	72	17	F	1
+input1.bam	FBtr0080609	72	19	F	1
+input1.bam	FBtr0080609	72	20	F	1
+input1.bam	FBtr0080609	72	42	F	1
+input1.bam	FBtr0080609	72	72	F	0
+input1.bam	FBtr0080644	72	1	F	1
+input1.bam	FBtr0080644	72	4	F	1
+input1.bam	FBtr0080644	72	72	F	0
+input1.bam	FBtr0080646	72	1	F	0
+input1.bam	FBtr0080646	72	6	F	1
+input1.bam	FBtr0080646	72	7	F	1
+input1.bam	FBtr0080646	72	72	F	0
+input1.bam	FBtr0080647	72	1	F	0
+input1.bam	FBtr0080647	72	6	F	1
+input1.bam	FBtr0080647	72	8	F	1
+input1.bam	FBtr0080647	72	72	F	0
+input1.bam	FBtr0080660	72	1	F	0
+input1.bam	FBtr0080660	72	4	F	4
+input1.bam	FBtr0080660	72	7	F	2
+input1.bam	FBtr0080660	72	72	F	0
+input1.bam	FBtr0080663	71	1	F	6
+input1.bam	FBtr0080663	71	3	F	56
+input1.bam	FBtr0080663	71	4	F	4
+input1.bam	FBtr0080663	71	8	F	2
+input1.bam	FBtr0080663	71	51	F	1
+input1.bam	FBtr0080663	71	71	F	0
+input1.bam	FBtr0080664	71	1	F	6
+input1.bam	FBtr0080664	71	3	F	56
+input1.bam	FBtr0080664	71	4	F	4
+input1.bam	FBtr0080664	71	6	F	1
+input1.bam	FBtr0080664	71	7	F	1
+input1.bam	FBtr0080664	71	8	F	3
+input1.bam	FBtr0080664	71	9	F	1
+input1.bam	FBtr0080664	71	12	F	1
+input1.bam	FBtr0080664	71	13	F	2
+input1.bam	FBtr0080664	71	33	F	1
+input1.bam	FBtr0080664	71	36	F	1
+input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min20_max30_single_plot_size.pdf
Binary file test-data/input1_min20_max30_single_plot_size.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_min20_max30_size.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_min20_max30_size.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,263 @@
+Dataset	Chromosome	Polarity	Size	Counts
+input1.bam	FBtr0070001	F	20	4
+input1.bam	FBtr0070001	F	21	4
+input1.bam	FBtr0070001	F	22	29
+input1.bam	FBtr0070001	F	23	15
+input1.bam	FBtr0070001	F	24	1
+input1.bam	FBtr0070001	R	20	0
+input1.bam	FBtr0070001	R	21	0
+input1.bam	FBtr0070001	R	22	0
+input1.bam	FBtr0070001	R	23	0
+input1.bam	FBtr0070001	R	24	0
+input1.bam	FBtr0070533	F	20	2
+input1.bam	FBtr0070533	F	21	2
+input1.bam	FBtr0070533	F	22	4
+input1.bam	FBtr0070533	F	23	2
+input1.bam	FBtr0070533	F	24	0
+input1.bam	FBtr0070533	F	25	1
+input1.bam	FBtr0070533	R	20	0
+input1.bam	FBtr0070533	R	21	0
+input1.bam	FBtr0070533	R	22	0
+input1.bam	FBtr0070533	R	23	0
+input1.bam	FBtr0070533	R	24	0
+input1.bam	FBtr0070533	R	25	0
+input1.bam	FBtr0070603	F	20	6
+input1.bam	FBtr0070603	F	21	3
+input1.bam	FBtr0070603	F	22	3
+input1.bam	FBtr0070603	F	23	10
+input1.bam	FBtr0070603	F	24	2
+input1.bam	FBtr0070603	F	25	5
+input1.bam	FBtr0070603	F	26	5
+input1.bam	FBtr0070603	F	27	3
+input1.bam	FBtr0070603	R	20	0
+input1.bam	FBtr0070603	R	21	0
+input1.bam	FBtr0070603	R	22	0
+input1.bam	FBtr0070603	R	23	0
+input1.bam	FBtr0070603	R	24	0
+input1.bam	FBtr0070603	R	25	0
+input1.bam	FBtr0070603	R	26	0
+input1.bam	FBtr0070603	R	27	0
+input1.bam	FBtr0070604	F	21	1
+input1.bam	FBtr0070604	F	22	23
+input1.bam	FBtr0070604	F	23	10
+input1.bam	FBtr0070604	R	21	0
+input1.bam	FBtr0070604	R	22	0
+input1.bam	FBtr0070604	R	23	0
+input1.bam	FBtr0070911	F	21	1
+input1.bam	FBtr0070911	R	21	0
+input1.bam	FBtr0078490	F	23	1
+input1.bam	FBtr0078490	R	23	0
+input1.bam	FBtr0078580	F	20	9
+input1.bam	FBtr0078580	F	21	5
+input1.bam	FBtr0078580	F	22	13
+input1.bam	FBtr0078580	F	23	5
+input1.bam	FBtr0078580	F	24	180
+input1.bam	FBtr0078580	F	25	212
+input1.bam	FBtr0078580	F	26	1
+input1.bam	FBtr0078580	F	27	2
+input1.bam	FBtr0078580	F	28	17
+input1.bam	FBtr0078580	R	20	0
+input1.bam	FBtr0078580	R	21	0
+input1.bam	FBtr0078580	R	22	0
+input1.bam	FBtr0078580	R	23	0
+input1.bam	FBtr0078580	R	24	0
+input1.bam	FBtr0078580	R	25	0
+input1.bam	FBtr0078580	R	26	0
+input1.bam	FBtr0078580	R	27	0
+input1.bam	FBtr0078580	R	28	0
+input1.bam	FBtr0078790	F	20	2
+input1.bam	FBtr0078790	F	21	0
+input1.bam	FBtr0078790	F	22	2
+input1.bam	FBtr0078790	F	23	1
+input1.bam	FBtr0078790	R	20	0
+input1.bam	FBtr0078790	R	21	0
+input1.bam	FBtr0078790	R	22	0
+input1.bam	FBtr0078790	R	23	0
+input1.bam	FBtr0079064	F	21	1
+input1.bam	FBtr0079064	R	21	0
+input1.bam	FBtr0079090	F	21	0
+input1.bam	FBtr0079090	F	22	0
+input1.bam	FBtr0079090	F	23	0
+input1.bam	FBtr0079090	F	24	1
+input1.bam	FBtr0079090	F	25	0
+input1.bam	FBtr0079090	F	26	0
+input1.bam	FBtr0079090	F	27	0
+input1.bam	FBtr0079090	F	28	1
+input1.bam	FBtr0079090	R	21	1
+input1.bam	FBtr0079090	R	22	0
+input1.bam	FBtr0079090	R	23	0
+input1.bam	FBtr0079090	R	24	0
+input1.bam	FBtr0079090	R	25	0
+input1.bam	FBtr0079090	R	26	0
+input1.bam	FBtr0079090	R	27	0
+input1.bam	FBtr0079090	R	28	0
+input1.bam	FBtr0079338	F	21	3
+input1.bam	FBtr0079338	F	22	6
+input1.bam	FBtr0079338	R	21	0
+input1.bam	FBtr0079338	R	22	0
+input1.bam	FBtr0079528	F	20	12
+input1.bam	FBtr0079528	F	21	3
+input1.bam	FBtr0079528	F	22	2
+input1.bam	FBtr0079528	F	23	3
+input1.bam	FBtr0079528	F	24	36
+input1.bam	FBtr0079528	F	25	8
+input1.bam	FBtr0079528	F	26	5
+input1.bam	FBtr0079528	F	27	2
+input1.bam	FBtr0079528	F	28	2
+input1.bam	FBtr0079528	F	29	1
+input1.bam	FBtr0079528	R	20	0
+input1.bam	FBtr0079528	R	21	0
+input1.bam	FBtr0079528	R	22	0
+input1.bam	FBtr0079528	R	23	0
+input1.bam	FBtr0079528	R	24	0
+input1.bam	FBtr0079528	R	25	0
+input1.bam	FBtr0079528	R	26	0
+input1.bam	FBtr0079528	R	27	0
+input1.bam	FBtr0079528	R	28	0
+input1.bam	FBtr0079528	R	29	0
+input1.bam	FBtr0079596	F	20	13
+input1.bam	FBtr0079596	F	21	3
+input1.bam	FBtr0079596	F	22	16
+input1.bam	FBtr0079596	F	23	8
+input1.bam	FBtr0079596	F	24	0
+input1.bam	FBtr0079596	F	25	0
+input1.bam	FBtr0079596	F	26	3
+input1.bam	FBtr0079596	F	27	1
+input1.bam	FBtr0079596	R	20	0
+input1.bam	FBtr0079596	R	21	0
+input1.bam	FBtr0079596	R	22	0
+input1.bam	FBtr0079596	R	23	0
+input1.bam	FBtr0079596	R	24	0
+input1.bam	FBtr0079596	R	25	0
+input1.bam	FBtr0079596	R	26	0
+input1.bam	FBtr0079596	R	27	0
+input1.bam	FBtr0079677	F	23	1
+input1.bam	FBtr0079677	R	23	0
+input1.bam	FBtr0079690	F	25	1
+input1.bam	FBtr0079690	R	25	0
+input1.bam	FBtr0079692	F	20	1
+input1.bam	FBtr0079692	F	21	0
+input1.bam	FBtr0079692	F	22	0
+input1.bam	FBtr0079692	F	23	1
+input1.bam	FBtr0079692	R	20	0
+input1.bam	FBtr0079692	R	21	0
+input1.bam	FBtr0079692	R	22	0
+input1.bam	FBtr0079692	R	23	0
+input1.bam	FBtr0079693	F	23	1
+input1.bam	FBtr0079693	F	24	1
+input1.bam	FBtr0079693	R	23	0
+input1.bam	FBtr0079693	R	24	0
+input1.bam	FBtr0079694	F	23	1
+input1.bam	FBtr0079694	F	24	1
+input1.bam	FBtr0079694	F	25	1
+input1.bam	FBtr0079694	R	23	0
+input1.bam	FBtr0079694	R	24	0
+input1.bam	FBtr0079694	R	25	0
+input1.bam	FBtr0079728	F	20	1
+input1.bam	FBtr0079728	F	21	0
+input1.bam	FBtr0079728	F	22	0
+input1.bam	FBtr0079728	F	23	0
+input1.bam	FBtr0079728	F	24	1
+input1.bam	FBtr0079728	R	20	0
+input1.bam	FBtr0079728	R	21	0
+input1.bam	FBtr0079728	R	22	0
+input1.bam	FBtr0079728	R	23	0
+input1.bam	FBtr0079728	R	24	0
+input1.bam	FBtr0079729	F	22	1
+input1.bam	FBtr0079729	R	22	0
+input1.bam	FBtr0079752	F	20	2
+input1.bam	FBtr0079752	F	21	0
+input1.bam	FBtr0079752	F	22	0
+input1.bam	FBtr0079752	F	23	0
+input1.bam	FBtr0079752	F	24	1
+input1.bam	FBtr0079752	R	20	0
+input1.bam	FBtr0079752	R	21	0
+input1.bam	FBtr0079752	R	22	0
+input1.bam	FBtr0079752	R	23	0
+input1.bam	FBtr0079752	R	24	0
+input1.bam	FBtr0079820	F	20	2
+input1.bam	FBtr0079820	F	21	0
+input1.bam	FBtr0079820	F	22	0
+input1.bam	FBtr0079820	F	23	0
+input1.bam	FBtr0079820	F	24	1
+input1.bam	FBtr0079820	R	20	0
+input1.bam	FBtr0079820	R	21	0
+input1.bam	FBtr0079820	R	22	0
+input1.bam	FBtr0079820	R	23	0
+input1.bam	FBtr0079820	R	24	0
+input1.bam	FBtr0080609	F	20	10
+input1.bam	FBtr0080609	F	21	4
+input1.bam	FBtr0080609	F	22	0
+input1.bam	FBtr0080609	F	23	4
+input1.bam	FBtr0080609	F	24	1
+input1.bam	FBtr0080609	F	25	1
+input1.bam	FBtr0080609	F	26	1
+input1.bam	FBtr0080609	R	20	0
+input1.bam	FBtr0080609	R	21	0
+input1.bam	FBtr0080609	R	22	0
+input1.bam	FBtr0080609	R	23	0
+input1.bam	FBtr0080609	R	24	0
+input1.bam	FBtr0080609	R	25	0
+input1.bam	FBtr0080609	R	26	0
+input1.bam	FBtr0080644	F	24	1
+input1.bam	FBtr0080644	F	25	0
+input1.bam	FBtr0080644	F	26	0
+input1.bam	FBtr0080644	F	27	1
+input1.bam	FBtr0080644	R	24	0
+input1.bam	FBtr0080644	R	25	0
+input1.bam	FBtr0080644	R	26	0
+input1.bam	FBtr0080644	R	27	0
+input1.bam	FBtr0080646	F	21	1
+input1.bam	FBtr0080646	F	22	1
+input1.bam	FBtr0080646	R	21	0
+input1.bam	FBtr0080646	R	22	0
+input1.bam	FBtr0080647	F	20	1
+input1.bam	FBtr0080647	F	21	0
+input1.bam	FBtr0080647	F	22	1
+input1.bam	FBtr0080647	R	20	0
+input1.bam	FBtr0080647	R	21	0
+input1.bam	FBtr0080647	R	22	0
+input1.bam	FBtr0080660	F	21	2
+input1.bam	FBtr0080660	F	22	0
+input1.bam	FBtr0080660	F	23	0
+input1.bam	FBtr0080660	F	24	4
+input1.bam	FBtr0080660	R	21	0
+input1.bam	FBtr0080660	R	22	0
+input1.bam	FBtr0080660	R	23	0
+input1.bam	FBtr0080660	R	24	0
+input1.bam	FBtr0080663	F	20	10
+input1.bam	FBtr0080663	F	21	0
+input1.bam	FBtr0080663	F	22	1
+input1.bam	FBtr0080663	F	23	7
+input1.bam	FBtr0080663	F	24	33
+input1.bam	FBtr0080663	F	25	10
+input1.bam	FBtr0080663	F	26	6
+input1.bam	FBtr0080663	F	27	0
+input1.bam	FBtr0080663	F	28	2
+input1.bam	FBtr0080663	R	20	0
+input1.bam	FBtr0080663	R	21	0
+input1.bam	FBtr0080663	R	22	0
+input1.bam	FBtr0080663	R	23	0
+input1.bam	FBtr0080663	R	24	0
+input1.bam	FBtr0080663	R	25	0
+input1.bam	FBtr0080663	R	26	0
+input1.bam	FBtr0080663	R	27	0
+input1.bam	FBtr0080663	R	28	0
+input1.bam	FBtr0080664	F	20	12
+input1.bam	FBtr0080664	F	21	5
+input1.bam	FBtr0080664	F	22	0
+input1.bam	FBtr0080664	F	23	11
+input1.bam	FBtr0080664	F	24	33
+input1.bam	FBtr0080664	F	25	10
+input1.bam	FBtr0080664	F	26	4
+input1.bam	FBtr0080664	F	27	0
+input1.bam	FBtr0080664	F	28	2
+input1.bam	FBtr0080664	R	20	0
+input1.bam	FBtr0080664	R	21	0
+input1.bam	FBtr0080664	R	22	0
+input1.bam	FBtr0080664	R	23	0
+input1.bam	FBtr0080664	R	24	0
+input1.bam	FBtr0080664	R	25	0
+input1.bam	FBtr0080664	R	26	0
+input1.bam	FBtr0080664	R	27	0
+input1.bam	FBtr0080664	R	28	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_single_plot_median.pdf
Binary file test-data/input1_single_plot_median.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_size.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1_size.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,605 @@
+Dataset	Chromosome	Polarity	Size	Counts
+input1.bam	FBtr0070001	F	16	2
+input1.bam	FBtr0070001	F	17	1
+input1.bam	FBtr0070001	F	18	0
+input1.bam	FBtr0070001	F	19	1
+input1.bam	FBtr0070001	F	20	4
+input1.bam	FBtr0070001	F	21	4
+input1.bam	FBtr0070001	F	22	29
+input1.bam	FBtr0070001	F	23	15
+input1.bam	FBtr0070001	F	24	1
+input1.bam	FBtr0070001	R	16	0
+input1.bam	FBtr0070001	R	17	0
+input1.bam	FBtr0070001	R	18	0
+input1.bam	FBtr0070001	R	19	0
+input1.bam	FBtr0070001	R	20	0
+input1.bam	FBtr0070001	R	21	0
+input1.bam	FBtr0070001	R	22	0
+input1.bam	FBtr0070001	R	23	0
+input1.bam	FBtr0070001	R	24	0
+input1.bam	FBtr0070533	F	15	2
+input1.bam	FBtr0070533	F	16	1
+input1.bam	FBtr0070533	F	17	1
+input1.bam	FBtr0070533	F	18	6
+input1.bam	FBtr0070533	F	19	3
+input1.bam	FBtr0070533	F	20	2
+input1.bam	FBtr0070533	F	21	2
+input1.bam	FBtr0070533	F	22	4
+input1.bam	FBtr0070533	F	23	2
+input1.bam	FBtr0070533	F	24	0
+input1.bam	FBtr0070533	F	25	1
+input1.bam	FBtr0070533	R	15	0
+input1.bam	FBtr0070533	R	16	0
+input1.bam	FBtr0070533	R	17	0
+input1.bam	FBtr0070533	R	18	0
+input1.bam	FBtr0070533	R	19	0
+input1.bam	FBtr0070533	R	20	0
+input1.bam	FBtr0070533	R	21	0
+input1.bam	FBtr0070533	R	22	0
+input1.bam	FBtr0070533	R	23	0
+input1.bam	FBtr0070533	R	24	0
+input1.bam	FBtr0070533	R	25	0
+input1.bam	FBtr0070603	F	15	9
+input1.bam	FBtr0070603	F	16	6
+input1.bam	FBtr0070603	F	17	10
+input1.bam	FBtr0070603	F	18	7
+input1.bam	FBtr0070603	F	19	1
+input1.bam	FBtr0070603	F	20	6
+input1.bam	FBtr0070603	F	21	3
+input1.bam	FBtr0070603	F	22	3
+input1.bam	FBtr0070603	F	23	10
+input1.bam	FBtr0070603	F	24	2
+input1.bam	FBtr0070603	F	25	5
+input1.bam	FBtr0070603	F	26	5
+input1.bam	FBtr0070603	F	27	3
+input1.bam	FBtr0070603	R	15	0
+input1.bam	FBtr0070603	R	16	0
+input1.bam	FBtr0070603	R	17	0
+input1.bam	FBtr0070603	R	18	0
+input1.bam	FBtr0070603	R	19	0
+input1.bam	FBtr0070603	R	20	0
+input1.bam	FBtr0070603	R	21	0
+input1.bam	FBtr0070603	R	22	0
+input1.bam	FBtr0070603	R	23	0
+input1.bam	FBtr0070603	R	24	0
+input1.bam	FBtr0070603	R	25	0
+input1.bam	FBtr0070603	R	26	0
+input1.bam	FBtr0070603	R	27	0
+input1.bam	FBtr0070604	F	15	2
+input1.bam	FBtr0070604	F	16	0
+input1.bam	FBtr0070604	F	17	0
+input1.bam	FBtr0070604	F	18	2
+input1.bam	FBtr0070604	F	19	2
+input1.bam	FBtr0070604	F	20	0
+input1.bam	FBtr0070604	F	21	1
+input1.bam	FBtr0070604	F	22	23
+input1.bam	FBtr0070604	F	23	10
+input1.bam	FBtr0070604	R	15	0
+input1.bam	FBtr0070604	R	16	0
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+input1.bam	FBtr0080644	R	16	0
+input1.bam	FBtr0080644	R	17	0
+input1.bam	FBtr0080644	R	18	0
+input1.bam	FBtr0080644	R	19	0
+input1.bam	FBtr0080644	R	20	0
+input1.bam	FBtr0080644	R	21	0
+input1.bam	FBtr0080644	R	22	0
+input1.bam	FBtr0080644	R	23	0
+input1.bam	FBtr0080644	R	24	0
+input1.bam	FBtr0080644	R	25	0
+input1.bam	FBtr0080644	R	26	0
+input1.bam	FBtr0080644	R	27	0
+input1.bam	FBtr0080646	F	16	1
+input1.bam	FBtr0080646	F	17	0
+input1.bam	FBtr0080646	F	18	0
+input1.bam	FBtr0080646	F	19	0
+input1.bam	FBtr0080646	F	20	0
+input1.bam	FBtr0080646	F	21	1
+input1.bam	FBtr0080646	F	22	1
+input1.bam	FBtr0080646	R	16	0
+input1.bam	FBtr0080646	R	17	0
+input1.bam	FBtr0080646	R	18	0
+input1.bam	FBtr0080646	R	19	0
+input1.bam	FBtr0080646	R	20	0
+input1.bam	FBtr0080646	R	21	0
+input1.bam	FBtr0080646	R	22	0
+input1.bam	FBtr0080647	F	15	1
+input1.bam	FBtr0080647	F	16	4
+input1.bam	FBtr0080647	F	17	2
+input1.bam	FBtr0080647	F	18	1
+input1.bam	FBtr0080647	F	19	0
+input1.bam	FBtr0080647	F	20	1
+input1.bam	FBtr0080647	F	21	0
+input1.bam	FBtr0080647	F	22	1
+input1.bam	FBtr0080647	R	15	0
+input1.bam	FBtr0080647	R	16	0
+input1.bam	FBtr0080647	R	17	0
+input1.bam	FBtr0080647	R	18	0
+input1.bam	FBtr0080647	R	19	0
+input1.bam	FBtr0080647	R	20	0
+input1.bam	FBtr0080647	R	21	0
+input1.bam	FBtr0080647	R	22	0
+input1.bam	FBtr0080660	F	16	1
+input1.bam	FBtr0080660	F	17	0
+input1.bam	FBtr0080660	F	18	0
+input1.bam	FBtr0080660	F	19	0
+input1.bam	FBtr0080660	F	20	0
+input1.bam	FBtr0080660	F	21	2
+input1.bam	FBtr0080660	F	22	0
+input1.bam	FBtr0080660	F	23	0
+input1.bam	FBtr0080660	F	24	4
+input1.bam	FBtr0080660	R	16	0
+input1.bam	FBtr0080660	R	17	0
+input1.bam	FBtr0080660	R	18	0
+input1.bam	FBtr0080660	R	19	0
+input1.bam	FBtr0080660	R	20	0
+input1.bam	FBtr0080660	R	21	0
+input1.bam	FBtr0080660	R	22	0
+input1.bam	FBtr0080660	R	23	0
+input1.bam	FBtr0080660	R	24	0
+input1.bam	FBtr0080663	F	15	18
+input1.bam	FBtr0080663	F	16	16
+input1.bam	FBtr0080663	F	17	6
+input1.bam	FBtr0080663	F	18	3
+input1.bam	FBtr0080663	F	19	3
+input1.bam	FBtr0080663	F	20	10
+input1.bam	FBtr0080663	F	21	0
+input1.bam	FBtr0080663	F	22	1
+input1.bam	FBtr0080663	F	23	7
+input1.bam	FBtr0080663	F	24	33
+input1.bam	FBtr0080663	F	25	10
+input1.bam	FBtr0080663	F	26	6
+input1.bam	FBtr0080663	F	27	0
+input1.bam	FBtr0080663	F	28	2
+input1.bam	FBtr0080663	R	15	0
+input1.bam	FBtr0080663	R	16	0
+input1.bam	FBtr0080663	R	17	0
+input1.bam	FBtr0080663	R	18	0
+input1.bam	FBtr0080663	R	19	0
+input1.bam	FBtr0080663	R	20	0
+input1.bam	FBtr0080663	R	21	0
+input1.bam	FBtr0080663	R	22	0
+input1.bam	FBtr0080663	R	23	0
+input1.bam	FBtr0080663	R	24	0
+input1.bam	FBtr0080663	R	25	0
+input1.bam	FBtr0080663	R	26	0
+input1.bam	FBtr0080663	R	27	0
+input1.bam	FBtr0080663	R	28	0
+input1.bam	FBtr0080664	F	15	22
+input1.bam	FBtr0080664	F	16	15
+input1.bam	FBtr0080664	F	17	6
+input1.bam	FBtr0080664	F	18	5
+input1.bam	FBtr0080664	F	19	3
+input1.bam	FBtr0080664	F	20	12
+input1.bam	FBtr0080664	F	21	5
+input1.bam	FBtr0080664	F	22	0
+input1.bam	FBtr0080664	F	23	11
+input1.bam	FBtr0080664	F	24	33
+input1.bam	FBtr0080664	F	25	10
+input1.bam	FBtr0080664	F	26	4
+input1.bam	FBtr0080664	F	27	0
+input1.bam	FBtr0080664	F	28	2
+input1.bam	FBtr0080664	R	15	0
+input1.bam	FBtr0080664	R	16	0
+input1.bam	FBtr0080664	R	17	0
+input1.bam	FBtr0080664	R	18	0
+input1.bam	FBtr0080664	R	19	0
+input1.bam	FBtr0080664	R	20	0
+input1.bam	FBtr0080664	R	21	0
+input1.bam	FBtr0080664	R	22	0
+input1.bam	FBtr0080664	R	23	0
+input1.bam	FBtr0080664	R	24	0
+input1.bam	FBtr0080664	R	25	0
+input1.bam	FBtr0080664	R	26	0
+input1.bam	FBtr0080664	R	27	0
+input1.bam	FBtr0080664	R	28	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input1_yminneg5_5_single_plot_counts.pdf
Binary file test-data/input1_yminneg5_5_single_plot_counts.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input_5_chr.bam
Binary file test-data/input_5_chr.bam has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input_single_chr_x_6_single_plot_coverage.pdf
Binary file test-data/input_single_chr_x_6_single_plot_coverage.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/input_single_chr_x_6_single_plot_coverage.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_single_chr_x_6_single_plot_coverage.tab	Sat Apr 07 06:14:50 2018 -0400
@@ -0,0 +1,481 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Coverage
+input_single_chr.bam_0	1	80	1	F	1
+input_single_chr.bam_0	1	80	2	F	1
+input_single_chr.bam_0	1	80	3	F	1
+input_single_chr.bam_0	1	80	4	F	1
+input_single_chr.bam_0	1	80	5	F	1
+input_single_chr.bam_0	1	80	6	F	1
+input_single_chr.bam_0	1	80	7	F	1
+input_single_chr.bam_0	1	80	8	F	1
+input_single_chr.bam_0	1	80	9	F	1
+input_single_chr.bam_0	1	80	10	F	1
+input_single_chr.bam_0	1	80	11	F	1
+input_single_chr.bam_0	1	80	12	F	1
+input_single_chr.bam_0	1	80	13	F	1
+input_single_chr.bam_0	1	80	14	F	1
+input_single_chr.bam_0	1	80	15	F	1
+input_single_chr.bam_0	1	80	16	F	1
+input_single_chr.bam_0	1	80	17	F	1
+input_single_chr.bam_0	1	80	18	F	1
+input_single_chr.bam_0	1	80	19	F	1
+input_single_chr.bam_0	1	80	20	F	1
+input_single_chr.bam_0	1	80	21	F	1
+input_single_chr.bam_0	1	80	22	F	1
+input_single_chr.bam_0	1	80	23	F	1
+input_single_chr.bam_0	1	80	24	F	1
+input_single_chr.bam_0	1	80	25	F	1
+input_single_chr.bam_0	1	80	26	F	1
+input_single_chr.bam_0	1	80	27	F	1
+input_single_chr.bam_0	1	80	28	F	1
+input_single_chr.bam_0	1	80	29	F	1
+input_single_chr.bam_0	1	80	30	F	1
+input_single_chr.bam_0	1	80	31	F	1
+input_single_chr.bam_0	1	80	32	F	1
+input_single_chr.bam_0	1	80	33	F	1
+input_single_chr.bam_0	1	80	34	F	1
+input_single_chr.bam_0	1	80	35	F	1
+input_single_chr.bam_0	1	80	36	F	1
+input_single_chr.bam_0	1	80	37	F	1
+input_single_chr.bam_0	1	80	38	F	1
+input_single_chr.bam_0	1	80	39	F	1
+input_single_chr.bam_0	1	80	40	F	1
+input_single_chr.bam_0	1	80	41	F	1
+input_single_chr.bam_0	1	80	42	F	1
+input_single_chr.bam_0	1	80	43	F	1
+input_single_chr.bam_0	1	80	44	F	1
+input_single_chr.bam_0	1	80	45	F	1
+input_single_chr.bam_0	1	80	46	F	1
+input_single_chr.bam_0	1	80	47	F	1
+input_single_chr.bam_0	1	80	48	F	1
+input_single_chr.bam_0	1	80	49	F	1
+input_single_chr.bam_0	1	80	50	F	1
+input_single_chr.bam_0	1	80	51	F	1
+input_single_chr.bam_0	1	80	52	F	1
+input_single_chr.bam_0	1	80	53	F	1
+input_single_chr.bam_0	1	80	54	F	1
+input_single_chr.bam_0	1	80	55	F	1
+input_single_chr.bam_0	1	80	56	F	1
+input_single_chr.bam_0	1	80	57	F	1
+input_single_chr.bam_0	1	80	58	F	1
+input_single_chr.bam_0	1	80	59	F	1
+input_single_chr.bam_0	1	80	60	F	1
+input_single_chr.bam_0	1	80	61	F	1
+input_single_chr.bam_0	1	80	62	F	1
+input_single_chr.bam_0	1	80	63	F	1
+input_single_chr.bam_0	1	80	64	F	1
+input_single_chr.bam_0	1	80	65	F	1
+input_single_chr.bam_0	1	80	66	F	1
+input_single_chr.bam_0	1	80	67	F	1
+input_single_chr.bam_0	1	80	68	F	1
+input_single_chr.bam_0	1	80	69	F	1
+input_single_chr.bam_0	1	80	70	F	1
+input_single_chr.bam_0	1	80	71	F	1
+input_single_chr.bam_0	1	80	72	F	1
+input_single_chr.bam_0	1	80	73	F	1
+input_single_chr.bam_0	1	80	74	F	1
+input_single_chr.bam_0	1	80	75	F	1
+input_single_chr.bam_0	1	80	76	F	1
+input_single_chr.bam_0	1	80	77	F	1
+input_single_chr.bam_0	1	80	78	F	1
+input_single_chr.bam_0	1	80	79	F	1
+input_single_chr.bam_0	1	80	80	F	1
+input_single_chr.bam_1	1	80	1	F	1
+input_single_chr.bam_1	1	80	2	F	1
+input_single_chr.bam_1	1	80	3	F	1
+input_single_chr.bam_1	1	80	4	F	1
+input_single_chr.bam_1	1	80	5	F	1
+input_single_chr.bam_1	1	80	6	F	1
+input_single_chr.bam_1	1	80	7	F	1
+input_single_chr.bam_1	1	80	8	F	1
+input_single_chr.bam_1	1	80	9	F	1
+input_single_chr.bam_1	1	80	10	F	1
+input_single_chr.bam_1	1	80	11	F	1
+input_single_chr.bam_1	1	80	12	F	1
+input_single_chr.bam_1	1	80	13	F	1
+input_single_chr.bam_1	1	80	14	F	1
+input_single_chr.bam_1	1	80	15	F	1
+input_single_chr.bam_1	1	80	16	F	1
+input_single_chr.bam_1	1	80	17	F	1
+input_single_chr.bam_1	1	80	18	F	1
+input_single_chr.bam_1	1	80	19	F	1
+input_single_chr.bam_1	1	80	20	F	1
+input_single_chr.bam_1	1	80	21	F	1
+input_single_chr.bam_1	1	80	22	F	1
+input_single_chr.bam_1	1	80	23	F	1
+input_single_chr.bam_1	1	80	24	F	1
+input_single_chr.bam_1	1	80	25	F	1
+input_single_chr.bam_1	1	80	26	F	1
+input_single_chr.bam_1	1	80	27	F	1
+input_single_chr.bam_1	1	80	28	F	1
+input_single_chr.bam_1	1	80	29	F	1
+input_single_chr.bam_1	1	80	30	F	1
+input_single_chr.bam_1	1	80	31	F	1
+input_single_chr.bam_1	1	80	32	F	1
+input_single_chr.bam_1	1	80	33	F	1
+input_single_chr.bam_1	1	80	34	F	1
+input_single_chr.bam_1	1	80	35	F	1
+input_single_chr.bam_1	1	80	36	F	1
+input_single_chr.bam_1	1	80	37	F	1
+input_single_chr.bam_1	1	80	38	F	1
+input_single_chr.bam_1	1	80	39	F	1
+input_single_chr.bam_1	1	80	40	F	1
+input_single_chr.bam_1	1	80	41	F	1
+input_single_chr.bam_1	1	80	42	F	1
+input_single_chr.bam_1	1	80	43	F	1
+input_single_chr.bam_1	1	80	44	F	1
+input_single_chr.bam_1	1	80	45	F	1
+input_single_chr.bam_1	1	80	46	F	1
+input_single_chr.bam_1	1	80	47	F	1
+input_single_chr.bam_1	1	80	48	F	1
+input_single_chr.bam_1	1	80	49	F	1
+input_single_chr.bam_1	1	80	50	F	1
+input_single_chr.bam_1	1	80	51	F	1
+input_single_chr.bam_1	1	80	52	F	1
+input_single_chr.bam_1	1	80	53	F	1
+input_single_chr.bam_1	1	80	54	F	1
+input_single_chr.bam_1	1	80	55	F	1
+input_single_chr.bam_1	1	80	56	F	1
+input_single_chr.bam_1	1	80	57	F	1
+input_single_chr.bam_1	1	80	58	F	1
+input_single_chr.bam_1	1	80	59	F	1
+input_single_chr.bam_1	1	80	60	F	1
+input_single_chr.bam_1	1	80	61	F	1
+input_single_chr.bam_1	1	80	62	F	1
+input_single_chr.bam_1	1	80	63	F	1
+input_single_chr.bam_1	1	80	64	F	1
+input_single_chr.bam_1	1	80	65	F	1
+input_single_chr.bam_1	1	80	66	F	1
+input_single_chr.bam_1	1	80	67	F	1
+input_single_chr.bam_1	1	80	68	F	1
+input_single_chr.bam_1	1	80	69	F	1
+input_single_chr.bam_1	1	80	70	F	1
+input_single_chr.bam_1	1	80	71	F	1
+input_single_chr.bam_1	1	80	72	F	1
+input_single_chr.bam_1	1	80	73	F	1
+input_single_chr.bam_1	1	80	74	F	1
+input_single_chr.bam_1	1	80	75	F	1
+input_single_chr.bam_1	1	80	76	F	1
+input_single_chr.bam_1	1	80	77	F	1
+input_single_chr.bam_1	1	80	78	F	1
+input_single_chr.bam_1	1	80	79	F	1
+input_single_chr.bam_1	1	80	80	F	1
+input_single_chr.bam_2	1	80	1	F	1
+input_single_chr.bam_2	1	80	2	F	1
+input_single_chr.bam_2	1	80	3	F	1
+input_single_chr.bam_2	1	80	4	F	1
+input_single_chr.bam_2	1	80	5	F	1
+input_single_chr.bam_2	1	80	6	F	1
+input_single_chr.bam_2	1	80	7	F	1
+input_single_chr.bam_2	1	80	8	F	1
+input_single_chr.bam_2	1	80	9	F	1
+input_single_chr.bam_2	1	80	10	F	1
+input_single_chr.bam_2	1	80	11	F	1
+input_single_chr.bam_2	1	80	12	F	1
+input_single_chr.bam_2	1	80	13	F	1
+input_single_chr.bam_2	1	80	14	F	1
+input_single_chr.bam_2	1	80	15	F	1
+input_single_chr.bam_2	1	80	16	F	1
+input_single_chr.bam_2	1	80	17	F	1
+input_single_chr.bam_2	1	80	18	F	1
+input_single_chr.bam_2	1	80	19	F	1
+input_single_chr.bam_2	1	80	20	F	1
+input_single_chr.bam_2	1	80	21	F	1
+input_single_chr.bam_2	1	80	22	F	1
+input_single_chr.bam_2	1	80	23	F	1
+input_single_chr.bam_2	1	80	24	F	1
+input_single_chr.bam_2	1	80	25	F	1
+input_single_chr.bam_2	1	80	26	F	1
+input_single_chr.bam_2	1	80	27	F	1
+input_single_chr.bam_2	1	80	28	F	1
+input_single_chr.bam_2	1	80	29	F	1
+input_single_chr.bam_2	1	80	30	F	1
+input_single_chr.bam_2	1	80	31	F	1
+input_single_chr.bam_2	1	80	32	F	1
+input_single_chr.bam_2	1	80	33	F	1
+input_single_chr.bam_2	1	80	34	F	1
+input_single_chr.bam_2	1	80	35	F	1
+input_single_chr.bam_2	1	80	36	F	1
+input_single_chr.bam_2	1	80	37	F	1
+input_single_chr.bam_2	1	80	38	F	1
+input_single_chr.bam_2	1	80	39	F	1
+input_single_chr.bam_2	1	80	40	F	1
+input_single_chr.bam_2	1	80	41	F	1
+input_single_chr.bam_2	1	80	42	F	1
+input_single_chr.bam_2	1	80	43	F	1
+input_single_chr.bam_2	1	80	44	F	1
+input_single_chr.bam_2	1	80	45	F	1
+input_single_chr.bam_2	1	80	46	F	1
+input_single_chr.bam_2	1	80	47	F	1
+input_single_chr.bam_2	1	80	48	F	1
+input_single_chr.bam_2	1	80	49	F	1
+input_single_chr.bam_2	1	80	50	F	1
+input_single_chr.bam_2	1	80	51	F	1
+input_single_chr.bam_2	1	80	52	F	1
+input_single_chr.bam_2	1	80	53	F	1
+input_single_chr.bam_2	1	80	54	F	1
+input_single_chr.bam_2	1	80	55	F	1
+input_single_chr.bam_2	1	80	56	F	1
+input_single_chr.bam_2	1	80	57	F	1
+input_single_chr.bam_2	1	80	58	F	1
+input_single_chr.bam_2	1	80	59	F	1
+input_single_chr.bam_2	1	80	60	F	1
+input_single_chr.bam_2	1	80	61	F	1
+input_single_chr.bam_2	1	80	62	F	1
+input_single_chr.bam_2	1	80	63	F	1
+input_single_chr.bam_2	1	80	64	F	1
+input_single_chr.bam_2	1	80	65	F	1
+input_single_chr.bam_2	1	80	66	F	1
+input_single_chr.bam_2	1	80	67	F	1
+input_single_chr.bam_2	1	80	68	F	1
+input_single_chr.bam_2	1	80	69	F	1
+input_single_chr.bam_2	1	80	70	F	1
+input_single_chr.bam_2	1	80	71	F	1
+input_single_chr.bam_2	1	80	72	F	1
+input_single_chr.bam_2	1	80	73	F	1
+input_single_chr.bam_2	1	80	74	F	1
+input_single_chr.bam_2	1	80	75	F	1
+input_single_chr.bam_2	1	80	76	F	1
+input_single_chr.bam_2	1	80	77	F	1
+input_single_chr.bam_2	1	80	78	F	1
+input_single_chr.bam_2	1	80	79	F	1
+input_single_chr.bam_2	1	80	80	F	1
+input_single_chr.bam_3	1	80	1	F	1
+input_single_chr.bam_3	1	80	2	F	1
+input_single_chr.bam_3	1	80	3	F	1
+input_single_chr.bam_3	1	80	4	F	1
+input_single_chr.bam_3	1	80	5	F	1
+input_single_chr.bam_3	1	80	6	F	1
+input_single_chr.bam_3	1	80	7	F	1
+input_single_chr.bam_3	1	80	8	F	1
+input_single_chr.bam_3	1	80	9	F	1
+input_single_chr.bam_3	1	80	10	F	1
+input_single_chr.bam_3	1	80	11	F	1
+input_single_chr.bam_3	1	80	12	F	1
+input_single_chr.bam_3	1	80	13	F	1
+input_single_chr.bam_3	1	80	14	F	1
+input_single_chr.bam_3	1	80	15	F	1
+input_single_chr.bam_3	1	80	16	F	1
+input_single_chr.bam_3	1	80	17	F	1
+input_single_chr.bam_3	1	80	18	F	1
+input_single_chr.bam_3	1	80	19	F	1
+input_single_chr.bam_3	1	80	20	F	1
+input_single_chr.bam_3	1	80	21	F	1
+input_single_chr.bam_3	1	80	22	F	1
+input_single_chr.bam_3	1	80	23	F	1
+input_single_chr.bam_3	1	80	24	F	1
+input_single_chr.bam_3	1	80	25	F	1
+input_single_chr.bam_3	1	80	26	F	1
+input_single_chr.bam_3	1	80	27	F	1
+input_single_chr.bam_3	1	80	28	F	1
+input_single_chr.bam_3	1	80	29	F	1
+input_single_chr.bam_3	1	80	30	F	1
+input_single_chr.bam_3	1	80	31	F	1
+input_single_chr.bam_3	1	80	32	F	1
+input_single_chr.bam_3	1	80	33	F	1
+input_single_chr.bam_3	1	80	34	F	1
+input_single_chr.bam_3	1	80	35	F	1
+input_single_chr.bam_3	1	80	36	F	1
+input_single_chr.bam_3	1	80	37	F	1
+input_single_chr.bam_3	1	80	38	F	1
+input_single_chr.bam_3	1	80	39	F	1
+input_single_chr.bam_3	1	80	40	F	1
+input_single_chr.bam_3	1	80	41	F	1
+input_single_chr.bam_3	1	80	42	F	1
+input_single_chr.bam_3	1	80	43	F	1
+input_single_chr.bam_3	1	80	44	F	1
+input_single_chr.bam_3	1	80	45	F	1
+input_single_chr.bam_3	1	80	46	F	1
+input_single_chr.bam_3	1	80	47	F	1
+input_single_chr.bam_3	1	80	48	F	1
+input_single_chr.bam_3	1	80	49	F	1
+input_single_chr.bam_3	1	80	50	F	1
+input_single_chr.bam_3	1	80	51	F	1
+input_single_chr.bam_3	1	80	52	F	1
+input_single_chr.bam_3	1	80	53	F	1
+input_single_chr.bam_3	1	80	54	F	1
+input_single_chr.bam_3	1	80	55	F	1
+input_single_chr.bam_3	1	80	56	F	1
+input_single_chr.bam_3	1	80	57	F	1
+input_single_chr.bam_3	1	80	58	F	1
+input_single_chr.bam_3	1	80	59	F	1
+input_single_chr.bam_3	1	80	60	F	1
+input_single_chr.bam_3	1	80	61	F	1
+input_single_chr.bam_3	1	80	62	F	1
+input_single_chr.bam_3	1	80	63	F	1
+input_single_chr.bam_3	1	80	64	F	1
+input_single_chr.bam_3	1	80	65	F	1
+input_single_chr.bam_3	1	80	66	F	1
+input_single_chr.bam_3	1	80	67	F	1
+input_single_chr.bam_3	1	80	68	F	1
+input_single_chr.bam_3	1	80	69	F	1
+input_single_chr.bam_3	1	80	70	F	1
+input_single_chr.bam_3	1	80	71	F	1
+input_single_chr.bam_3	1	80	72	F	1
+input_single_chr.bam_3	1	80	73	F	1
+input_single_chr.bam_3	1	80	74	F	1
+input_single_chr.bam_3	1	80	75	F	1
+input_single_chr.bam_3	1	80	76	F	1
+input_single_chr.bam_3	1	80	77	F	1
+input_single_chr.bam_3	1	80	78	F	1
+input_single_chr.bam_3	1	80	79	F	1
+input_single_chr.bam_3	1	80	80	F	1
+input_single_chr.bam_4	1	80	1	F	1
+input_single_chr.bam_4	1	80	2	F	1
+input_single_chr.bam_4	1	80	3	F	1
+input_single_chr.bam_4	1	80	4	F	1
+input_single_chr.bam_4	1	80	5	F	1
+input_single_chr.bam_4	1	80	6	F	1
+input_single_chr.bam_4	1	80	7	F	1
+input_single_chr.bam_4	1	80	8	F	1
+input_single_chr.bam_4	1	80	9	F	1
+input_single_chr.bam_4	1	80	10	F	1
+input_single_chr.bam_4	1	80	11	F	1
+input_single_chr.bam_4	1	80	12	F	1
+input_single_chr.bam_4	1	80	13	F	1
+input_single_chr.bam_4	1	80	14	F	1
+input_single_chr.bam_4	1	80	15	F	1
+input_single_chr.bam_4	1	80	16	F	1
+input_single_chr.bam_4	1	80	17	F	1
+input_single_chr.bam_4	1	80	18	F	1
+input_single_chr.bam_4	1	80	19	F	1
+input_single_chr.bam_4	1	80	20	F	1
+input_single_chr.bam_4	1	80	21	F	1
+input_single_chr.bam_4	1	80	22	F	1
+input_single_chr.bam_4	1	80	23	F	1
+input_single_chr.bam_4	1	80	24	F	1
+input_single_chr.bam_4	1	80	25	F	1
+input_single_chr.bam_4	1	80	26	F	1
+input_single_chr.bam_4	1	80	27	F	1
+input_single_chr.bam_4	1	80	28	F	1
+input_single_chr.bam_4	1	80	29	F	1
+input_single_chr.bam_4	1	80	30	F	1
+input_single_chr.bam_4	1	80	31	F	1
+input_single_chr.bam_4	1	80	32	F	1
+input_single_chr.bam_4	1	80	33	F	1
+input_single_chr.bam_4	1	80	34	F	1
+input_single_chr.bam_4	1	80	35	F	1
+input_single_chr.bam_4	1	80	36	F	1
+input_single_chr.bam_4	1	80	37	F	1
+input_single_chr.bam_4	1	80	38	F	1
+input_single_chr.bam_4	1	80	39	F	1
+input_single_chr.bam_4	1	80	40	F	1
+input_single_chr.bam_4	1	80	41	F	1
+input_single_chr.bam_4	1	80	42	F	1
+input_single_chr.bam_4	1	80	43	F	1
+input_single_chr.bam_4	1	80	44	F	1
+input_single_chr.bam_4	1	80	45	F	1
+input_single_chr.bam_4	1	80	46	F	1
+input_single_chr.bam_4	1	80	47	F	1
+input_single_chr.bam_4	1	80	48	F	1
+input_single_chr.bam_4	1	80	49	F	1
+input_single_chr.bam_4	1	80	50	F	1
+input_single_chr.bam_4	1	80	51	F	1
+input_single_chr.bam_4	1	80	52	F	1
+input_single_chr.bam_4	1	80	53	F	1
+input_single_chr.bam_4	1	80	54	F	1
+input_single_chr.bam_4	1	80	55	F	1
+input_single_chr.bam_4	1	80	56	F	1
+input_single_chr.bam_4	1	80	57	F	1
+input_single_chr.bam_4	1	80	58	F	1
+input_single_chr.bam_4	1	80	59	F	1
+input_single_chr.bam_4	1	80	60	F	1
+input_single_chr.bam_4	1	80	61	F	1
+input_single_chr.bam_4	1	80	62	F	1
+input_single_chr.bam_4	1	80	63	F	1
+input_single_chr.bam_4	1	80	64	F	1
+input_single_chr.bam_4	1	80	65	F	1
+input_single_chr.bam_4	1	80	66	F	1
+input_single_chr.bam_4	1	80	67	F	1
+input_single_chr.bam_4	1	80	68	F	1
+input_single_chr.bam_4	1	80	69	F	1
+input_single_chr.bam_4	1	80	70	F	1
+input_single_chr.bam_4	1	80	71	F	1
+input_single_chr.bam_4	1	80	72	F	1
+input_single_chr.bam_4	1	80	73	F	1
+input_single_chr.bam_4	1	80	74	F	1
+input_single_chr.bam_4	1	80	75	F	1
+input_single_chr.bam_4	1	80	76	F	1
+input_single_chr.bam_4	1	80	77	F	1
+input_single_chr.bam_4	1	80	78	F	1
+input_single_chr.bam_4	1	80	79	F	1
+input_single_chr.bam_4	1	80	80	F	1
+input_single_chr.bam_5	1	80	1	F	1
+input_single_chr.bam_5	1	80	2	F	1
+input_single_chr.bam_5	1	80	3	F	1
+input_single_chr.bam_5	1	80	4	F	1
+input_single_chr.bam_5	1	80	5	F	1
+input_single_chr.bam_5	1	80	6	F	1
+input_single_chr.bam_5	1	80	7	F	1
+input_single_chr.bam_5	1	80	8	F	1
+input_single_chr.bam_5	1	80	9	F	1
+input_single_chr.bam_5	1	80	10	F	1
+input_single_chr.bam_5	1	80	11	F	1
+input_single_chr.bam_5	1	80	12	F	1
+input_single_chr.bam_5	1	80	13	F	1
+input_single_chr.bam_5	1	80	14	F	1
+input_single_chr.bam_5	1	80	15	F	1
+input_single_chr.bam_5	1	80	16	F	1
+input_single_chr.bam_5	1	80	17	F	1
+input_single_chr.bam_5	1	80	18	F	1
+input_single_chr.bam_5	1	80	19	F	1
+input_single_chr.bam_5	1	80	20	F	1
+input_single_chr.bam_5	1	80	21	F	1
+input_single_chr.bam_5	1	80	22	F	1
+input_single_chr.bam_5	1	80	23	F	1
+input_single_chr.bam_5	1	80	24	F	1
+input_single_chr.bam_5	1	80	25	F	1
+input_single_chr.bam_5	1	80	26	F	1
+input_single_chr.bam_5	1	80	27	F	1
+input_single_chr.bam_5	1	80	28	F	1
+input_single_chr.bam_5	1	80	29	F	1
+input_single_chr.bam_5	1	80	30	F	1
+input_single_chr.bam_5	1	80	31	F	1
+input_single_chr.bam_5	1	80	32	F	1
+input_single_chr.bam_5	1	80	33	F	1
+input_single_chr.bam_5	1	80	34	F	1
+input_single_chr.bam_5	1	80	35	F	1
+input_single_chr.bam_5	1	80	36	F	1
+input_single_chr.bam_5	1	80	37	F	1
+input_single_chr.bam_5	1	80	38	F	1
+input_single_chr.bam_5	1	80	39	F	1
+input_single_chr.bam_5	1	80	40	F	1
+input_single_chr.bam_5	1	80	41	F	1
+input_single_chr.bam_5	1	80	42	F	1
+input_single_chr.bam_5	1	80	43	F	1
+input_single_chr.bam_5	1	80	44	F	1
+input_single_chr.bam_5	1	80	45	F	1
+input_single_chr.bam_5	1	80	46	F	1
+input_single_chr.bam_5	1	80	47	F	1
+input_single_chr.bam_5	1	80	48	F	1
+input_single_chr.bam_5	1	80	49	F	1
+input_single_chr.bam_5	1	80	50	F	1
+input_single_chr.bam_5	1	80	51	F	1
+input_single_chr.bam_5	1	80	52	F	1
+input_single_chr.bam_5	1	80	53	F	1
+input_single_chr.bam_5	1	80	54	F	1
+input_single_chr.bam_5	1	80	55	F	1
+input_single_chr.bam_5	1	80	56	F	1
+input_single_chr.bam_5	1	80	57	F	1
+input_single_chr.bam_5	1	80	58	F	1
+input_single_chr.bam_5	1	80	59	F	1
+input_single_chr.bam_5	1	80	60	F	1
+input_single_chr.bam_5	1	80	61	F	1
+input_single_chr.bam_5	1	80	62	F	1
+input_single_chr.bam_5	1	80	63	F	1
+input_single_chr.bam_5	1	80	64	F	1
+input_single_chr.bam_5	1	80	65	F	1
+input_single_chr.bam_5	1	80	66	F	1
+input_single_chr.bam_5	1	80	67	F	1
+input_single_chr.bam_5	1	80	68	F	1
+input_single_chr.bam_5	1	80	69	F	1
+input_single_chr.bam_5	1	80	70	F	1
+input_single_chr.bam_5	1	80	71	F	1
+input_single_chr.bam_5	1	80	72	F	1
+input_single_chr.bam_5	1	80	73	F	1
+input_single_chr.bam_5	1	80	74	F	1
+input_single_chr.bam_5	1	80	75	F	1
+input_single_chr.bam_5	1	80	76	F	1
+input_single_chr.bam_5	1	80	77	F	1
+input_single_chr.bam_5	1	80	78	F	1
+input_single_chr.bam_5	1	80	79	F	1
+input_single_chr.bam_5	1	80	80	F	1
diff -r a561a71bd7d7 -r d33263e6e812 test-data/mean.tab
--- a/test-data/mean.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	20.3
-input1.bam	FBtr0070001	72	8	F	21.3
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	16	F	19.0
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
-input1.bam	FBtr0070533	72	19	F	21.8
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	20.5
-input1.bam	FBtr0070533	72	35	F	19.0
-input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.1
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
-input1.bam	FBtr0070603	72	17	F	24.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	22.6
-input1.bam	FBtr0070603	72	20	F	21.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	20.7
-input1.bam	FBtr0070603	72	24	F	19.5
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	25.8
-input1.bam	FBtr0070603	72	27	F	26.3
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	19.3
-input1.bam	FBtr0070603	72	38	F	18.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
-input1.bam	FBtr0070604	72	31	F	22.6
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	18.9
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.3
-input1.bam	FBtr0078580	72	5	F	21.0
-input1.bam	FBtr0078580	72	6	F	19.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	18.0
-input1.bam	FBtr0078580	72	14	F	15.3
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	19.4
-input1.bam	FBtr0078580	72	24	F	17.0
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
-input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
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-input2.bam	FBtr0079596	73	2	F	16.0
-input2.bam	FBtr0079596	73	3	F	17.9
-input2.bam	FBtr0079596	73	4	F	19.0
-input2.bam	FBtr0079596	73	5	F	20.0
-input2.bam	FBtr0079596	73	6	F	19.0
-input2.bam	FBtr0079596	73	8	F	17.0
-input2.bam	FBtr0079596	73	9	F	20.0
-input2.bam	FBtr0079596	73	11	F	22.0
-input2.bam	FBtr0079596	73	12	F	20.9
-input2.bam	FBtr0079596	73	13	F	19.9
-input2.bam	FBtr0079596	73	14	F	19.0
-input2.bam	FBtr0079596	73	15	F	18.1
-input2.bam	FBtr0079596	73	16	F	17.1
-input2.bam	FBtr0079596	73	17	F	16.1
-input2.bam	FBtr0079596	73	18	F	15.1
-input2.bam	FBtr0079596	73	19	F	15.0
-input2.bam	FBtr0079596	73	22	F	19.5
-input2.bam	FBtr0079596	73	42	F	19.0
-input2.bam	FBtr0079596	73	53	F	18.7
-input2.bam	FBtr0079596	73	59	R	21.0
-input2.bam	FBtr0079596	73	73	F	0
-input2.bam	FBtr0079677	72	1	F	15.0
-input2.bam	FBtr0079677	72	15	F	20.0
-input2.bam	FBtr0079677	72	24	F	17.0
-input2.bam	FBtr0079677	72	43	F	19.0
-input2.bam	FBtr0079677	72	52	F	17.0
-input2.bam	FBtr0079677	72	54	F	16.0
-input2.bam	FBtr0079677	72	72	F	0
-input2.bam	FBtr0079690	72	1	F	15.0
-input2.bam	FBtr0079690	72	15	F	20.0
-input2.bam	FBtr0079690	72	17	F	20.0
-input2.bam	FBtr0079690	72	19	F	21.0
-input2.bam	FBtr0079690	72	21	F	16.0
-input2.bam	FBtr0079690	72	72	F	0
-input2.bam	FBtr0079692	73	1	F	0
-input2.bam	FBtr0079692	73	4	F	18.0
-input2.bam	FBtr0079692	73	7	F	15.0
-input2.bam	FBtr0079692	73	12	F	22.0
-input2.bam	FBtr0079692	73	15	F	21.0
-input2.bam	FBtr0079692	73	73	F	0
-input2.bam	FBtr0079693	72	1	F	15.0
-input2.bam	FBtr0079693	72	17	F	19.0
-input2.bam	FBtr0079693	72	20	F	15.0
-input2.bam	FBtr0079693	72	45	F	16.0
-input2.bam	FBtr0079693	72	52	F	20.0
-input2.bam	FBtr0079693	72	54	F	16.0
-input2.bam	FBtr0079693	72	72	F	0
-input2.bam	FBtr0079694	72	1	F	15.0
-input2.bam	FBtr0079694	72	16	F	19.0
-input2.bam	FBtr0079694	72	17	F	18.0
-input2.bam	FBtr0079694	72	18	F	17.0
-input2.bam	FBtr0079694	72	52	F	18.0
-input2.bam	FBtr0079694	72	72	F	0
-input2.bam	FBtr0079702	72	1	F	15.0
-input2.bam	FBtr0079702	72	52	F	17.5
-input2.bam	FBtr0079702	72	72	F	0
-input2.bam	FBtr0079728	72	1	F	15.0
-input2.bam	FBtr0079728	72	20	F	16.0
-input2.bam	FBtr0079728	72	52	F	17.5
-input2.bam	FBtr0079728	72	72	F	0
-input2.bam	FBtr0079729	72	1	F	15.0
-input2.bam	FBtr0079729	72	19	F	16.0
-input2.bam	FBtr0079729	72	33	F	17.0
-input2.bam	FBtr0079729	72	53	F	16.0
-input2.bam	FBtr0079729	72	72	F	0
-input2.bam	FBtr0079752	72	1	F	0
-input2.bam	FBtr0079752	72	49	F	24.0
-input2.bam	FBtr0079752	72	52	F	17.0
-input2.bam	FBtr0079752	72	72	F	0
-input2.bam	FBtr0079820	74	1	F	0
-input2.bam	FBtr0079820	74	39	F	16.0
-input2.bam	FBtr0079820	74	52	F	21.0
-input2.bam	FBtr0079820	74	53	F	20.0
-input2.bam	FBtr0079820	74	54	F	19.3
-input2.bam	FBtr0079820	74	55	F	18.6
-input2.bam	FBtr0079820	74	56	F	16.5
-input2.bam	FBtr0079820	74	57	F	16.8
-input2.bam	FBtr0079820	74	58	F	16.0
-input2.bam	FBtr0079820	74	59	F	15.5
-input2.bam	FBtr0079820	74	60	F	15.0
-input2.bam	FBtr0079820	74	74	F	0
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	20	F	19.0
-input2.bam	FBtr0080609	72	21	F	21.0
-input2.bam	FBtr0080609	72	22	F	23.0
-input2.bam	FBtr0080609	72	33	F	22.0
-input2.bam	FBtr0080609	72	39	F	17.0
-input2.bam	FBtr0080609	72	52	F	18.0
-input2.bam	FBtr0080609	72	53	F	19.0
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	57	F	15.0
-input2.bam	FBtr0080644	72	58	F	15.0
-input2.bam	FBtr0080644	72	72	F	0
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	21.0
-input2.bam	FBtr0080646	72	57	F	15.5
-input2.bam	FBtr0080646	72	58	F	15.0
-input2.bam	FBtr0080646	72	72	F	0
-input2.bam	FBtr0080647	72	1	F	18.0
-input2.bam	FBtr0080647	72	57	F	15.5
-input2.bam	FBtr0080647	72	58	F	15.0
-input2.bam	FBtr0080647	72	72	F	0
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	15.0
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	22.0
-input2.bam	FBtr0080663	71	11	F	21.0
-input2.bam	FBtr0080663	71	12	F	20.5
-input2.bam	FBtr0080663	71	13	F	19.8
-input2.bam	FBtr0080663	71	14	F	18.6
-input2.bam	FBtr0080663	71	15	F	17.9
-input2.bam	FBtr0080663	71	16	F	17.0
-input2.bam	FBtr0080663	71	17	F	16.0
-input2.bam	FBtr0080663	71	18	F	18.2
-input2.bam	FBtr0080663	71	19	F	17.7
-input2.bam	FBtr0080663	71	20	F	16.7
-input2.bam	FBtr0080663	71	21	F	15.5
-input2.bam	FBtr0080663	71	22	F	15.3
-input2.bam	FBtr0080663	71	31	F	17.0
-input2.bam	FBtr0080663	71	50	F	15.5
-input2.bam	FBtr0080663	71	51	F	19.0
-input2.bam	FBtr0080663	71	52	F	15.0
-input2.bam	FBtr0080663	71	57	F	15.0
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	22.0
-input2.bam	FBtr0080664	71	3	F	23.0
-input2.bam	FBtr0080664	71	10	F	23.0
-input2.bam	FBtr0080664	71	11	F	22.0
-input2.bam	FBtr0080664	71	12	F	21.0
-input2.bam	FBtr0080664	71	13	F	19.7
-input2.bam	FBtr0080664	71	14	F	18.3
-input2.bam	FBtr0080664	71	15	F	18.1
-input2.bam	FBtr0080664	71	16	F	17.3
-input2.bam	FBtr0080664	71	17	F	15.8
-input2.bam	FBtr0080664	71	18	F	18.9
-input2.bam	FBtr0080664	71	19	F	19.0
-input2.bam	FBtr0080664	71	20	F	16.0
-input2.bam	FBtr0080664	71	21	F	15.3
-input2.bam	FBtr0080664	71	22	F	16.2
-input2.bam	FBtr0080664	71	24	F	15.0
-input2.bam	FBtr0080664	71	30	F	21.0
-input2.bam	FBtr0080664	71	31	F	18.7
-input2.bam	FBtr0080664	71	32	F	18.3
-input2.bam	FBtr0080664	71	33	F	17.5
-input2.bam	FBtr0080664	71	34	F	16.1
-input2.bam	FBtr0080664	71	35	F	15.2
-input2.bam	FBtr0080664	71	36	F	19.9
-input2.bam	FBtr0080664	71	37	F	17.7
-input2.bam	FBtr0080664	71	38	F	18.1
-input2.bam	FBtr0080664	71	39	F	17.0
-input2.bam	FBtr0080664	71	42	F	20.0
-input2.bam	FBtr0080664	71	47	F	15.0
-input2.bam	FBtr0080664	71	50	F	15.5
-input2.bam	FBtr0080664	71	52	F	16.0
-input2.bam	FBtr0080664	71	53	F	19.0
-input2.bam	FBtr0080664	71	56	F	16.0
-input2.bam	FBtr0080664	71	57	F	15.0
-input2.bam	FBtr0080664	71	62	R	23.0
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	22.0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/mean20-30.tab
--- a/test-data/mean20-30.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,350 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Mean
-input2.bam	FBtr0070001	72	1	F	0
-input2.bam	FBtr0070001	72	13	F	22.0
-input2.bam	FBtr0070001	72	19	F	23.0
-input2.bam	FBtr0070001	72	28	F	23.0
-input2.bam	FBtr0070001	72	32	F	22.0
-input2.bam	FBtr0070001	72	53	F	20.0
-input2.bam	FBtr0070001	72	72	F	0
-input2.bam	FBtr0070533	72	1	F	0
-input2.bam	FBtr0070533	72	16	F	22.0
-input2.bam	FBtr0070533	72	19	F	22.0
-input2.bam	FBtr0070533	72	20	F	21.0
-input2.bam	FBtr0070533	72	21	F	20.0
-input2.bam	FBtr0070533	72	22	F	20.0
-input2.bam	FBtr0070533	72	72	F	0
-input2.bam	FBtr0070603	72	1	F	0
-input2.bam	FBtr0070603	72	17	F	21.5
-input2.bam	FBtr0070603	72	19	F	23.0
-input2.bam	FBtr0070603	72	20	F	21.0
-input2.bam	FBtr0070603	72	22	F	20.1
-input2.bam	FBtr0070603	72	27	F	23.0
-input2.bam	FBtr0070603	72	28	F	24.0
-input2.bam	FBtr0070603	72	30	F	20.0
-input2.bam	FBtr0070603	72	31	F	20.0
-input2.bam	FBtr0070603	72	34	F	21.0
-input2.bam	FBtr0070603	72	35	F	21.0
-input2.bam	FBtr0070603	72	37	F	20.0
-input2.bam	FBtr0070603	72	41	F	22.0
-input2.bam	FBtr0070603	72	51	F	20.0
-input2.bam	FBtr0070603	72	72	F	0
-input2.bam	FBtr0070604	72	1	F	0
-input2.bam	FBtr0070604	72	31	F	23.0
-input2.bam	FBtr0070604	72	32	F	21.8
-input2.bam	FBtr0070604	72	53	F	20.0
-input2.bam	FBtr0070604	72	72	F	0
-input2.bam	FBtr0070911	73	1	F	0
-input2.bam	FBtr0070911	73	32	F	23.0
-input2.bam	FBtr0070911	73	73	F	0
-input2.bam	FBtr0078490	72	1	F	22.7
-input2.bam	FBtr0078490	72	13	F	20.0
-input2.bam	FBtr0078490	72	20	F	20.0
-input2.bam	FBtr0078490	72	30	F	21.0
-input2.bam	FBtr0078490	72	72	F	0
-input2.bam	FBtr0078580	72	1	F	24.3
-input2.bam	FBtr0078580	72	11	F	23.0
-input2.bam	FBtr0078580	72	13	F	23.0
-input2.bam	FBtr0078580	72	15	F	22.5
-input2.bam	FBtr0078580	72	16	F	23.3
-input2.bam	FBtr0078580	72	17	F	23.0
-input2.bam	FBtr0078580	72	18	F	22.8
-input2.bam	FBtr0078580	72	19	F	21.7
-input2.bam	FBtr0078580	72	20	F	21.3
-input2.bam	FBtr0078580	72	21	F	20.4
-input2.bam	FBtr0078580	72	25	F	26.0
-input2.bam	FBtr0078580	72	26	F	25.0
-input2.bam	FBtr0078580	72	28	F	21.5
-input2.bam	FBtr0078580	72	29	F	23.0
-input2.bam	FBtr0078580	72	40	F	20.0
-input2.bam	FBtr0078580	72	72	F	0
-input2.bam	FBtr0078790	73	1	F	0
-input2.bam	FBtr0078790	73	42	F	20.0
-input2.bam	FBtr0078790	73	51	F	22.0
-input2.bam	FBtr0078790	73	52	F	21.0
-input2.bam	FBtr0078790	73	73	F	0
-input2.bam	FBtr0079064	72	1	F	0
-input2.bam	FBtr0079064	72	72	F	0
-input2.bam	FBtr0079090	72	1	F	0
-input2.bam	FBtr0079090	72	16	F	21.0
-input2.bam	FBtr0079090	72	72	F	0
-input2.bam	FBtr0079338	73	1	F	0
-input2.bam	FBtr0079338	73	41	F	22.5
-input2.bam	FBtr0079338	73	42	F	20.0
-input2.bam	FBtr0079338	73	73	F	0
-input2.bam	FBtr0079528	71	1	F	0
-input2.bam	FBtr0079528	71	3	F	24.0
-input2.bam	FBtr0079528	71	10	F	22.5
-input2.bam	FBtr0079528	71	11	F	21.0
-input2.bam	FBtr0079528	71	13	F	20.0
-input2.bam	FBtr0079528	71	14	F	21.5
-input2.bam	FBtr0079528	71	15	F	22.0
-input2.bam	FBtr0079528	71	18	F	21.3
-input2.bam	FBtr0079528	71	19	F	23.0
-input2.bam	FBtr0079528	71	30	F	23.0
-input2.bam	FBtr0079528	71	31	F	22.0
-input2.bam	FBtr0079528	71	32	F	20.6
-input2.bam	FBtr0079528	71	36	F	23.0
-input2.bam	FBtr0079528	71	37	F	26.0
-input2.bam	FBtr0079528	71	38	F	22.3
-input2.bam	FBtr0079528	71	71	F	0
-input2.bam	FBtr0079596	73	1	F	0
-input2.bam	FBtr0079596	73	3	F	22.3
-input2.bam	FBtr0079596	73	4	F	20.0
-input2.bam	FBtr0079596	73	5	F	20.0
-input2.bam	FBtr0079596	73	9	F	24.0
-input2.bam	FBtr0079596	73	11	F	22.0
-input2.bam	FBtr0079596	73	12	F	21.2
-input2.bam	FBtr0079596	73	13	F	20.2
-input2.bam	FBtr0079596	73	14	F	20.0
-input2.bam	FBtr0079596	73	22	F	20.0
-input2.bam	FBtr0079596	73	53	F	20.0
-input2.bam	FBtr0079596	73	59	R	21.0
-input2.bam	FBtr0079596	73	73	F	0
-input2.bam	FBtr0079677	72	1	F	0
-input2.bam	FBtr0079677	72	15	F	20.0
-input2.bam	FBtr0079677	72	72	F	0
-input2.bam	FBtr0079690	72	1	F	0
-input2.bam	FBtr0079690	72	15	F	20.0
-input2.bam	FBtr0079690	72	17	F	20.0
-input2.bam	FBtr0079690	72	19	F	21.0
-input2.bam	FBtr0079690	72	72	F	0
-input2.bam	FBtr0079692	73	1	F	0
-input2.bam	FBtr0079692	73	12	F	22.0
-input2.bam	FBtr0079692	73	15	F	21.0
-input2.bam	FBtr0079692	73	73	F	0
-input2.bam	FBtr0079693	72	1	F	0
-input2.bam	FBtr0079693	72	17	F	20.0
-input2.bam	FBtr0079693	72	52	F	20.0
-input2.bam	FBtr0079693	72	72	F	0
-input2.bam	FBtr0079694	72	1	F	0
-input2.bam	FBtr0079694	72	72	F	0
-input2.bam	FBtr0079702	72	1	F	0
-input2.bam	FBtr0079702	72	72	F	0
-input2.bam	FBtr0079728	72	1	F	0
-input2.bam	FBtr0079728	72	72	F	0
-input2.bam	FBtr0079729	72	1	F	0
-input2.bam	FBtr0079729	72	72	F	0
-input2.bam	FBtr0079752	72	1	F	0
-input2.bam	FBtr0079752	72	49	F	24.0
-input2.bam	FBtr0079752	72	72	F	0
-input2.bam	FBtr0079820	74	1	F	0
-input2.bam	FBtr0079820	74	52	F	21.0
-input2.bam	FBtr0079820	74	53	F	20.3
-input2.bam	FBtr0079820	74	54	F	20.2
-input2.bam	FBtr0079820	74	55	F	20.0
-input2.bam	FBtr0079820	74	74	F	0
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	21	F	25.0
-input2.bam	FBtr0080609	72	22	F	23.0
-input2.bam	FBtr0080609	72	33	F	22.0
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	72	F	0
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	21.0
-input2.bam	FBtr0080646	72	72	F	0
-input2.bam	FBtr0080647	72	1	F	0
-input2.bam	FBtr0080647	72	72	F	0
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	22.0
-input2.bam	FBtr0080663	71	11	F	21.0
-input2.bam	FBtr0080663	71	12	F	20.5
-input2.bam	FBtr0080663	71	13	F	20.0
-input2.bam	FBtr0080663	71	14	F	22.0
-input2.bam	FBtr0080663	71	15	F	22.0
-input2.bam	FBtr0080663	71	16	F	20.0
-input2.bam	FBtr0080663	71	18	F	24.0
-input2.bam	FBtr0080663	71	19	F	21.0
-input2.bam	FBtr0080663	71	21	F	20.0
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	22.0
-input2.bam	FBtr0080664	71	3	F	23.0
-input2.bam	FBtr0080664	71	10	F	23.0
-input2.bam	FBtr0080664	71	11	F	22.0
-input2.bam	FBtr0080664	71	12	F	21.0
-input2.bam	FBtr0080664	71	13	F	20.4
-input2.bam	FBtr0080664	71	15	F	21.5
-input2.bam	FBtr0080664	71	16	F	20.0
-input2.bam	FBtr0080664	71	18	F	20.3
-input2.bam	FBtr0080664	71	19	F	21.0
-input2.bam	FBtr0080664	71	30	F	21.0
-input2.bam	FBtr0080664	71	32	F	20.7
-input2.bam	FBtr0080664	71	33	F	20.0
-input2.bam	FBtr0080664	71	36	F	24.3
-input2.bam	FBtr0080664	71	37	F	24.5
-input2.bam	FBtr0080664	71	38	F	25.0
-input2.bam	FBtr0080664	71	42	F	20.0
-input2.bam	FBtr0080664	71	62	R	23.0
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	22.0
-input1.bam	FBtr0070001	72	1	F	0
-input1.bam	FBtr0070001	72	7	F	21.2
-input1.bam	FBtr0070001	72	8	F	21.3
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	0
-input1.bam	FBtr0070533	72	19	F	21.8
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	21.3
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	0
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	12	F	23.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	20.0
-input1.bam	FBtr0070603	72	16	F	24.0
-input1.bam	FBtr0070603	72	17	F	24.0
-input1.bam	FBtr0070603	72	19	F	23.3
-input1.bam	FBtr0070603	72	20	F	24.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	21.5
-input1.bam	FBtr0070603	72	24	F	21.0
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	25.8
-input1.bam	FBtr0070603	72	27	F	26.3
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	20.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	31	F	23.0
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	28	F	23.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	24.6
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.3
-input1.bam	FBtr0078580	72	5	F	21.5
-input1.bam	FBtr0078580	72	6	F	21.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	22.5
-input1.bam	FBtr0078580	72	16	F	23.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	20.3
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	22.0
-input1.bam	FBtr0078790	73	44	F	20.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	0
-input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	28.0
-input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	56	R	21.0
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	42	F	21.8
-input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	25.3
-input1.bam	FBtr0079528	71	3	F	23.7
-input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	22.0
-input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	22.0
-input1.bam	FBtr0079528	71	18	F	20.3
-input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	0
-input1.bam	FBtr0079596	73	3	F	23.1
-input1.bam	FBtr0079596	73	4	F	21.6
-input1.bam	FBtr0079596	73	13	F	21.0
-input1.bam	FBtr0079596	73	53	F	20.0
-input1.bam	FBtr0079596	73	54	F	20.0
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	23.0
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	0
-input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	23.0
-input1.bam	FBtr0079692	73	32	F	20.0
-input1.bam	FBtr0079692	73	73	F	0
-input1.bam	FBtr0079693	72	1	F	24.0
-input1.bam	FBtr0079693	72	25	F	23.0
-input1.bam	FBtr0079693	72	72	F	0
-input1.bam	FBtr0079694	72	1	F	24.0
-input1.bam	FBtr0079694	72	72	F	0
-input1.bam	FBtr0079702	72	1	F	0
-input1.bam	FBtr0079702	72	72	F	0
-input1.bam	FBtr0079728	72	1	F	0
-input1.bam	FBtr0079728	72	8	F	20.0
-input1.bam	FBtr0079728	72	19	F	24.0
-input1.bam	FBtr0079728	72	72	F	0
-input1.bam	FBtr0079729	72	1	F	0
-input1.bam	FBtr0079729	72	13	F	22.0
-input1.bam	FBtr0079729	72	72	F	0
-input1.bam	FBtr0079752	72	1	F	24.0
-input1.bam	FBtr0079752	72	7	F	20.0
-input1.bam	FBtr0079752	72	52	F	20.0
-input1.bam	FBtr0079752	72	72	F	0
-input1.bam	FBtr0079820	74	1	F	0
-input1.bam	FBtr0079820	74	45	F	20.0
-input1.bam	FBtr0079820	74	49	F	24.0
-input1.bam	FBtr0079820	74	51	F	20.0
-input1.bam	FBtr0079820	74	74	F	0
-input1.bam	FBtr0080609	72	1	F	22.3
-input1.bam	FBtr0080609	72	3	F	21.0
-input1.bam	FBtr0080609	72	4	F	20.0
-input1.bam	FBtr0080609	72	12	F	23.0
-input1.bam	FBtr0080609	72	16	F	23.0
-input1.bam	FBtr0080609	72	17	F	24.0
-input1.bam	FBtr0080609	72	19	F	26.0
-input1.bam	FBtr0080609	72	20	F	25.0
-input1.bam	FBtr0080609	72	42	F	21.0
-input1.bam	FBtr0080609	72	72	F	0
-input1.bam	FBtr0080644	72	1	F	27.0
-input1.bam	FBtr0080644	72	4	F	24.0
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	0
-input1.bam	FBtr0080646	72	6	F	22.0
-input1.bam	FBtr0080646	72	7	F	21.0
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	0
-input1.bam	FBtr0080647	72	6	F	22.0
-input1.bam	FBtr0080647	72	8	F	20.0
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	24.0
-input1.bam	FBtr0080660	72	7	F	21.0
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	26.0
-input1.bam	FBtr0080663	71	3	F	23.7
-input1.bam	FBtr0080663	71	4	F	23.3
-input1.bam	FBtr0080663	71	8	F	20.0
-input1.bam	FBtr0080663	71	51	F	20.0
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	24.7
-input1.bam	FBtr0080664	71	3	F	23.8
-input1.bam	FBtr0080664	71	4	F	23.5
-input1.bam	FBtr0080664	71	6	F	23.0
-input1.bam	FBtr0080664	71	7	F	21.0
-input1.bam	FBtr0080664	71	8	F	21.0
-input1.bam	FBtr0080664	71	9	F	20.0
-input1.bam	FBtr0080664	71	12	F	20.0
-input1.bam	FBtr0080664	71	13	F	20.0
-input1.bam	FBtr0080664	71	33	F	20.0
-input1.bam	FBtr0080664	71	36	F	21.0
-input1.bam	FBtr0080664	71	71	F	0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/median.tab
--- a/test-data/median.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,617 +0,0 @@
-Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Median
-input1.bam	FBtr0070001	72	1	F	17.0
-input1.bam	FBtr0070001	72	7	F	21.0
-input1.bam	FBtr0070001	72	8	F	21.0
-input1.bam	FBtr0070001	72	11	F	20.5
-input1.bam	FBtr0070001	72	16	F	19.0
-input1.bam	FBtr0070001	72	17	F	23.0
-input1.bam	FBtr0070001	72	18	F	16.0
-input1.bam	FBtr0070001	72	27	F	23.5
-input1.bam	FBtr0070001	72	30	F	23.0
-input1.bam	FBtr0070001	72	31	F	23.0
-input1.bam	FBtr0070001	72	32	F	22.0
-input1.bam	FBtr0070001	72	34	F	20.0
-input1.bam	FBtr0070001	72	72	F	0
-input1.bam	FBtr0070533	72	1	F	15.0
-input1.bam	FBtr0070533	72	12	F	18.0
-input1.bam	FBtr0070533	72	15	F	15.0
-input1.bam	FBtr0070533	72	19	F	22.0
-input1.bam	FBtr0070533	72	20	F	23.0
-input1.bam	FBtr0070533	72	21	F	18.0
-input1.bam	FBtr0070533	72	22	F	20.0
-input1.bam	FBtr0070533	72	25	F	17.0
-input1.bam	FBtr0070533	72	26	F	16.0
-input1.bam	FBtr0070533	72	28	F	25.0
-input1.bam	FBtr0070533	72	32	F	21.0
-input1.bam	FBtr0070533	72	35	F	19.0
-input1.bam	FBtr0070533	72	37	F	19.0
-input1.bam	FBtr0070533	72	38	F	18.0
-input1.bam	FBtr0070533	72	72	F	0
-input1.bam	FBtr0070603	72	1	F	16.5
-input1.bam	FBtr0070603	72	3	F	21.0
-input1.bam	FBtr0070603	72	4	F	20.0
-input1.bam	FBtr0070603	72	6	F	18.0
-input1.bam	FBtr0070603	72	7	F	17.0
-input1.bam	FBtr0070603	72	8	F	16.0
-input1.bam	FBtr0070603	72	9	F	15.0
-input1.bam	FBtr0070603	72	12	F	20.0
-input1.bam	FBtr0070603	72	13	F	22.0
-input1.bam	FBtr0070603	72	15	F	18.5
-input1.bam	FBtr0070603	72	16	F	20.5
-input1.bam	FBtr0070603	72	17	F	25.0
-input1.bam	FBtr0070603	72	18	F	16.0
-input1.bam	FBtr0070603	72	19	F	23.0
-input1.bam	FBtr0070603	72	20	F	22.0
-input1.bam	FBtr0070603	72	21	F	25.0
-input1.bam	FBtr0070603	72	22	F	20.0
-input1.bam	FBtr0070603	72	24	F	19.5
-input1.bam	FBtr0070603	72	25	F	23.0
-input1.bam	FBtr0070603	72	26	F	26.0
-input1.bam	FBtr0070603	72	27	F	26.0
-input1.bam	FBtr0070603	72	32	F	20.0
-input1.bam	FBtr0070603	72	34	F	20.0
-input1.bam	FBtr0070603	72	38	F	18.0
-input1.bam	FBtr0070603	72	42	F	21.0
-input1.bam	FBtr0070603	72	51	F	18.0
-input1.bam	FBtr0070603	72	56	F	16.0
-input1.bam	FBtr0070603	72	72	F	0
-input1.bam	FBtr0070604	72	1	F	15.0
-input1.bam	FBtr0070604	72	18	F	23.0
-input1.bam	FBtr0070604	72	22	F	19.0
-input1.bam	FBtr0070604	72	30	F	18.0
-input1.bam	FBtr0070604	72	31	F	23.0
-input1.bam	FBtr0070604	72	32	F	22.0
-input1.bam	FBtr0070604	72	57	F	15.0
-input1.bam	FBtr0070604	72	72	F	0
-input1.bam	FBtr0070911	73	1	F	0
-input1.bam	FBtr0070911	73	15	F	21.0
-input1.bam	FBtr0070911	73	38	F	15.0
-input1.bam	FBtr0070911	73	73	F	0
-input1.bam	FBtr0078490	72	1	F	0
-input1.bam	FBtr0078490	72	13	F	16.0
-input1.bam	FBtr0078490	72	17	F	16.0
-input1.bam	FBtr0078490	72	18	F	15.0
-input1.bam	FBtr0078490	72	25	F	15.0
-input1.bam	FBtr0078490	72	28	F	19.0
-input1.bam	FBtr0078490	72	38	F	18.0
-input1.bam	FBtr0078490	72	72	F	0
-input1.bam	FBtr0078580	72	1	F	15.0
-input1.bam	FBtr0078580	72	3	F	22.0
-input1.bam	FBtr0078580	72	4	F	25.0
-input1.bam	FBtr0078580	72	5	F	20.0
-input1.bam	FBtr0078580	72	6	F	19.0
-input1.bam	FBtr0078580	72	7	F	22.0
-input1.bam	FBtr0078580	72	8	F	18.0
-input1.bam	FBtr0078580	72	11	F	23.0
-input1.bam	FBtr0078580	72	12	F	17.0
-input1.bam	FBtr0078580	72	14	F	15.0
-input1.bam	FBtr0078580	72	15	F	16.0
-input1.bam	FBtr0078580	72	16	F	19.0
-input1.bam	FBtr0078580	72	17	F	17.0
-input1.bam	FBtr0078580	72	19	F	24.0
-input1.bam	FBtr0078580	72	20	F	21.0
-input1.bam	FBtr0078580	72	21	F	20.0
-input1.bam	FBtr0078580	72	24	F	17.0
-input1.bam	FBtr0078580	72	25	F	27.5
-input1.bam	FBtr0078580	72	29	F	17.0
-input1.bam	FBtr0078580	72	31	F	17.0
-input1.bam	FBtr0078580	72	52	F	16.0
-input1.bam	FBtr0078580	72	72	F	0
-input1.bam	FBtr0078790	73	1	F	19.0
-input1.bam	FBtr0078790	73	17	F	16.0
-input1.bam	FBtr0078790	73	33	F	23.0
-input1.bam	FBtr0078790	73	42	F	18.5
-input1.bam	FBtr0078790	73	44	F	19.5
-input1.bam	FBtr0078790	73	46	F	17.0
-input1.bam	FBtr0078790	73	47	F	18.0
-input1.bam	FBtr0078790	73	52	F	20.0
-input1.bam	FBtr0078790	73	69	R	15.0
-input1.bam	FBtr0078790	73	73	F	0
-input1.bam	FBtr0079064	72	1	F	15.0
-input1.bam	FBtr0079064	72	3	F	21.0
-input1.bam	FBtr0079064	72	33	F	15.0
-input1.bam	FBtr0079064	72	52	F	17.0
-input1.bam	FBtr0079064	72	72	F	0
-input1.bam	FBtr0079090	72	1	F	21.5
-input1.bam	FBtr0079090	72	26	F	24.0
-input1.bam	FBtr0079090	72	33	F	16.0
-input1.bam	FBtr0079090	72	53	F	18.0
-input1.bam	FBtr0079090	72	56	R	21.0
-input1.bam	FBtr0079090	72	72	F	0
-input1.bam	FBtr0079338	73	1	F	0
-input1.bam	FBtr0079338	73	12	F	17.0
-input1.bam	FBtr0079338	73	13	F	17.5
-input1.bam	FBtr0079338	73	14	F	15.0
-input1.bam	FBtr0079338	73	17	F	15.0
-input1.bam	FBtr0079338	73	25	F	16.0
-input1.bam	FBtr0079338	73	42	F	22.0
-input1.bam	FBtr0079338	73	43	F	21.0
-input1.bam	FBtr0079338	73	46	F	18.0
-input1.bam	FBtr0079338	73	73	F	0
-input1.bam	FBtr0079528	71	1	F	20.0
-input1.bam	FBtr0079528	71	3	F	24.0
-input1.bam	FBtr0079528	71	4	F	24.0
-input1.bam	FBtr0079528	71	8	F	19.5
-input1.bam	FBtr0079528	71	10	F	21.0
-input1.bam	FBtr0079528	71	11	F	19.0
-input1.bam	FBtr0079528	71	13	F	16.0
-input1.bam	FBtr0079528	71	14	F	18.5
-input1.bam	FBtr0079528	71	16	F	15.0
-input1.bam	FBtr0079528	71	17	F	15.0
-input1.bam	FBtr0079528	71	18	F	20.0
-input1.bam	FBtr0079528	71	28	F	16.0
-input1.bam	FBtr0079528	71	35	F	15.0
-input1.bam	FBtr0079528	71	36	F	20.0
-input1.bam	FBtr0079528	71	37	F	18.0
-input1.bam	FBtr0079528	71	51	F	15.0
-input1.bam	FBtr0079528	71	71	F	0
-input1.bam	FBtr0079596	73	1	F	15.0
-input1.bam	FBtr0079596	73	3	F	23.0
-input1.bam	FBtr0079596	73	4	F	22.0
-input1.bam	FBtr0079596	73	5	F	18.5
-input1.bam	FBtr0079596	73	6	F	18.0
-input1.bam	FBtr0079596	73	8	F	17.0
-input1.bam	FBtr0079596	73	9	F	16.0
-input1.bam	FBtr0079596	73	10	F	15.0
-input1.bam	FBtr0079596	73	11	F	15.0
-input1.bam	FBtr0079596	73	12	F	17.0
-input1.bam	FBtr0079596	73	13	F	16.0
-input1.bam	FBtr0079596	73	14	F	15.0
-input1.bam	FBtr0079596	73	15	F	18.0
-input1.bam	FBtr0079596	73	16	F	17.0
-input1.bam	FBtr0079596	73	17	F	16.0
-input1.bam	FBtr0079596	73	18	F	15.0
-input1.bam	FBtr0079596	73	19	F	15.0
-input1.bam	FBtr0079596	73	53	F	18.5
-input1.bam	FBtr0079596	73	54	F	19.5
-input1.bam	FBtr0079596	73	73	F	0
-input1.bam	FBtr0079677	72	1	F	23.0
-input1.bam	FBtr0079677	72	5	F	19.0
-input1.bam	FBtr0079677	72	52	F	19.0
-input1.bam	FBtr0079677	72	53	F	18.0
-input1.bam	FBtr0079677	72	72	F	0
-input1.bam	FBtr0079690	72	1	F	15.0
-input1.bam	FBtr0079690	72	22	F	15.0
-input1.bam	FBtr0079690	72	27	F	25.0
-input1.bam	FBtr0079690	72	33	F	16.0
-input1.bam	FBtr0079690	72	72	F	0
-input1.bam	FBtr0079692	73	1	F	19.0
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-input2.bam	FBtr0079820	74	52	F	21.0
-input2.bam	FBtr0079820	74	53	F	20.0
-input2.bam	FBtr0079820	74	54	F	19.0
-input2.bam	FBtr0079820	74	55	F	18.5
-input2.bam	FBtr0079820	74	56	F	16.5
-input2.bam	FBtr0079820	74	57	F	17.0
-input2.bam	FBtr0079820	74	58	F	16.0
-input2.bam	FBtr0079820	74	59	F	15.0
-input2.bam	FBtr0079820	74	60	F	15.0
-input2.bam	FBtr0079820	74	74	F	0
-input2.bam	FBtr0080609	72	1	F	0
-input2.bam	FBtr0080609	72	20	F	19.0
-input2.bam	FBtr0080609	72	21	F	21.0
-input2.bam	FBtr0080609	72	22	F	23.0
-input2.bam	FBtr0080609	72	33	F	22.0
-input2.bam	FBtr0080609	72	39	F	17.0
-input2.bam	FBtr0080609	72	52	F	18.0
-input2.bam	FBtr0080609	72	53	F	19.0
-input2.bam	FBtr0080609	72	72	F	0
-input2.bam	FBtr0080644	72	1	F	0
-input2.bam	FBtr0080644	72	57	F	15.0
-input2.bam	FBtr0080644	72	58	F	15.0
-input2.bam	FBtr0080644	72	72	F	0
-input2.bam	FBtr0080646	72	1	F	0
-input2.bam	FBtr0080646	72	51	F	21.0
-input2.bam	FBtr0080646	72	57	F	15.5
-input2.bam	FBtr0080646	72	58	F	15.0
-input2.bam	FBtr0080646	72	72	F	0
-input2.bam	FBtr0080647	72	1	F	18.0
-input2.bam	FBtr0080647	72	57	F	15.5
-input2.bam	FBtr0080647	72	58	F	15.0
-input2.bam	FBtr0080647	72	72	F	0
-input2.bam	FBtr0080660	72	1	F	0
-input2.bam	FBtr0080660	72	58	F	15.0
-input2.bam	FBtr0080660	72	72	F	0
-input2.bam	FBtr0080663	71	1	F	22.0
-input2.bam	FBtr0080663	71	11	F	21.0
-input2.bam	FBtr0080663	71	12	F	20.5
-input2.bam	FBtr0080663	71	13	F	20.0
-input2.bam	FBtr0080663	71	14	F	18.0
-input2.bam	FBtr0080663	71	15	F	18.0
-input2.bam	FBtr0080663	71	16	F	16.0
-input2.bam	FBtr0080663	71	17	F	15.5
-input2.bam	FBtr0080663	71	18	F	17.0
-input2.bam	FBtr0080663	71	19	F	17.0
-input2.bam	FBtr0080663	71	20	F	16.0
-input2.bam	FBtr0080663	71	21	F	15.0
-input2.bam	FBtr0080663	71	22	F	15.0
-input2.bam	FBtr0080663	71	31	F	17.0
-input2.bam	FBtr0080663	71	50	F	15.5
-input2.bam	FBtr0080663	71	51	F	19.0
-input2.bam	FBtr0080663	71	52	F	15.0
-input2.bam	FBtr0080663	71	57	F	15.0
-input2.bam	FBtr0080663	71	71	F	0
-input2.bam	FBtr0080664	71	1	F	22.0
-input2.bam	FBtr0080664	71	3	F	23.0
-input2.bam	FBtr0080664	71	10	F	23.0
-input2.bam	FBtr0080664	71	11	F	22.0
-input2.bam	FBtr0080664	71	12	F	21.0
-input2.bam	FBtr0080664	71	13	F	20.0
-input2.bam	FBtr0080664	71	14	F	18.0
-input2.bam	FBtr0080664	71	15	F	18.0
-input2.bam	FBtr0080664	71	16	F	17.0
-input2.bam	FBtr0080664	71	17	F	16.0
-input2.bam	FBtr0080664	71	18	F	18.5
-input2.bam	FBtr0080664	71	19	F	19.0
-input2.bam	FBtr0080664	71	20	F	16.0
-input2.bam	FBtr0080664	71	21	F	15.0
-input2.bam	FBtr0080664	71	22	F	15.5
-input2.bam	FBtr0080664	71	24	F	15.0
-input2.bam	FBtr0080664	71	30	F	21.0
-input2.bam	FBtr0080664	71	31	F	19.0
-input2.bam	FBtr0080664	71	32	F	18.0
-input2.bam	FBtr0080664	71	33	F	17.0
-input2.bam	FBtr0080664	71	34	F	16.0
-input2.bam	FBtr0080664	71	35	F	15.0
-input2.bam	FBtr0080664	71	36	F	18.5
-input2.bam	FBtr0080664	71	37	F	18.0
-input2.bam	FBtr0080664	71	38	F	16.0
-input2.bam	FBtr0080664	71	39	F	17.0
-input2.bam	FBtr0080664	71	42	F	20.0
-input2.bam	FBtr0080664	71	47	F	15.0
-input2.bam	FBtr0080664	71	50	F	15.5
-input2.bam	FBtr0080664	71	52	F	16.0
-input2.bam	FBtr0080664	71	53	F	19.0
-input2.bam	FBtr0080664	71	56	F	16.0
-input2.bam	FBtr0080664	71	57	F	15.0
-input2.bam	FBtr0080664	71	62	R	23.0
-input2.bam	FBtr0080664	71	71	F	0
-input2.bam	FBtr0080664	71	71	R	22.0
diff -r a561a71bd7d7 -r d33263e6e812 test-data/single_chr-count-size.pdf
Binary file test-data/single_chr-count-size.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/size-count.pdf
Binary file test-data/size-count.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/size-count_normed.pdf
Binary file test-data/size-count_normed.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/size.pdf
Binary file test-data/size.pdf has changed
diff -r a561a71bd7d7 -r d33263e6e812 test-data/size_single_chr.tab
--- a/test-data/size_single_chr.tab	Tue Mar 06 06:11:55 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-Dataset	Chromosome	Polarity	Size	Counts
-input_single_chr.bam	Anopheles_C_Virus|KU169878	F	21	0
-input_single_chr.bam	Anopheles_C_Virus|KU169878	R	21	1