# HG changeset patch
# User artbio
# Date 1507499773 14400
# Node ID 12c14642e6ac8db494db906cfd60b4543cae1a60
# Parent  a6b9a081064b9f353b8b5bd33c62f6c8234582fd
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449

diff -r a6b9a081064b -r 12c14642e6ac small_rna_maps.py
--- a/small_rna_maps.py	Fri Aug 25 12:22:03 2017 -0400
+++ b/small_rna_maps.py	Sun Oct 08 17:56:13 2017 -0400
@@ -186,7 +186,7 @@
     for method, output in zip(methods, outputs):
         F = open(output, 'w')
         if method == 'Size':
-            header = ["Dataset", "Chromosome", "Polarity", method, "Count"]
+            header = ["Dataset", "Chromosome", "Polarity", method, "Counts"]
         else:
             header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
                       "Polarity", method]
diff -r a6b9a081064b -r 12c14642e6ac small_rna_maps.r
--- a/small_rna_maps.r	Fri Aug 25 12:22:03 2017 -0400
+++ b/small_rna_maps.r	Sun Oct 08 17:56:13 2017 -0400
@@ -1,7 +1,7 @@
 ## Setup R error handling to go to stderr
 options( show.error.messages=F,
        error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
-warnings()
+# options(warn = -1)
 library(RColorBrewer)
 library(lattice)
 library(latticeExtra)
@@ -12,6 +12,7 @@
 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("--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("--output_pdf", type = "character", help="path to the pdf file with plots")
     )
@@ -20,122 +21,199 @@
 args = parse_args(parser)
  
 # data frames implementation
-
+## first table
 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
-Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
+    Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+}
 n_samples=length(unique(Table$Dataset))
 genes=unique(levels(Table$Chromosome))
 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
 n_genes=length(per_gene_readmap)
-
-ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
-if (args$extra_plot_method=='Size') {
-    ExtraTable <- within(ExtraTable, Count[Polarity=="R"] <- (Count[Polarity=="R"]*-1))
+# 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))
+        }
+    per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
     }
-per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
-    
-## end of data frames implementation
 
 ## functions
 
-first_plot = function(df, ...) {
-    combineLimits(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),
-    ...))
+plot_unit = function(df, method=args$first_plot_method, ...) {
+    if (method == 'Counts') {
+        p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+        data=df,
+        type='h',
+        lwd=1.5,
+        scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+        xlab=NULL, main=NULL, ylab=NULL,
+        as.table=T,
+        origin = 0,
+        horizontal=FALSE,
+        group=Polarity,
+        col=c("red","blue"),
+        par.strip.text = list(cex=0.7),
+        ...)
+    } else if (method != "Size") {
+        p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+        data=df,
+        type='p',
+        pch=19,
+        cex=0.35,
+        scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+        xlab=NULL, main=NULL, ylab=NULL,
+        as.table=T,
+        origin = 0,
+        horizontal=FALSE,
+        group=Polarity,
+        col=c("red","blue"),
+        par.strip.text = list(cex=0.7),
+        ...)
+    } else {
+        p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
+                     horizontal=FALSE,
+                     group=Polarity,
+                     stack=TRUE,
+                     col=c('red', 'blue'),
+                     scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=0.5)),
+        xlab = NULL,
+        ylab = NULL,
+        main = NULL,
+        as.table=TRUE,
+        par.strip.text = list(cex=0.6),
+        ...)
     }
+    combineLimits(p)
+}
+
+plot_single <- function(df, method=args$first_plot_method, rows_per_page=rows_per_page, ...) {
+    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=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$first_plot_method]],
+                   origin = 0,
+                   group=Polarity,
+                   col=c("red","blue"),
+                   par.strip.text = list(cex=0.7),
+                   as.table=T,
+                   ...)
+        p = update(useOuterStrips(p, strip.left=strip.custom(par.strip.text = list(cex=0.5))), layout=c(n_samples, rows_per_page))
+        return(p)
+    } else if (method != "Size") {
+        p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
+                   data=df,
+                   type='p',
+                   pch=19,
+                   cex=0.35,
+                   scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+                   xlab=list(label=bottom_first_method[[args$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]],
+                   origin = 0,
+                   group=Polarity,
+                   col=c("red","blue"),
+                   par.strip.text = list(cex=0.7),
+                   as.table=T,
+                   ...)
+        p = update(useOuterStrips(p, strip.left=strip.custom(par.strip.text = list(cex=0.5))), layout=c(n_samples, rows_per_page))
+        return(p)
+    } 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=0.5, 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]],
+                    par.strip.text = list(cex=0.7),
+                    nrow = 8,
+                    as.table=TRUE,
+                    
+                    ...)
+          p = update(useOuterStrips(p, strip.left=strip.custom(par.strip.text = list(cex=0.5))), layout=c(n_samples, rows_per_page))
+          
+          p = combineLimits(p, extend=TRUE)
+          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")))
+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")
+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(...) {
+    if (n_genes > 5) {page_height=15; rows_per_page=10} else {
+                     rows_per_page= 2 * n_genes; page_height=1.5*n_genes}
+    if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 7 * 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}
+        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$extra_plot_method, par.settings=par.settings.secondplot))
+        plot.list=rbind(second_plot.list, first_plot.list)
+        args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1,  heights=unit(c(40,30,40,30,40,30,40,30,40,30,10), rep("mm", 11)),
+                                    top=textGrob(paste(title_first_method[[args$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$extra_plot_method]]), gp=gpar(cex=1), vjust=2, rot=90),
+                                    sub=textGrob(paste(bottom_first_method[[args$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()
+}
 
 
-second_plot = function(df, ...) {
-    #smR.prepanel=function(x,y,...) {; yscale=c(y*0, max(abs(y)));list(ylim=yscale);}
-    sizeplot = xyplot(eval(as.name(args$extra_plot_method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
-    data=df,
-    type='p',
-    cex=0.35,
-    pch=19,
-    scales= list(relation="free", x=list(rot=0, cex=0, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
-    xlab=NULL, main=NULL, ylab=NULL,
-    as.table=T,
-    origin = 0,
-    horizontal=FALSE,
-    group=Polarity,
-    col=c("darkred","darkblue"),
-    par.strip.text = list(cex=0.7),
-    ...)
-    combineLimits(sizeplot)
-    }
+single_plot <- function(...) {
+    width = 8.2677 * n_samples / 2
+    rows_per_page=8
+    pdf(file=args$output_pdf, paper="special", height=11.69, 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}
+        bunch = do.call(rbind, per_gene_readmap[start:end]) # sub dataframe from the list
+        p = plot_single(bunch, method=args$first_plot_method, par.settings=par.settings.single_plot, rows_per_page=rows_per_page)
+        plot(p)
+        }
+    devname=dev.off()
+}
 
-second_plot_size = function(df, ...) {
-#  smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
-  bc= barchart(Count~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
-    horizontal=FALSE,
-group=Polarity,
-stack=TRUE,
-    col=c('red', 'blue'),
-    cex=0.75,
-    scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
-#    prepanel=smR.prepanel,
-    xlab = NULL,
-    ylab = NULL,
-    main = NULL,
-    as.table=TRUE,
-    newpage = T,
-    par.strip.text = list(cex=0.7),
-    ...)
-  combineLimits(bc)
-  }
+# main
+
+if (args$extra_plot_method != '') { double_plot() }
+if (args$extra_plot_method == '') {
+    single_plot()
+}
 
 
-## end of functions
 
-## function parameters
-par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=0), strip.background = list(col=c("lightblue","lightgreen")) )
-par.settings.size=list(layout.heights=list(top.padding=0, bottom.padding=0))
-graph_title=list(Coverage="Read Maps and Coverages", Median="Read Maps and Median sizes", Mean="Read Maps and Mean sizes", SizeDistribution="Read Maps and Size Distributions")
-graph_legend=list(Coverage="Read counts / Coverage", Median="Read counts / Median size", Mean="Read counts / Mean size", SizeDistribution="Read counts")
-graph_bottom=list(Coverage="Nucleotide coordinates", Median="Nucleotide coordinates", Mean="Nucleotide coordinates", Size="Read sizes / Nucleotide coordinates")
-## end of function parameters'
 
-## GRAPHS
-
-if (n_genes > 5) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=6} else {
-                 rows_per_page= n_genes; page_height_simple = 2.5*n_genes; page_height_combi=page_height_simple*2 }
-if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/2} # to test
 
 
-pdf(file=args$output_pdf, paper="special", height=page_height_simple, width=page_width)
-if (rows_per_page %% 2 != 0) { rows_per_page = rows_per_page + 1}
-for (i in seq(1,n_genes,rows_per_page/2)) {
-    start=i
-    end=i+rows_per_page/2-1
-    if (end>n_genes) {end=n_genes}
-    first_plot.list=lapply(per_gene_readmap[start:end], function(x) first_plot(x, strip=FALSE, par.settings=par.settings.readmap))
-    if (args$extra_plot_method == "Size") {
-        second_plot.list=lapply(per_gene_size[start:end], function(x) second_plot_size(x, par.settings=par.settings.size))
-        }
-    else {
-        second_plot.list=lapply(per_gene_size[start:end], function(x) second_plot(x, par.settings=par.settings.size))
-        }
-    
-        
-    plot.list=rbind(second_plot.list, first_plot.list)
-    args_list=c(plot.list, list(nrow=rows_per_page+1, ncol=1,
-                                    top=textGrob(graph_title[[args$extra_plot_method]], gp=gpar(cex=1), just="top"),
-                                    left=textGrob(graph_legend[[args$extra_plot_method]], gp=gpar(cex=1), vjust=1, rot=90),
-                                    sub=textGrob(graph_bottom[[args$extra_plot_method]], gp=gpar(cex=1), just="bottom")
-                                    )
-           )
-do.call(grid.arrange, args_list)
-}
-devname=dev.off()
+
 
+
diff -r a6b9a081064b -r 12c14642e6ac small_rna_maps.xml
--- a/small_rna_maps.xml	Fri Aug 25 12:22:03 2017 -0400
+++ b/small_rna_maps.xml	Sun Oct 08 17:56:13 2017 -0400
@@ -1,11 +1,11 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="1.1.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.0.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
         <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
-        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
-        <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
-        <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
+        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
+        <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
   </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -23,27 +23,65 @@
       #for $sample in $inputs
           '$sample.name'
       #end for
-          --plot_methods Counts '$extra_plot'
+      #if str($plots_options.plots_options_selector ) == "two_plot":
+          --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
           --outputs '$output_tab' '$extra_output_tab' &&
+      #else:
+          --plot_methods '${plots_options.first_plot}'
+          --outputs '$output_tab' &&
+      #end if
       Rscript '$__tool_directory__'/small_rna_maps.r
           --first_dataframe '$output_tab' 
           --extra_dataframe '$extra_output_tab'
-          --extra_plot_method '$extra_plot'
+          #if str($plots_options.plots_options_selector ) == "two_plot":
+              --first_plot_method '${plots_options.first_plot}'
+              --extra_plot_method '${plots_options.extra_plot}'
+          #else:
+              --first_plot_method '${plots_options.first_plot}'
+              --extra_plot_method ''
+          #end if
           --output_pdf '$output_pdf'
   ]]></command>
  <inputs>
-   <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 
-   <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map">
-       <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="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
+    <conditional name="plots_options">
+        <param name="plots_options_selector" type="select" label="Number of plots per chromosome">
+            <option value="one_plot">Just one plot per chromosome</option>
+            <option value="two_plot" selected="True">Two plots per chromosome</option>
+        </param>
+        <when value="two_plot">
+            <param name="first_plot" type="select" label="select the type of the first 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" label="select the type of the second 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>
+        </when>
+        <when value="one_plot">
+            <param name="first_plot" type="select" label="select the type of the first 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>
+        </when>
+    </conditional>
  </inputs>
 
  <outputs>
    <data format="tabular" name="output_tab" label="Read Count dataframe" />
-   <data format="tabular" name="extra_output_tab" label="$extra_plot dataframe" />
+   <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
+    <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
+   </data> 
    <data format="pdf" name="output_pdf" label="PDF file" />
 
 </outputs>
@@ -51,38 +89,78 @@
     <tests>
         <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
-            <output file="readmap.tab" name="output_tab" />
+            <output file="count.tab" name="output_tab" />
             <output file="mean.tab" name="extra_output_tab" />
-            <output file="mean.pdf" name="output_pdf" />
+            <output file="count-mean.pdf" name="output_pdf" />
         </test>
         <test>
             <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
+            <param name="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
-            <output file="doubled_readmap.tab" name="output_tab" />
-            <output file="double_mean.tab" name="extra_output_tab" />
-            <output file="doubled_mean.pdf" name="output_pdf" />
+            <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="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
+            <param name="extra_plot" value="Median" />
+            <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="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
+            <param name="extra_plot" value="Coverage" />
+            <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="extra_plot" value="Median" />
-            <output file="readmap.tab" name="output_tab" />
-            <output file="median.tab" name="extra_output_tab" />
-            <output file="median.pdf" name="output_pdf" />
+            <param name="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Counts" />
+            <param name="extra_plot" value="Size" />
+            <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="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Size" />
+            <param name="extra_plot" value="Counts" />
+            <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="extra_plot" value="Coverage" />
-            <output file="readmap.tab" name="output_tab" />
-            <output file="coverage.tab" name="extra_output_tab" />
-            <output file="coverage.pdf" name="output_pdf" />
+            <param name="plots_options_selector" value="one_plot" />
+            <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="extra_plot" value="Size" />
-            <output file="readmap.tab" name="output_tab" />
-            <output file="size.tab" name="extra_output_tab" />
-            <output file="sizes.pdf" name="output_pdf" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Size" />
+            <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="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Coverage" />
+            <output file="coverage.tab" name="output_tab" />
+            <output file="coverage.pdf" name="output_pdf" />
         </test>
     </tests>
 
diff -r a6b9a081064b -r 12c14642e6ac test-data/count-coverage.pdf
Binary file test-data/count-coverage.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/count-mean.pdf
Binary file test-data/count-mean.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/count-median.pdf
Binary file test-data/count-median.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/count-size.pdf
Binary file test-data/count-size.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/count.pdf
Binary file test-data/count.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/count.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count.tab	Sun Oct 08 17:56:13 2017 -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
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+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
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+input1.bam	FBtr0079690	72	33	F	2
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+input1.bam	FBtr0079692	73	1	F	3
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+input1.bam	FBtr0079692	73	32	F	1
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+input1.bam	FBtr0079693	72	1	F	5
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+input1.bam	FBtr0079694	72	1	F	5
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+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
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+input1.bam	FBtr0079728	72	33	F	3
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+input1.bam	FBtr0079729	72	1	F	1
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+input1.bam	FBtr0079729	72	72	F	0
+input1.bam	FBtr0079752	72	1	F	2
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+input1.bam	FBtr0079820	74	1	F	0
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+input1.bam	FBtr0079820	74	48	F	1
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+input1.bam	FBtr0079820	74	74	F	0
+input1.bam	FBtr0080609	72	1	F	13
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diff -r a6b9a081064b -r 12c14642e6ac test-data/coverage.pdf
Binary file test-data/coverage.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/double_mean.tab
--- a/test-data/double_mean.tab	Fri Aug 25 12:22:03 2017 -0400
+++ /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
-input1.bam_0	FBtr0070533	72	25	F	17.0
-input1.bam_0	FBtr0070533	72	26	F	16.0
-input1.bam_0	FBtr0070533	72	28	F	25.0
-input1.bam_0	FBtr0070533	72	32	F	20.5
-input1.bam_0	FBtr0070533	72	35	F	19.0
-input1.bam_0	FBtr0070533	72	37	F	19.0
-input1.bam_0	FBtr0070533	72	38	F	18.0
-input1.bam_0	FBtr0070533	72	72	F	0
-input1.bam_0	FBtr0070603	72	1	F	16.5
-input1.bam_0	FBtr0070603	72	3	F	21.0
-input1.bam_0	FBtr0070603	72	4	F	20.0
-input1.bam_0	FBtr0070603	72	6	F	18.0
-input1.bam_0	FBtr0070603	72	7	F	17.1
-input1.bam_0	FBtr0070603	72	8	F	16.0
-input1.bam_0	FBtr0070603	72	9	F	15.0
-input1.bam_0	FBtr0070603	72	12	F	20.0
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-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 a6b9a081064b -r 12c14642e6ac test-data/doubled_count-mean.pdf
Binary file test-data/doubled_count-mean.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/doubled_count.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/doubled_count.tab	Sun Oct 08 17:56:13 2017 -0400
@@ -0,0 +1,599 @@
+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
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+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 a6b9a081064b -r 12c14642e6ac test-data/doubled_mean.pdf
Binary file test-data/doubled_mean.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/doubled_mean.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/doubled_mean.tab	Sun Oct 08 17:56:13 2017 -0400
@@ -0,0 +1,599 @@
+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
+input1.bam_0	FBtr0070533	72	25	F	17.0
+input1.bam_0	FBtr0070533	72	26	F	16.0
+input1.bam_0	FBtr0070533	72	28	F	25.0
+input1.bam_0	FBtr0070533	72	32	F	20.5
+input1.bam_0	FBtr0070533	72	35	F	19.0
+input1.bam_0	FBtr0070533	72	37	F	19.0
+input1.bam_0	FBtr0070533	72	38	F	18.0
+input1.bam_0	FBtr0070533	72	72	F	0
+input1.bam_0	FBtr0070603	72	1	F	16.5
+input1.bam_0	FBtr0070603	72	3	F	21.0
+input1.bam_0	FBtr0070603	72	4	F	20.0
+input1.bam_0	FBtr0070603	72	6	F	18.0
+input1.bam_0	FBtr0070603	72	7	F	17.1
+input1.bam_0	FBtr0070603	72	8	F	16.0
+input1.bam_0	FBtr0070603	72	9	F	15.0
+input1.bam_0	FBtr0070603	72	12	F	20.0
+input1.bam_0	FBtr0070603	72	13	F	22.0
+input1.bam_0	FBtr0070603	72	15	F	18.5
+input1.bam_0	FBtr0070603	72	16	F	20.5
+input1.bam_0	FBtr0070603	72	17	F	24.0
+input1.bam_0	FBtr0070603	72	18	F	16.0
+input1.bam_0	FBtr0070603	72	19	F	22.6
+input1.bam_0	FBtr0070603	72	20	F	21.0
+input1.bam_0	FBtr0070603	72	21	F	25.0
+input1.bam_0	FBtr0070603	72	22	F	20.7
+input1.bam_0	FBtr0070603	72	24	F	19.5
+input1.bam_0	FBtr0070603	72	25	F	23.0
+input1.bam_0	FBtr0070603	72	26	F	25.8
+input1.bam_0	FBtr0070603	72	27	F	26.3
+input1.bam_0	FBtr0070603	72	32	F	20.0
+input1.bam_0	FBtr0070603	72	34	F	19.3
+input1.bam_0	FBtr0070603	72	38	F	18.0
+input1.bam_0	FBtr0070603	72	42	F	21.0
+input1.bam_0	FBtr0070603	72	51	F	18.0
+input1.bam_0	FBtr0070603	72	56	F	16.0
+input1.bam_0	FBtr0070603	72	72	F	0
+input1.bam_0	FBtr0070604	72	1	F	15.0
+input1.bam_0	FBtr0070604	72	18	F	23.0
+input1.bam_0	FBtr0070604	72	22	F	19.0
+input1.bam_0	FBtr0070604	72	30	F	18.0
+input1.bam_0	FBtr0070604	72	31	F	22.6
+input1.bam_0	FBtr0070604	72	32	F	22.0
+input1.bam_0	FBtr0070604	72	57	F	15.0
+input1.bam_0	FBtr0070604	72	72	F	0
+input1.bam_0	FBtr0070911	73	1	F	0
+input1.bam_0	FBtr0070911	73	15	F	21.0
+input1.bam_0	FBtr0070911	73	38	F	15.0
+input1.bam_0	FBtr0070911	73	73	F	0
+input1.bam_0	FBtr0078490	72	1	F	0
+input1.bam_0	FBtr0078490	72	13	F	16.0
+input1.bam_0	FBtr0078490	72	17	F	16.0
+input1.bam_0	FBtr0078490	72	18	F	15.0
+input1.bam_0	FBtr0078490	72	25	F	15.0
+input1.bam_0	FBtr0078490	72	28	F	19.0
+input1.bam_0	FBtr0078490	72	38	F	18.0
+input1.bam_0	FBtr0078490	72	72	F	0
+input1.bam_0	FBtr0078580	72	1	F	18.9
+input1.bam_0	FBtr0078580	72	3	F	22.0
+input1.bam_0	FBtr0078580	72	4	F	25.3
+input1.bam_0	FBtr0078580	72	5	F	21.0
+input1.bam_0	FBtr0078580	72	6	F	19.0
+input1.bam_0	FBtr0078580	72	7	F	22.0
+input1.bam_0	FBtr0078580	72	8	F	18.0
+input1.bam_0	FBtr0078580	72	11	F	23.0
+input1.bam_0	FBtr0078580	72	12	F	18.0
+input1.bam_0	FBtr0078580	72	14	F	15.3
+input1.bam_0	FBtr0078580	72	15	F	16.0
+input1.bam_0	FBtr0078580	72	16	F	19.0
+input1.bam_0	FBtr0078580	72	17	F	17.0
+input1.bam_0	FBtr0078580	72	19	F	24.0
+input1.bam_0	FBtr0078580	72	20	F	21.0
+input1.bam_0	FBtr0078580	72	21	F	19.4
+input1.bam_0	FBtr0078580	72	24	F	17.0
+input1.bam_0	FBtr0078580	72	25	F	27.5
+input1.bam_0	FBtr0078580	72	29	F	17.0
+input1.bam_0	FBtr0078580	72	31	F	17.0
+input1.bam_0	FBtr0078580	72	52	F	16.0
+input1.bam_0	FBtr0078580	72	72	F	0
+input1.bam_0	FBtr0078790	73	1	F	19.0
+input1.bam_0	FBtr0078790	73	17	F	16.0
+input1.bam_0	FBtr0078790	73	33	F	23.0
+input1.bam_0	FBtr0078790	73	42	F	18.5
+input1.bam_0	FBtr0078790	73	44	F	19.5
+input1.bam_0	FBtr0078790	73	46	F	17.0
+input1.bam_0	FBtr0078790	73	47	F	18.0
+input1.bam_0	FBtr0078790	73	52	F	20.0
+input1.bam_0	FBtr0078790	73	69	R	15.0
+input1.bam_0	FBtr0078790	73	73	F	0
+input1.bam_0	FBtr0079064	72	1	F	15.0
+input1.bam_0	FBtr0079064	72	3	F	21.0
+input1.bam_0	FBtr0079064	72	33	F	15.0
+input1.bam_0	FBtr0079064	72	52	F	17.0
+input1.bam_0	FBtr0079064	72	72	F	0
+input1.bam_0	FBtr0079090	72	1	F	21.5
+input1.bam_0	FBtr0079090	72	26	F	24.0
+input1.bam_0	FBtr0079090	72	33	F	16.0
+input1.bam_0	FBtr0079090	72	53	F	18.0
+input1.bam_0	FBtr0079090	72	56	R	21.0
+input1.bam_0	FBtr0079090	72	72	F	0
+input1.bam_0	FBtr0079338	73	1	F	0
+input1.bam_0	FBtr0079338	73	12	F	17.0
+input1.bam_0	FBtr0079338	73	13	F	17.5
+input1.bam_0	FBtr0079338	73	14	F	15.0
+input1.bam_0	FBtr0079338	73	17	F	15.0
+input1.bam_0	FBtr0079338	73	25	F	16.0
+input1.bam_0	FBtr0079338	73	42	F	21.8
+input1.bam_0	FBtr0079338	73	43	F	21.0
+input1.bam_0	FBtr0079338	73	46	F	18.0
+input1.bam_0	FBtr0079338	73	73	F	0
+input1.bam_0	FBtr0079528	71	1	F	20.8
+input1.bam_0	FBtr0079528	71	3	F	23.6
+input1.bam_0	FBtr0079528	71	4	F	24.0
+input1.bam_0	FBtr0079528	71	8	F	20.3
+input1.bam_0	FBtr0079528	71	10	F	21.0
+input1.bam_0	FBtr0079528	71	11	F	19.0
+input1.bam_0	FBtr0079528	71	13	F	16.0
+input1.bam_0	FBtr0079528	71	14	F	18.5
+input1.bam_0	FBtr0079528	71	16	F	15.0
+input1.bam_0	FBtr0079528	71	17	F	15.3
+input1.bam_0	FBtr0079528	71	18	F	19.8
+input1.bam_0	FBtr0079528	71	28	F	16.0
+input1.bam_0	FBtr0079528	71	35	F	15.0
+input1.bam_0	FBtr0079528	71	36	F	20.0
+input1.bam_0	FBtr0079528	71	37	F	18.0
+input1.bam_0	FBtr0079528	71	51	F	15.0
+input1.bam_0	FBtr0079528	71	71	F	0
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+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 a6b9a081064b -r 12c14642e6ac test-data/doubled_readmap.tab
--- a/test-data/doubled_readmap.tab	Fri Aug 25 12:22:03 2017 -0400
+++ /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
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-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 a6b9a081064b -r 12c14642e6ac test-data/mean.pdf
Binary file test-data/mean.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/median.pdf
Binary file test-data/median.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/readmap.tab
--- a/test-data/readmap.tab	Fri Aug 25 12:22:03 2017 -0400
+++ /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
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-input2.bam	FBtr0080664	71	11	F	2
-input2.bam	FBtr0080664	71	12	F	3
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-input2.bam	FBtr0080664	71	15	F	17
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-input2.bam	FBtr0080664	71	19	F	8
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-input2.bam	FBtr0080664	71	21	F	15
-input2.bam	FBtr0080664	71	22	F	6
-input2.bam	FBtr0080664	71	24	F	1
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-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 a6b9a081064b -r 12c14642e6ac test-data/size-count.pdf
Binary file test-data/size-count.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/size.pdf
Binary file test-data/size.pdf has changed
diff -r a6b9a081064b -r 12c14642e6ac test-data/size.tab
--- a/test-data/size.tab	Fri Aug 25 12:22:03 2017 -0400
+++ b/test-data/size.tab	Sun Oct 08 17:56:13 2017 -0400
@@ -1,4 +1,4 @@
-Dataset	Chromosome	Polarity	Size	Count
+Dataset	Chromosome	Polarity	Size	Counts
 input1.bam	FBtr0070001	F	16	2
 input1.bam	FBtr0070001	F	17	1
 input1.bam	FBtr0070001	F	18	0
diff -r a6b9a081064b -r 12c14642e6ac test-data/sizes.pdf
Binary file test-data/sizes.pdf has changed