Mercurial > repos > kyost > atac_primer_tool
changeset 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ATAC_Primer_Tool.ga Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +{"uuid": "adf14070-f445-41b0-ba62-c9a96d71bae5", "tags": [], "format-version": "0.1", "name": "ATAC Primer Tool", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "4a35572c-71e7-4459-8588-5f5934dfa525", "label": null}], "input_connections": {}, "tool_state": "{\"collection_type\": \"list\"}", "id": 0, "uuid": "2c0a2479-903a-46d6-af83-2fd16f0c4111", "errors": null, "name": "Input dataset collection", "label": "ATAC-seq bam files", "inputs": [], "position": {"top": 294, "left": 214}, "annotation": "", "content_id": null, "type": "data_collection_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [{"output_name": "output", "uuid": "cb2d4088-fe8d-454b-aea3-118709f04e53", "label": null}], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/concatenate_ordered.bash Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,18 @@ +#!/bin/bash + +input1=$1 +output1=$2 + +echo $input1 |tr , '\n' > input_series + +cat input_series | while read file +do + cat $file >> count_list +done + +sort -k1 count_list > sorted_list +cut -f 2 sorted_list > $output1 + +rm input_series +rm count_list +rm sorted_list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/concatenate_ordered.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,29 @@ +<tool id="concatenate_ordered" name="Concatenate Ordered Dataset Collection" version="0.1.0"> + <description> Concatenates files in dataset collection based on orginial file name stored in first column.</description> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + $__tool_directory__/./concatenate_ordered.bash "$input1" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="tabular" multiple="true" label="Read Counts Files"/> + </inputs> + <outputs> + <data name="output1" format="tabular" label="Read Counts"/> + </outputs> + <tests> + <test> + <param name="input1" value="dataset_692.dat,dataset_684.dat,dataset_688.dat,dataset_686.dat,dataset_690.dat"/> + <output name="output1" file="read_counts_ordered.txt"/> + </test> + </tests> + <help><![CDATA[ + This tools takes a series of input files and concatenates the contents in order according to the alphabetical order of the first column of the input files containing the original file name. + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4663</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_bam.bash Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,35 @@ +#Requires bam files and bed file containing coordinates of peaks of interest +#Generates filtered bams and library size file to upload into Galaxy + +#required arguements: +#($1): bam file +#($2): bed file containing regions of interest + +#Usage: filter_bam /pathtofolder/ qPCR_peaks.bed + +#outputs: +#Filtered bam files containing reads in regions of interest +#read_counts: txt file containing number of mapped reads in each bam file, used for normalization + +bam_file=$1 +peak_file=$2 +chrom_sizes=$3 +ext_peak_file=$4 +filtered_bam_file=$5 +read_counts=$6 +name=$7 + +bedtools slop -i $peak_file -g $chrom_sizes -b 2000 | sort -k1,1 -k2,2n - > $ext_peak_file + +samtools index $bam_file + +samtools view -c -F 1284 $bam_file > count +echo $name > name +paste name count > $read_counts + +#create bed file of fragments for each bam file + +samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file + +rm name +rm count
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_bam.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,40 @@ +<tool id="filter_bam" name="Filter bam files" version="0.1.0"> + <description> Filters bam files for reads in regions of interest.</description> + <requirements> + <requirement type="package" version="1.3">samtools</requirement> + <requirement type="package" version="2.27.0.0">bedtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + #set input_name = str( $input1.name ) + $__tool_directory__/./filter_bam.bash "$input1" "$input2" "$input3" "$output1" "$output2" "$output3" "$input_name" + ]]></command> + <inputs> + <param type="data" name="input1" format="bam" label="Bam File"/> + <param type="data" name="input2" format="bed" label="Peak Bed File"/> + <param type="data" name="input3" format="tabular" label="chrom.sizes"/> + </inputs> + <outputs> + <data name="output1" format="bed" label="Extended Peak File"/> + <data name="output2" format="bam" label="Filtered Bam File"/> + <data name="output3" format="tabular" label="Read Counts" /> + </outputs> + <tests> + <test> + <param name="input1" value="test.bam"/> + <param name="input2" value="test.bed"/> + <param name="input3" value="mm9.chrom.sizes.txt"/> + <output name="output1" file="ext_peak"/> + <output name="output2" file="test.filter.bam"/> + <output name="output3" file="test.readcounts.txt"/> + </test> + </tests> + <help><![CDATA[ + This tools takes a bam file and filters to reads mapping to regions specified by input bed file. Outputs include filtered bam file and count of total numbers of reads in original bam file. + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4663</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_qPCR_regions.R Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,121 @@ +## Command to run tool: +# Rscript --vanilla find_qPCR_regions.R o.coverage.bed f9.coverage.bed lib_sizes.txt cor_cutoff cov_cutoff output_file + +# Set up R error handling to go to stderr +options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) + +# Avoid crashing Galaxy with an UTF8 error on German LC settings +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +args <- commandArgs(TRUE) + +o.coverage <- args[1] +f9.coverage <- args[2] +lib_sizes <- args[3] +corr_cutoff <- as.numeric(args[4]) +cov_cutoff <- as.numeric(args[5]) +output_file <- args[6] + +o.coverage.data <- read.delim(o.coverage, header=FALSE) +f9.coverage.data <- read.delim(f9.coverage, header=FALSE) +lib.sizes.data <- read.delim(lib_sizes, header=FALSE) + +m <- ncol(o.coverage.data) + +#normalize library sizes to 50 mil reads +lib.sizes.data <- lib.sizes.data/50000000 +#normalize peak reads and spanning reads by library size +o.coverage.data[,5:m] <- t(apply(o.coverage.data[,5:m], 1, function(x) x/t(lib.sizes.data))) +f9.coverage.data[,5:m] <- t(apply(f9.coverage.data[,5:m], 1, function(x) x/t(lib.sizes.data))) + +#returns list of dataframes containing windows for each peak +split_coverage <- function(a) { + returnlist <- list() + temp <- a[1,] + for (i in 2:nrow(a)) { + if (temp[1,4] == strsplit(as.character(a[i,4]),"_window")[[1]][1]){ + temp <- rbind(temp, a[i,]) + }else{ + returnlist[[length(returnlist)+1]] <- temp + temp <- a[i,] + } + } + returnlist[[length(returnlist)+1]] <- temp + return(returnlist) +} + +make_cor_plot <- function(a,b, corr_cut, cov_cut, output_file) { #a=o.coverage b=f9.coverage + + asplit <- split_coverage(a) + bsplit <- split_coverage(b) + + combined_regions <- data.frame() + + for (i in 1:length(asplit)){ + n <- nrow(asplit[[i]])-1 + m <- ncol(asplit[[i]]) + + a_split <- asplit[[i]] + b_split <- bsplit[[i]] + + #calculate correlation between total peak reads and spanning reads in each window + corb <- data.frame(cor(t(a_split[1,5:m]) + , t(b_split[-1,5:m]) + , method = "pearson")) + + data <- data.frame(t(corb), row.names = NULL, stringsAsFactors = FALSE) + + data <- cbind(rep(c(1:n)) + , a_split[-1,1:4] + , data) + colnames(data)<-c("position","chr", "start", "stop", "name", "correlation") + rownames(data)<-NULL + a_split$average <- rowMeans(a_split[,5:m]) + b_split$average <- rowMeans(b_split[,5:m]) + data2 <- data.frame(cbind(c(1:n), a_split[-1,m+1]), stringsAsFactors=FALSE) + data3 <- data.frame(cbind(c(1:n), b_split[-1,m+1]), stringsAsFactors=FALSE) + colnames(data2)<-c("position","averageReadDepth") + colnames(data3)<-c("position","averageReadDepth") + + #keep windows for which correlation with total peak reads is above threshold and + #number of spanning reads is above cutoff + regions <- data[which(data$correlation > corr_cut & data3$averageReadDepth > cov_cut),] + regions <- regions[,2:4] + + #collapse windows to non-overlappin regions + if (nrow(regions)>0){ + regions$V4 <- paste(as.character(a_split[1,4]),"_region1",sep="") + collapsed_regions <- regions[1,] + nregion <- 1 + if (nrow(regions)>=2){ + for (j in 2:nrow(regions)) { + if (as.numeric(regions[j,2]) <= (as.numeric(regions[j-1,3]))) { + collapsed_regions[nrow(collapsed_regions),3] <- regions[j,3] + }else{ + collapsed_regions <- rbind(collapsed_regions, regions[j,]) + nregion <- nregion + 1 + collapsed_regions[nrow(collapsed_regions),4] <- paste(as.character(a_split[1,4]) + ,"_region" + , as.character(nregion) + ,sep="") + } + } + } + rownames(collapsed_regions) <- NULL + + combined_regions <- rbind(combined_regions, collapsed_regions) +} + + + } + + write.table(combined_regions + , output_file + , sep = "\t" + , col.names = FALSE + , row.names = FALSE + , quote = FALSE) + print("Successfully found optimal ATAC-qPCR regions.") +} + +make_cor_plot(o.coverage.data, f9.coverage.data, corr_cutoff, cov_cutoff, output_file)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_qPCR_regions.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,35 @@ +<tool id="find_qPCR_regions" name="Find ATAC qPCR regions" version="0.1.0"> + <description> Determines optimal regions for designing ATAC-qPCR primers.</description> + <requirements> + <requirement type="package" version="3.4.2" >r-base</requirement> + </requirements> + <command><![CDATA[ + Rscript --vanilla $__tool_directory__/find_qPCR_regions.R $input1 $input2 $input3 $input4 $input5 $output + ]]></command> + <inputs> + <param type="data" name="input1" format="tabular" label="Coverage Bed File"/> + <param type="data" name="input2" format="tabular" label="Spanning Fragment Coverage Bed File"/> + <param type="data" name="input3" format="tabular" label="Total Read Counts"/> + <param type="float" name="input4" value="0.8" label="Correlation Cutoff"/> + <param type="integer" name="input5" value="3" label="Coverage Cutoff"/> + </inputs> + <outputs> + <data name="output" format="bed" /> + </outputs> + <tests> + <test> + <param name="input1" value="combined.o.bed.coverage"/> + <param name="input2" value="combined.f9.bed.coverage"/> + <param name="input3" value="lib_sizes.txt"/> + <param name="input4" value="0.7"/> + <param name="input5" value="2"/> + <output name="output" file="qPCR_regions.bed"/> + </test> + </tests> + <help><![CDATA[ + Determines optimal regions for designing ATAC-qPCR primers based on correlation between spanning fragments and total peak height. + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4663</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_window_bed.R Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,64 @@ +## Command to run tool: +# Rscript --vanilla make_window_bed.R qPCR_peaks.bed window_size output_file + +# Set up R error handling to go to stderr +options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) + +# Avoid crashing Galaxy with an UTF8 error on German LC settings +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +args <- commandArgs(TRUE) + +qPCR_bed <- args[1] +window_size <- strtoi(args[2]) +output_file <- args[3] + +qPCR_table <- read.delim(qPCR_bed, header=FALSE, stringsAsFactors=FALSE) + +make_windows_bed <- function(a, size) { #a is a bed file containing peaks of interest and coordinates + #generates bed file with overlapping windows spanning each peak of specified size + return_bed <- data.frame() + for (i in 1:nrow(a)) { + line <- data.frame(a[i,],stringsAsFactors=FALSE) + peak_name <- as.character(line[1,4]) + line <- rbind(line + , data.frame(V1=as.character(line[1,1]) + , V2=line[1,2] + , V3=line[1,2]+size + , V4=as.character(paste(as.character(line[1,4]) + , "_window1" + , sep = "") + ) + ) + ) + count <- as.numeric(line[1,2])+size + nline <- 2 + while (count < as.numeric(line[1,3])) { + line <- rbind(line + , data.frame(V1=as.character(line[nline,1]) + , V2=line[nline,2]+floor(size/4) + , V3=line[nline,2]+floor(size/4)+size + , V4=as.character(paste(as.character(line[1,4]) + , "_window" + , as.character(nline) + , sep = "") + ) + ) + ) + nline <- nline + 1 + count <- as.numeric(line[nline,3]) + } + return_bed <- rbind(return_bed,line) + } + return(return_bed) +} + +output <- make_windows_bed(qPCR_table, window_size) + + +write.table(output + , output_file + , sep = "\t" + , col.names = FALSE + , row.names = FALSE + , quote = FALSE)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_window_bed.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,29 @@ +<tool id="make_window_bed" name="Create bed file of qPCR windows" version="0.1.0"> + <description> Creates bed file of windows spanning peaks of interest.</description> + <requirements> + <requirement type="package" version="3.4.2">r-base</requirement> + </requirements> + <command><![CDATA[ + Rscript --vanilla $__tool_directory__/make_window_bed.R $input1 $input2 $output + ]]></command> + <inputs> + <param type="data" name="input1" format="bed" label="Peak Bed File"/> + <param type="integer" name="input2" value="100" label="Window Size"/> + </inputs> + <outputs> + <data name="output" format="bed" label="qPCR Window Bed File"/> + </outputs> + <tests> + <test> + <param name="input1" value="RAMA_peaks.bed"/> + <param name="input2" value="100"/> + <output name="output" file="qPCR_windows.bed"/> + </test> + </tests> + <help><![CDATA[ + Generates bed file containing overlapping windows of specified size spanning peaks in input bed file. + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4663</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAMA_peaks.bed Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,7 @@ +chr15 95484290 95485433 Dbx2 +chr10 20444676 20445116 Pde7b +chr18 58715130 58715849 Slc27a6 +chr2 32816762 32817713 Rpl12 +chr9 106331200 106332399 Rpl29 +chr2 153116826 153117777 Kif3b +chr1 133049497 133050192 Eif2d \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined.f9.bed.coverage Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,125 @@ +chr15 95484290 95485433 Dbx2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr15 95484290 95484390 Dbx2_window1 0 2 7 0 5 1 0 1 2 1 0 0 0 1 0 0 +chr15 95484340 95484440 Dbx2_window2 0 3 12 2 4 2 0 1 0 1 1 1 0 1 1 2 +chr15 95484390 95484490 Dbx2_window3 0 1 11 3 5 1 1 0 1 2 1 3 1 1 1 2 +chr15 95484440 95484540 Dbx2_window4 0 1 9 2 4 1 1 0 2 2 0 4 1 1 2 2 +chr15 95484490 95484590 Dbx2_window5 0 0 7 2 4 1 0 0 4 1 0 3 1 3 2 2 +chr15 95484540 95484640 Dbx2_window6 0 5 15 2 3 2 0 0 7 0 2 5 1 2 2 3 +chr15 95484590 95484690 Dbx2_window7 1 8 16 2 2 2 0 0 9 3 4 4 1 0 1 3 +chr15 95484640 95484740 Dbx2_window8 1 8 15 0 1 1 0 0 9 3 4 4 1 0 1 1 +chr15 95484690 95484790 Dbx2_window9 1 6 16 2 3 1 0 0 6 3 4 4 3 1 0 1 +chr15 95484740 95484840 Dbx2_window10 1 8 19 5 5 1 0 0 6 3 4 4 2 2 1 1 +chr15 95484790 95484890 Dbx2_window11 2 13 33 6 3 0 0 0 7 5 7 9 5 5 2 3 +chr15 95484840 95484940 Dbx2_window12 1 20 32 9 1 0 0 0 9 5 8 10 5 6 3 4 +chr15 95484890 95484990 Dbx2_window13 1 14 27 8 2 0 0 0 7 4 11 8 4 9 4 5 +chr15 95484940 95485040 Dbx2_window14 1 12 21 10 2 0 1 0 9 4 9 6 5 7 3 6 +chr15 95484990 95485090 Dbx2_window15 0 9 27 8 3 0 1 0 11 7 6 7 7 7 2 4 +chr15 95485040 95485140 Dbx2_window16 0 9 30 7 4 0 1 0 7 6 6 8 7 6 1 2 +chr15 95485090 95485190 Dbx2_window17 0 11 31 8 2 1 1 0 6 5 8 7 7 5 0 2 +chr15 95485140 95485240 Dbx2_window18 0 10 24 6 5 1 0 0 5 8 6 7 5 1 1 2 +chr15 95485190 95485290 Dbx2_window19 2 5 19 4 5 1 0 0 2 6 9 4 6 1 1 3 +chr15 95485240 95485340 Dbx2_window20 1 5 7 1 1 0 0 0 1 4 7 4 3 0 0 1 +chr15 95485290 95485390 Dbx2_window21 0 2 3 1 0 0 0 0 1 1 4 4 2 0 0 0 +chr15 95485340 95485440 Dbx2_window22 0 2 1 1 0 1 0 0 1 0 4 2 2 0 0 0 +chr10 20444676 20445116 Pde7b 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr10 20444676 20444776 Pde7b_window1 2 6 10 2 1 1 0 1 5 7 5 6 3 2 2 0 +chr10 20444726 20444826 Pde7b_window2 5 8 12 1 1 2 0 2 4 7 4 4 4 1 1 1 +chr10 20444776 20444876 Pde7b_window3 1 7 8 0 0 1 1 1 2 3 3 0 2 0 1 1 +chr10 20444826 20444926 Pde7b_window4 1 7 16 1 4 1 3 1 5 3 4 5 3 2 3 0 +chr10 20444876 20444976 Pde7b_window5 4 3 17 1 2 1 2 0 7 5 4 4 2 1 1 0 +chr10 20444926 20445026 Pde7b_window6 3 6 15 1 2 1 3 0 6 2 5 1 4 2 0 1 +chr10 20444976 20445076 Pde7b_window7 0 4 7 1 1 0 1 0 2 1 3 0 1 0 0 0 +chr10 20445026 20445126 Pde7b_window8 0 2 3 1 0 0 1 0 1 1 3 0 0 0 0 0 +chr18 58715130 58715849 Slc27a6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr18 58715130 58715230 Slc27a6_window1 0 3 2 1 2 2 1 1 1 2 4 1 1 1 2 0 +chr18 58715180 58715280 Slc27a6_window2 0 3 3 2 2 3 1 2 4 3 8 2 4 1 1 0 +chr18 58715230 58715330 Slc27a6_window3 1 7 10 2 3 2 1 1 5 6 10 4 7 3 4 2 +chr18 58715280 58715380 Slc27a6_window4 1 9 13 2 3 7 1 3 9 9 14 8 11 5 7 0 +chr18 58715330 58715430 Slc27a6_window5 0 7 16 2 2 4 1 4 9 8 13 11 10 6 3 3 +chr18 58715380 58715480 Slc27a6_window6 0 13 19 3 1 6 2 4 12 8 11 10 7 8 3 4 +chr18 58715430 58715530 Slc27a6_window7 0 15 9 0 1 7 4 5 14 7 9 8 2 5 1 4 +chr18 58715480 58715580 Slc27a6_window8 1 11 11 1 2 6 3 7 11 9 7 7 2 2 0 4 +chr18 58715530 58715630 Slc27a6_window9 1 12 9 3 1 4 3 5 9 10 8 10 4 4 0 5 +chr18 58715580 58715680 Slc27a6_window10 0 9 6 4 1 5 1 4 8 9 8 7 3 2 0 4 +chr18 58715630 58715730 Slc27a6_window11 0 7 8 3 0 4 1 3 7 9 7 7 2 2 0 3 +chr18 58715680 58715780 Slc27a6_window12 1 3 6 1 0 2 2 2 6 6 1 4 2 1 0 0 +chr18 58715730 58715830 Slc27a6_window13 1 1 1 0 0 0 1 0 5 2 3 2 0 0 0 0 +chr18 58715780 58715880 Slc27a6_window14 1 0 1 0 2 0 1 0 6 3 3 1 0 0 0 0 +chr2 32816762 32817713 Rpl12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr2 32816762 32816862 Rpl12_window1 0 6 1 0 3 2 3 0 3 1 2 2 0 0 0 0 +chr2 32816812 32816912 Rpl12_window2 0 3 1 0 1 3 3 0 7 2 1 2 0 0 0 0 +chr2 32816862 32816962 Rpl12_window3 0 2 2 2 0 4 4 1 6 3 1 2 0 0 0 0 +chr2 32816912 32817012 Rpl12_window4 1 8 11 3 1 9 5 1 10 6 2 4 3 1 0 1 +chr2 32816962 32817062 Rpl12_window5 3 25 24 3 5 12 7 3 17 8 11 8 6 1 0 2 +chr2 32817012 32817112 Rpl12_window6 3 26 22 4 6 13 7 4 14 8 13 8 6 0 2 2 +chr2 32817062 32817162 Rpl12_window7 1 10 18 5 2 4 3 3 8 1 7 8 4 1 2 0 +chr2 32817112 32817212 Rpl12_window8 1 20 18 5 2 7 4 1 7 4 7 10 5 2 3 0 +chr2 32817162 32817262 Rpl12_window9 4 24 24 7 7 8 10 5 11 12 8 11 3 3 3 2 +chr2 32817212 32817312 Rpl12_window10 2 20 15 4 8 8 9 5 14 9 9 10 3 3 1 1 +chr2 32817262 32817362 Rpl12_window11 2 19 21 3 4 15 8 5 19 9 13 11 4 6 1 3 +chr2 32817312 32817412 Rpl12_window12 1 22 18 3 5 13 9 6 21 10 13 11 4 4 2 4 +chr2 32817362 32817462 Rpl12_window13 1 15 10 2 3 8 5 3 9 7 7 7 2 3 1 3 +chr2 32817412 32817512 Rpl12_window14 0 10 5 0 1 6 2 1 6 4 4 3 2 2 1 2 +chr2 32817462 32817562 Rpl12_window15 1 11 6 0 2 6 4 1 7 5 4 4 2 3 2 1 +chr2 32817512 32817612 Rpl12_window16 2 9 6 1 1 4 5 0 6 7 1 5 2 4 2 0 +chr2 32817562 32817662 Rpl12_window17 2 9 8 1 2 2 5 1 7 6 1 5 2 2 1 0 +chr2 32817612 32817712 Rpl12_window18 2 5 7 1 2 2 4 1 4 4 1 4 1 2 0 0 +chr2 32817662 32817762 Rpl12_window19 2 6 8 0 0 1 2 1 3 3 2 2 0 3 0 0 +chr9 106331200 106332399 Rpl29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr9 106331200 106331300 Rpl29_window1 1 4 5 3 0 3 3 1 7 6 2 3 1 1 0 0 +chr9 106331250 106331350 Rpl29_window2 1 5 6 2 2 4 6 0 6 5 3 2 2 0 0 0 +chr9 106331300 106331400 Rpl29_window3 1 8 5 1 1 2 7 2 9 5 6 3 1 0 0 0 +chr9 106331350 106331450 Rpl29_window4 2 8 7 1 2 5 9 4 13 9 7 3 2 0 0 0 +chr9 106331400 106331500 Rpl29_window5 1 8 11 2 2 7 7 5 17 9 6 5 4 1 0 0 +chr9 106331450 106331550 Rpl29_window6 3 8 18 2 3 10 10 4 18 10 7 7 5 2 0 1 +chr9 106331500 106331600 Rpl29_window7 5 8 24 3 2 15 11 2 16 9 8 7 5 2 0 2 +chr9 106331550 106331650 Rpl29_window8 4 5 23 4 1 13 9 3 13 9 7 5 4 4 0 2 +chr9 106331600 106331700 Rpl29_window9 2 4 14 5 2 9 5 3 6 5 5 7 2 2 0 2 +chr9 106331650 106331750 Rpl29_window10 2 33 46 11 7 12 6 5 6 9 8 9 7 4 1 2 +chr9 106331700 106331800 Rpl29_window11 5 29 31 8 6 15 3 4 9 10 9 9 6 8 1 4 +chr9 106331750 106331850 Rpl29_window12 5 30 37 3 3 13 6 4 13 11 11 13 4 9 1 2 +chr9 106331800 106331900 Rpl29_window13 3 18 27 2 4 12 6 5 5 8 11 12 4 8 1 3 +chr9 106331850 106331950 Rpl29_window14 1 12 23 2 3 12 7 4 7 11 12 6 5 6 1 2 +chr9 106331900 106332000 Rpl29_window15 0 13 27 3 6 11 9 3 9 14 15 8 3 5 1 2 +chr9 106331950 106332050 Rpl29_window16 1 10 22 2 3 10 8 0 10 13 13 9 3 6 1 2 +chr9 106332000 106332100 Rpl29_window17 3 9 16 0 4 8 5 0 10 9 13 6 2 5 0 1 +chr9 106332050 106332150 Rpl29_window18 1 3 10 0 4 6 8 1 12 6 9 6 4 1 0 1 +chr9 106332100 106332200 Rpl29_window19 1 4 10 1 4 6 9 1 11 7 9 7 5 2 0 1 +chr9 106332150 106332250 Rpl29_window20 0 3 6 4 4 6 7 1 10 6 7 6 3 2 0 1 +chr9 106332200 106332300 Rpl29_window21 0 1 0 2 3 3 4 1 4 3 2 1 2 1 0 0 +chr9 106332250 106332350 Rpl29_window22 0 0 2 2 2 2 5 2 6 2 2 1 3 1 0 0 +chr9 106332300 106332400 Rpl29_window23 0 0 2 2 1 1 5 2 3 0 2 2 2 0 0 0 +chr2 153116826 153117777 Kif3b 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr2 153116826 153116926 Kif3b_window1 1 1 5 1 1 6 5 0 10 1 5 1 1 1 0 0 +chr2 153116876 153116976 Kif3b_window2 2 6 14 3 4 13 5 2 14 2 7 2 1 1 0 0 +chr2 153116926 153117026 Kif3b_window3 1 7 18 2 3 12 6 1 12 3 6 4 1 2 0 0 +chr2 153116976 153117076 Kif3b_window4 0 7 14 1 3 9 5 1 8 3 3 2 1 2 0 0 +chr2 153117026 153117126 Kif3b_window5 1 7 14 7 9 9 7 3 9 4 6 6 3 3 0 0 +chr2 153117076 153117176 Kif3b_window6 2 14 24 6 7 6 12 1 7 6 10 9 4 2 0 1 +chr2 153117126 153117226 Kif3b_window7 0 7 12 2 3 5 8 2 3 4 6 7 2 4 1 1 +chr2 153117176 153117276 Kif3b_window8 3 20 22 5 7 12 9 5 7 9 9 7 7 6 1 5 +chr2 153117226 153117326 Kif3b_window9 4 24 22 6 9 12 10 6 11 9 9 10 9 6 1 3 +chr2 153117276 153117376 Kif3b_window10 4 23 25 4 10 12 9 5 13 7 8 7 8 5 1 3 +chr2 153117326 153117426 Kif3b_window11 2 15 21 4 9 8 7 2 13 5 8 6 4 3 2 2 +chr2 153117376 153117476 Kif3b_window12 1 17 19 4 7 8 10 2 13 5 9 6 5 2 3 2 +chr2 153117426 153117526 Kif3b_window13 1 16 17 5 6 8 8 2 9 5 9 4 4 3 3 1 +chr2 153117476 153117576 Kif3b_window14 3 7 10 3 6 4 5 1 7 2 6 1 1 1 1 0 +chr2 153117526 153117626 Kif3b_window15 3 3 8 1 5 2 4 1 7 2 2 2 1 2 0 2 +chr2 153117576 153117676 Kif3b_window16 1 4 5 0 5 2 4 0 4 1 6 3 2 1 0 1 +chr2 153117626 153117726 Kif3b_window17 0 3 3 0 2 3 1 0 3 1 5 2 2 1 0 1 +chr2 153117676 153117776 Kif3b_window18 0 1 2 0 3 1 0 0 3 0 2 2 1 1 0 0 +chr2 153117726 153117826 Kif3b_window19 1 2 3 1 2 0 0 0 4 1 2 2 1 1 0 0 +chr1 133049497 133050192 Eif2d 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chr1 133049497 133049597 Eif2d_window1 0 3 2 3 1 4 3 1 9 1 2 1 3 1 0 0 +chr1 133049547 133049647 Eif2d_window2 1 9 5 4 2 7 3 1 10 2 2 2 4 0 0 1 +chr1 133049597 133049697 Eif2d_window3 1 14 6 2 3 6 4 1 9 2 1 3 4 0 0 1 +chr1 133049647 133049747 Eif2d_window4 1 11 6 3 0 3 4 0 4 0 0 3 2 0 0 1 +chr1 133049697 133049797 Eif2d_window5 14 36 42 10 6 4 11 5 7 2 4 4 7 0 0 1 +chr1 133049747 133049847 Eif2d_window6 6 24 18 7 4 6 10 4 6 5 6 5 4 2 1 1 +chr1 133049797 133049897 Eif2d_window7 5 19 26 4 5 9 9 4 8 6 7 7 5 2 2 0 +chr1 133049847 133049947 Eif2d_window8 5 16 32 4 7 7 12 4 9 5 6 7 5 2 1 0 +chr1 133049897 133049997 Eif2d_window9 4 13 31 3 7 5 12 2 6 3 4 5 4 1 1 0 +chr1 133049947 133050047 Eif2d_window10 2 6 19 3 4 4 9 1 4 2 1 5 3 0 0 0 +chr1 133049997 133050097 Eif2d_window11 1 4 8 2 0 4 6 0 2 3 1 3 1 0 0 0 +chr1 133050047 133050147 Eif2d_window12 1 3 9 1 1 2 5 0 2 3 1 2 2 0 0 0 +chr1 133050097 133050197 Eif2d_window13 0 2 4 1 2 1 3 0 3 2 1 1 1 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined.f9.coverage Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,233 @@ +chr15 95484290 95485433 Dbx2 0 0 +chr15 95484290 95484390 Dbx2_window1 0 2 +chr15 95484315 95484415 Dbx2_window2 0 2 +chr15 95484340 95484440 Dbx2_window3 0 3 +chr15 95484365 95484465 Dbx2_window4 0 3 +chr15 95484390 95484490 Dbx2_window5 0 1 +chr15 95484415 95484515 Dbx2_window6 0 1 +chr15 95484440 95484540 Dbx2_window7 0 1 +chr15 95484465 95484565 Dbx2_window8 0 0 +chr15 95484490 95484590 Dbx2_window9 0 0 +chr15 95484515 95484615 Dbx2_window10 0 2 +chr15 95484540 95484640 Dbx2_window11 0 5 +chr15 95484565 95484665 Dbx2_window12 1 6 +chr15 95484590 95484690 Dbx2_window13 1 8 +chr15 95484615 95484715 Dbx2_window14 1 9 +chr15 95484640 95484740 Dbx2_window15 1 8 +chr15 95484665 95484765 Dbx2_window16 1 6 +chr15 95484690 95484790 Dbx2_window17 1 6 +chr15 95484715 95484815 Dbx2_window18 1 6 +chr15 95484740 95484840 Dbx2_window19 1 8 +chr15 95484765 95484865 Dbx2_window20 1 11 +chr15 95484790 95484890 Dbx2_window21 2 13 +chr15 95484815 95484915 Dbx2_window22 1 17 +chr15 95484840 95484940 Dbx2_window23 1 20 +chr15 95484865 95484965 Dbx2_window24 1 19 +chr15 95484890 95484990 Dbx2_window25 1 14 +chr15 95484915 95485015 Dbx2_window26 0 14 +chr15 95484940 95485040 Dbx2_window27 1 12 +chr15 95484965 95485065 Dbx2_window28 1 9 +chr15 95484990 95485090 Dbx2_window29 0 9 +chr15 95485015 95485115 Dbx2_window30 0 9 +chr15 95485040 95485140 Dbx2_window31 0 9 +chr15 95485065 95485165 Dbx2_window32 0 10 +chr15 95485090 95485190 Dbx2_window33 0 11 +chr15 95485115 95485215 Dbx2_window34 0 7 +chr15 95485140 95485240 Dbx2_window35 0 10 +chr15 95485165 95485265 Dbx2_window36 1 9 +chr15 95485190 95485290 Dbx2_window37 2 5 +chr15 95485215 95485315 Dbx2_window38 1 4 +chr15 95485240 95485340 Dbx2_window39 1 5 +chr15 95485265 95485365 Dbx2_window40 0 5 +chr15 95485290 95485390 Dbx2_window41 0 2 +chr15 95485315 95485415 Dbx2_window42 0 2 +chr15 95485340 95485440 Dbx2_window43 0 2 +chr10 20444676 20445116 Pde7b 0 0 +chr10 20444676 20444776 Pde7b_window1 2 6 +chr10 20444701 20444801 Pde7b_window2 3 5 +chr10 20444726 20444826 Pde7b_window3 5 8 +chr10 20444751 20444851 Pde7b_window4 1 6 +chr10 20444776 20444876 Pde7b_window5 1 7 +chr10 20444801 20444901 Pde7b_window6 1 6 +chr10 20444826 20444926 Pde7b_window7 1 7 +chr10 20444851 20444951 Pde7b_window8 1 11 +chr10 20444876 20444976 Pde7b_window9 4 3 +chr10 20444901 20445001 Pde7b_window10 3 5 +chr10 20444926 20445026 Pde7b_window11 3 6 +chr10 20444951 20445051 Pde7b_window12 2 6 +chr10 20444976 20445076 Pde7b_window13 0 4 +chr10 20445001 20445101 Pde7b_window14 0 4 +chr10 20445026 20445126 Pde7b_window15 0 2 +chr18 58715130 58715849 Slc27a6 0 0 +chr18 58715130 58715230 Slc27a6_window1 0 3 +chr18 58715155 58715255 Slc27a6_window2 0 2 +chr18 58715180 58715280 Slc27a6_window3 0 3 +chr18 58715205 58715305 Slc27a6_window4 1 5 +chr18 58715230 58715330 Slc27a6_window5 1 7 +chr18 58715255 58715355 Slc27a6_window6 1 7 +chr18 58715280 58715380 Slc27a6_window7 1 9 +chr18 58715305 58715405 Slc27a6_window8 1 7 +chr18 58715330 58715430 Slc27a6_window9 0 7 +chr18 58715355 58715455 Slc27a6_window10 0 10 +chr18 58715380 58715480 Slc27a6_window11 0 13 +chr18 58715405 58715505 Slc27a6_window12 0 20 +chr18 58715430 58715530 Slc27a6_window13 0 15 +chr18 58715455 58715555 Slc27a6_window14 0 11 +chr18 58715480 58715580 Slc27a6_window15 1 11 +chr18 58715505 58715605 Slc27a6_window16 1 13 +chr18 58715530 58715630 Slc27a6_window17 1 12 +chr18 58715555 58715655 Slc27a6_window18 1 11 +chr18 58715580 58715680 Slc27a6_window19 0 9 +chr18 58715605 58715705 Slc27a6_window20 0 9 +chr18 58715630 58715730 Slc27a6_window21 0 7 +chr18 58715655 58715755 Slc27a6_window22 0 4 +chr18 58715680 58715780 Slc27a6_window23 1 3 +chr18 58715705 58715805 Slc27a6_window24 1 0 +chr18 58715730 58715830 Slc27a6_window25 1 1 +chr18 58715755 58715855 Slc27a6_window26 1 0 +chr2 32816762 32817713 Rpl12 0 0 +chr2 32816762 32816862 Rpl12_window1 0 6 +chr2 32816787 32816887 Rpl12_window2 0 5 +chr2 32816812 32816912 Rpl12_window3 0 3 +chr2 32816837 32816937 Rpl12_window4 0 2 +chr2 32816862 32816962 Rpl12_window5 0 2 +chr2 32816887 32816987 Rpl12_window6 1 1 +chr2 32816912 32817012 Rpl12_window7 1 8 +chr2 32816937 32817037 Rpl12_window8 3 14 +chr2 32816962 32817062 Rpl12_window9 3 25 +chr2 32816987 32817087 Rpl12_window10 3 26 +chr2 32817012 32817112 Rpl12_window11 3 26 +chr2 32817037 32817137 Rpl12_window12 3 22 +chr2 32817062 32817162 Rpl12_window13 1 10 +chr2 32817087 32817187 Rpl12_window14 1 13 +chr2 32817112 32817212 Rpl12_window15 1 20 +chr2 32817137 32817237 Rpl12_window16 4 20 +chr2 32817162 32817262 Rpl12_window17 4 24 +chr2 32817187 32817287 Rpl12_window18 2 18 +chr2 32817212 32817312 Rpl12_window19 2 20 +chr2 32817237 32817337 Rpl12_window20 1 17 +chr2 32817262 32817362 Rpl12_window21 2 19 +chr2 32817287 32817387 Rpl12_window22 1 20 +chr2 32817312 32817412 Rpl12_window23 1 22 +chr2 32817337 32817437 Rpl12_window24 1 18 +chr2 32817362 32817462 Rpl12_window25 1 15 +chr2 32817387 32817487 Rpl12_window26 2 14 +chr2 32817412 32817512 Rpl12_window27 0 10 +chr2 32817437 32817537 Rpl12_window28 1 11 +chr2 32817462 32817562 Rpl12_window29 1 11 +chr2 32817487 32817587 Rpl12_window30 1 11 +chr2 32817512 32817612 Rpl12_window31 2 9 +chr2 32817537 32817637 Rpl12_window32 2 8 +chr2 32817562 32817662 Rpl12_window33 2 9 +chr2 32817587 32817687 Rpl12_window34 2 7 +chr2 32817612 32817712 Rpl12_window35 2 5 +chr2 32817637 32817737 Rpl12_window36 2 6 +chr9 106331200 106332399 Rpl29 0 0 +chr9 106331200 106331300 Rpl29_window1 1 4 +chr9 106331225 106331325 Rpl29_window2 1 5 +chr9 106331250 106331350 Rpl29_window3 1 5 +chr9 106331275 106331375 Rpl29_window4 1 7 +chr9 106331300 106331400 Rpl29_window5 1 8 +chr9 106331325 106331425 Rpl29_window6 2 8 +chr9 106331350 106331450 Rpl29_window7 2 8 +chr9 106331375 106331475 Rpl29_window8 1 8 +chr9 106331400 106331500 Rpl29_window9 1 8 +chr9 106331425 106331525 Rpl29_window10 3 8 +chr9 106331450 106331550 Rpl29_window11 3 8 +chr9 106331475 106331575 Rpl29_window12 4 11 +chr9 106331500 106331600 Rpl29_window13 5 8 +chr9 106331525 106331625 Rpl29_window14 6 10 +chr9 106331550 106331650 Rpl29_window15 4 5 +chr9 106331575 106331675 Rpl29_window16 3 3 +chr9 106331600 106331700 Rpl29_window17 2 4 +chr9 106331625 106331725 Rpl29_window18 2 21 +chr9 106331650 106331750 Rpl29_window19 2 33 +chr9 106331675 106331775 Rpl29_window20 4 34 +chr9 106331700 106331800 Rpl29_window21 5 29 +chr9 106331725 106331825 Rpl29_window22 4 27 +chr9 106331750 106331850 Rpl29_window23 5 30 +chr9 106331775 106331875 Rpl29_window24 5 23 +chr9 106331800 106331900 Rpl29_window25 3 18 +chr9 106331825 106331925 Rpl29_window26 2 13 +chr9 106331850 106331950 Rpl29_window27 1 12 +chr9 106331875 106331975 Rpl29_window28 1 13 +chr9 106331900 106332000 Rpl29_window29 0 13 +chr9 106331925 106332025 Rpl29_window30 1 11 +chr9 106331950 106332050 Rpl29_window31 1 10 +chr9 106331975 106332075 Rpl29_window32 1 8 +chr9 106332000 106332100 Rpl29_window33 3 9 +chr9 106332025 106332125 Rpl29_window34 2 7 +chr9 106332050 106332150 Rpl29_window35 1 3 +chr9 106332075 106332175 Rpl29_window36 1 2 +chr9 106332100 106332200 Rpl29_window37 1 4 +chr9 106332125 106332225 Rpl29_window38 0 3 +chr9 106332150 106332250 Rpl29_window39 0 3 +chr9 106332175 106332275 Rpl29_window40 0 2 +chr9 106332200 106332300 Rpl29_window41 0 1 +chr9 106332225 106332325 Rpl29_window42 0 0 +chr9 106332250 106332350 Rpl29_window43 0 0 +chr9 106332275 106332375 Rpl29_window44 0 0 +chr9 106332300 106332400 Rpl29_window45 0 0 +chr2 153116826 153117777 Kif3b 0 0 +chr2 153116826 153116926 Kif3b_window1 1 1 +chr2 153116851 153116951 Kif3b_window2 2 5 +chr2 153116876 153116976 Kif3b_window3 2 6 +chr2 153116901 153117001 Kif3b_window4 2 7 +chr2 153116926 153117026 Kif3b_window5 1 7 +chr2 153116951 153117051 Kif3b_window6 1 7 +chr2 153116976 153117076 Kif3b_window7 0 7 +chr2 153117001 153117101 Kif3b_window8 1 7 +chr2 153117026 153117126 Kif3b_window9 1 7 +chr2 153117051 153117151 Kif3b_window10 5 13 +chr2 153117076 153117176 Kif3b_window11 2 14 +chr2 153117101 153117201 Kif3b_window12 1 8 +chr2 153117126 153117226 Kif3b_window13 0 7 +chr2 153117151 153117251 Kif3b_window14 2 12 +chr2 153117176 153117276 Kif3b_window15 3 20 +chr2 153117201 153117301 Kif3b_window16 4 23 +chr2 153117226 153117326 Kif3b_window17 4 24 +chr2 153117251 153117351 Kif3b_window18 5 24 +chr2 153117276 153117376 Kif3b_window19 4 23 +chr2 153117301 153117401 Kif3b_window20 2 17 +chr2 153117326 153117426 Kif3b_window21 2 15 +chr2 153117351 153117451 Kif3b_window22 1 14 +chr2 153117376 153117476 Kif3b_window23 1 17 +chr2 153117401 153117501 Kif3b_window24 1 18 +chr2 153117426 153117526 Kif3b_window25 1 16 +chr2 153117451 153117551 Kif3b_window26 1 12 +chr2 153117476 153117576 Kif3b_window27 3 7 +chr2 153117501 153117601 Kif3b_window28 3 5 +chr2 153117526 153117626 Kif3b_window29 3 3 +chr2 153117551 153117651 Kif3b_window30 2 4 +chr2 153117576 153117676 Kif3b_window31 1 4 +chr2 153117601 153117701 Kif3b_window32 1 4 +chr2 153117626 153117726 Kif3b_window33 0 3 +chr2 153117651 153117751 Kif3b_window34 0 3 +chr2 153117676 153117776 Kif3b_window35 0 1 +chr2 153117701 153117801 Kif3b_window36 1 2 +chr1 133049497 133050192 Eif2d 0 0 +chr1 133049497 133049597 Eif2d_window1 0 3 +chr1 133049522 133049622 Eif2d_window2 0 4 +chr1 133049547 133049647 Eif2d_window3 1 9 +chr1 133049572 133049672 Eif2d_window4 1 13 +chr1 133049597 133049697 Eif2d_window5 1 14 +chr1 133049622 133049722 Eif2d_window6 1 11 +chr1 133049647 133049747 Eif2d_window7 1 11 +chr1 133049672 133049772 Eif2d_window8 6 19 +chr1 133049697 133049797 Eif2d_window9 14 36 +chr1 133049722 133049822 Eif2d_window10 4 27 +chr1 133049747 133049847 Eif2d_window11 6 24 +chr1 133049772 133049872 Eif2d_window12 3 13 +chr1 133049797 133049897 Eif2d_window13 5 19 +chr1 133049822 133049922 Eif2d_window14 5 16 +chr1 133049847 133049947 Eif2d_window15 5 16 +chr1 133049872 133049972 Eif2d_window16 5 15 +chr1 133049897 133049997 Eif2d_window17 4 13 +chr1 133049922 133050022 Eif2d_window18 3 8 +chr1 133049947 133050047 Eif2d_window19 2 6 +chr1 133049972 133050072 Eif2d_window20 1 4 +chr1 133049997 133050097 Eif2d_window21 1 4 +chr1 133050022 133050122 Eif2d_window22 1 4 +chr1 133050047 133050147 Eif2d_window23 1 3 +chr1 133050072 133050172 Eif2d_window24 1 3 +chr1 133050097 133050197 Eif2d_window25 0 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined.o.bed.coverage Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,125 @@ +chr15 95484290 95485433 Dbx2 29 170 406 83 70 23 6 6 104 63 125 63 55 78 34 44 +chr15 95484290 95484390 Dbx2_window1 1 3 43 3 14 4 3 1 9 2 1 5 3 3 1 2 +chr15 95484340 95484440 Dbx2_window2 1 4 39 5 11 5 3 4 7 6 1 6 3 2 2 2 +chr15 95484390 95484490 Dbx2_window3 0 4 35 8 8 7 4 3 7 5 2 5 3 7 4 1 +chr15 95484440 95484540 Dbx2_window4 0 9 35 7 10 8 1 1 6 7 4 4 2 7 3 1 +chr15 95484490 95484590 Dbx2_window5 1 10 41 6 6 6 1 0 9 5 6 4 3 9 5 3 +chr15 95484540 95484640 Dbx2_window6 1 14 31 4 6 9 1 0 15 7 12 7 5 5 4 5 +chr15 95484590 95484690 Dbx2_window7 1 18 26 7 4 3 0 0 14 10 12 8 7 6 4 4 +chr15 95484640 95484740 Dbx2_window8 0 24 30 8 11 3 0 0 16 11 13 8 8 8 1 6 +chr15 95484690 95484790 Dbx2_window9 1 29 50 11 16 4 0 0 18 11 10 9 6 7 4 6 +chr15 95484740 95484840 Dbx2_window10 2 36 50 10 15 3 0 0 19 11 16 13 6 8 10 7 +chr15 95484790 95484890 Dbx2_window11 2 35 59 11 12 3 0 0 17 8 18 11 5 15 10 5 +chr15 95484840 95484940 Dbx2_window12 7 43 59 18 6 0 0 0 16 8 19 14 7 24 12 12 +chr15 95484890 95484990 Dbx2_window13 13 43 61 21 8 0 1 2 18 10 21 11 10 30 14 14 +chr15 95484940 95485040 Dbx2_window14 17 48 82 21 7 0 1 2 18 13 24 12 14 26 11 16 +chr15 95484990 95485090 Dbx2_window15 15 39 80 20 6 0 1 2 24 11 32 15 15 29 6 13 +chr15 95485040 95485140 Dbx2_window16 5 35 76 18 9 1 1 0 25 13 26 9 18 23 4 10 +chr15 95485090 95485190 Dbx2_window17 3 31 95 24 7 1 1 0 29 16 27 15 18 19 3 10 +chr15 95485140 95485240 Dbx2_window18 3 31 114 17 14 1 1 0 29 17 35 15 14 7 3 9 +chr15 95485190 95485290 Dbx2_window19 6 35 117 20 14 1 0 0 22 15 40 14 11 6 2 8 +chr15 95485240 95485340 Dbx2_window20 5 31 91 13 11 2 0 0 11 8 39 13 11 3 3 4 +chr15 95485290 95485390 Dbx2_window21 4 19 50 11 6 2 0 0 4 7 25 8 8 3 2 3 +chr15 95485340 95485440 Dbx2_window22 1 12 21 5 2 3 0 0 0 3 15 7 6 0 2 1 +chr10 20444676 20445116 Pde7b 72 177 214 15 34 16 16 20 67 43 82 40 36 18 19 14 +chr10 20444676 20444776 Pde7b_window1 21 34 31 3 7 6 4 5 12 9 22 12 12 1 5 1 +chr10 20444726 20444826 Pde7b_window2 27 90 100 5 14 10 6 5 24 16 43 18 15 9 11 3 +chr10 20444776 20444876 Pde7b_window3 57 145 151 9 20 12 7 12 42 24 51 25 21 13 14 11 +chr10 20444826 20444926 Pde7b_window4 50 139 165 7 23 10 9 13 50 29 55 28 20 13 12 12 +chr10 20444876 20444976 Pde7b_window5 33 72 111 10 19 7 9 9 39 22 39 19 21 8 6 11 +chr10 20444926 20445026 Pde7b_window6 15 38 59 5 13 3 7 5 26 18 26 15 16 6 7 2 +chr10 20444976 20445076 Pde7b_window7 7 11 27 6 6 1 5 0 11 8 10 3 8 4 2 1 +chr10 20445026 20445126 Pde7b_window8 4 7 19 2 4 1 4 2 6 7 9 2 4 3 3 0 +chr18 58715130 58715849 Slc27a6 36 166 227 60 58 56 51 72 170 133 201 133 113 162 53 100 +chr18 58715130 58715230 Slc27a6_window1 1 16 27 2 7 4 8 10 15 10 24 13 15 18 8 6 +chr18 58715180 58715280 Slc27a6_window2 1 24 47 3 8 7 14 13 35 20 46 22 28 35 14 15 +chr18 58715230 58715330 Slc27a6_window3 7 36 60 5 7 14 16 22 47 29 70 38 40 58 21 27 +chr18 58715280 58715380 Slc27a6_window4 10 50 80 8 8 21 12 22 56 32 78 52 52 73 25 44 +chr18 58715330 58715430 Slc27a6_window5 11 71 80 18 20 26 12 28 64 41 88 64 60 81 29 49 +chr18 58715380 58715480 Slc27a6_window6 14 75 80 22 24 20 16 31 66 37 74 59 54 63 28 56 +chr18 58715430 58715530 Slc27a6_window7 13 70 87 28 29 17 20 30 69 57 68 52 45 55 21 44 +chr18 58715480 58715580 Slc27a6_window8 16 65 75 28 25 17 18 31 63 53 59 47 30 44 14 40 +chr18 58715530 58715630 Slc27a6_window9 12 46 63 24 22 18 8 15 45 48 43 26 17 35 3 13 +chr18 58715580 58715680 Slc27a6_window10 8 32 46 19 10 15 7 9 32 35 31 25 10 20 0 8 +chr18 58715630 58715730 Slc27a6_window11 6 27 32 14 8 11 8 9 23 29 27 24 9 19 0 7 +chr18 58715680 58715780 Slc27a6_window12 5 15 24 11 5 9 8 8 21 25 21 17 8 11 2 6 +chr18 58715730 58715830 Slc27a6_window13 6 9 19 8 4 6 10 5 13 15 19 12 7 8 2 3 +chr18 58715780 58715880 Slc27a6_window14 4 2 10 5 4 5 4 3 10 9 14 6 4 4 2 0 +chr2 32816762 32817713 Rpl12 58 243 278 57 88 124 92 59 169 112 126 81 57 44 26 38 +chr2 32816762 32816862 Rpl12_window1 0 8 8 2 10 4 1 0 10 5 5 2 0 0 0 0 +chr2 32816812 32816912 Rpl12_window2 3 14 21 5 10 9 7 3 16 10 5 5 3 3 0 5 +chr2 32816862 32816962 Rpl12_window3 10 32 32 9 15 17 12 7 25 17 14 9 6 7 0 7 +chr2 32816912 32817012 Rpl12_window4 11 33 40 13 11 18 13 8 25 16 16 11 6 12 2 6 +chr2 32816962 32817062 Rpl12_window5 12 44 43 17 22 26 16 7 29 18 24 14 10 11 2 5 +chr2 32817012 32817112 Rpl12_window6 15 67 79 23 20 35 19 13 40 25 37 23 19 17 5 9 +chr2 32817062 32817162 Rpl12_window7 23 88 108 25 30 46 38 17 52 36 45 25 29 12 9 10 +chr2 32817112 32817212 Rpl12_window8 33 101 121 30 27 45 42 26 57 47 53 30 33 12 12 13 +chr2 32817162 32817262 Rpl12_window9 27 96 93 27 27 37 40 21 55 38 49 26 25 10 12 11 +chr2 32817212 32817312 Rpl12_window10 17 71 52 16 25 30 29 18 48 31 40 23 11 8 9 10 +chr2 32817262 32817362 Rpl12_window11 5 54 39 11 17 23 19 7 37 24 30 20 8 7 7 7 +chr2 32817312 32817412 Rpl12_window12 4 40 43 4 14 28 16 13 37 25 27 18 5 11 8 9 +chr2 32817362 32817462 Rpl12_window13 7 40 48 3 14 26 14 14 36 23 25 17 6 9 7 12 +chr2 32817412 32817512 Rpl12_window14 6 37 43 4 13 25 12 14 31 21 19 14 6 9 4 10 +chr2 32817462 32817562 Rpl12_window15 6 27 30 3 12 15 9 9 21 12 12 12 7 9 2 7 +chr2 32817512 32817612 Rpl12_window16 2 15 22 1 6 6 5 4 13 6 5 6 4 5 2 1 +chr2 32817562 32817662 Rpl12_window17 1 11 25 1 7 7 4 4 12 8 4 7 5 3 2 1 +chr2 32817612 32817712 Rpl12_window18 2 14 29 1 5 5 6 4 10 5 4 7 4 3 1 0 +chr2 32817662 32817762 Rpl12_window19 2 15 29 3 6 10 9 4 9 7 8 4 3 3 1 3 +chr9 106331200 106332399 Rpl29 94 304 471 97 119 193 184 89 260 178 178 117 98 101 28 50 +chr9 106331200 106331300 Rpl29_window1 4 11 12 8 5 13 13 3 20 13 11 6 5 5 0 0 +chr9 106331250 106331350 Rpl29_window2 5 15 21 10 10 20 15 8 31 15 15 5 7 5 0 0 +chr9 106331300 106331400 Rpl29_window3 6 17 27 10 9 20 23 8 32 16 18 6 5 9 0 0 +chr9 106331350 106331450 Rpl29_window4 8 18 33 7 14 19 17 5 35 12 19 9 7 10 0 1 +chr9 106331400 106331500 Rpl29_window5 12 21 35 6 12 16 24 11 37 24 16 12 6 8 0 3 +chr9 106331450 106331550 Rpl29_window6 15 22 32 7 12 19 23 11 38 23 19 14 7 7 0 6 +chr9 106331500 106331600 Rpl29_window7 14 34 70 10 14 28 38 15 45 30 25 18 12 4 4 6 +chr9 106331550 106331650 Rpl29_window8 27 73 131 19 21 40 44 22 53 35 36 26 22 15 6 7 +chr9 106331600 106331700 Rpl29_window9 32 96 173 30 30 56 50 25 56 38 41 35 30 37 11 10 +chr9 106331650 106331750 Rpl29_window10 42 120 197 33 36 66 49 32 61 51 40 42 33 48 16 25 +chr9 106331700 106331800 Rpl29_window11 36 130 200 36 48 66 50 40 69 55 46 48 35 53 19 32 +chr9 106331750 106331850 Rpl29_window12 32 119 172 30 38 59 47 31 70 48 52 47 29 36 13 28 +chr9 106331800 106331900 Rpl29_window13 14 74 141 19 34 44 37 25 62 48 44 33 25 28 9 18 +chr9 106331850 106331950 Rpl29_window14 8 62 84 17 28 31 28 11 42 36 31 22 18 19 2 8 +chr9 106331900 106332000 Rpl29_window15 9 41 61 13 22 22 25 9 36 34 27 14 14 15 3 8 +chr9 106331950 106332050 Rpl29_window16 8 29 42 9 16 16 18 11 31 25 29 8 13 9 2 7 +chr9 106332000 106332100 Rpl29_window17 6 24 40 9 15 17 14 4 24 20 29 6 10 9 1 3 +chr9 106332050 106332150 Rpl29_window18 9 23 33 9 10 22 14 3 16 13 33 7 8 8 1 0 +chr9 106332100 106332200 Rpl29_window19 5 19 29 10 7 26 15 2 21 15 24 8 8 6 0 1 +chr9 106332150 106332250 Rpl29_window20 1 18 24 9 6 20 16 1 25 13 16 12 6 2 0 1 +chr9 106332200 106332300 Rpl29_window21 0 9 18 9 9 14 17 1 24 12 13 9 6 1 0 1 +chr9 106332250 106332350 Rpl29_window22 3 12 15 6 7 8 17 3 25 9 8 10 7 2 0 1 +chr9 106332300 106332400 Rpl29_window23 3 8 10 5 6 6 12 6 16 4 6 3 6 1 2 0 +chr2 153116826 153117777 Kif3b 74 211 266 79 108 127 109 47 159 86 100 77 65 57 22 38 +chr2 153116826 153116926 Kif3b_window1 3 13 22 8 10 15 12 4 13 9 7 6 5 2 2 4 +chr2 153116876 153116976 Kif3b_window2 3 10 27 13 9 17 13 7 17 11 10 5 7 3 0 6 +chr2 153116926 153117026 Kif3b_window3 14 19 39 17 17 24 15 9 26 10 13 11 7 7 0 8 +chr2 153116976 153117076 Kif3b_window4 23 49 82 27 33 29 33 16 51 15 27 18 14 19 5 8 +chr2 153117026 153117126 Kif3b_window5 24 96 114 31 40 43 42 20 69 28 39 30 24 28 9 9 +chr2 153117076 153117176 Kif3b_window6 38 113 126 27 49 49 51 23 62 35 44 31 25 34 11 16 +chr2 153117126 153117226 Kif3b_window7 41 98 105 21 34 41 45 19 53 34 36 29 27 32 8 18 +chr2 153117176 153117276 Kif3b_window8 36 54 63 18 25 25 30 13 29 27 21 20 17 17 7 12 +chr2 153117226 153117326 Kif3b_window9 10 30 36 12 11 15 15 9 19 19 13 13 11 7 3 9 +chr2 153117276 153117376 Kif3b_window10 5 18 20 12 11 16 10 6 18 13 7 10 8 5 4 3 +chr2 153117326 153117426 Kif3b_window11 4 23 16 12 12 19 12 4 16 14 8 8 9 5 4 3 +chr2 153117376 153117476 Kif3b_window12 4 34 24 11 15 18 16 3 20 8 7 9 10 5 2 5 +chr2 153117426 153117526 Kif3b_window13 3 30 31 11 18 17 19 1 21 10 16 7 9 4 3 5 +chr2 153117476 153117576 Kif3b_window14 6 26 40 8 16 15 12 4 25 11 20 10 10 3 3 5 +chr2 153117526 153117626 Kif3b_window15 7 17 33 7 15 12 8 6 18 7 21 8 10 3 2 3 +chr2 153117576 153117676 Kif3b_window16 5 13 29 5 14 13 7 5 21 6 16 12 6 2 1 3 +chr2 153117626 153117726 Kif3b_window17 4 13 16 4 14 10 6 3 16 3 9 12 5 3 0 1 +chr2 153117676 153117776 Kif3b_window18 2 11 20 4 9 8 8 1 17 6 8 10 6 2 0 1 +chr2 153117726 153117826 Kif3b_window19 1 10 11 3 6 6 4 1 11 6 6 8 5 2 0 0 +chr1 133049497 133050192 Eif2d 146 406 445 66 96 86 114 49 125 59 72 41 65 25 14 14 +chr1 133049497 133049597 Eif2d_window1 1 15 7 5 3 8 3 0 11 1 2 3 3 3 0 1 +chr1 133049547 133049647 Eif2d_window2 3 31 25 11 12 12 11 3 16 5 4 6 6 3 0 3 +chr1 133049597 133049697 Eif2d_window3 37 112 115 22 36 25 27 16 33 16 20 12 17 2 2 5 +chr1 133049647 133049747 Eif2d_window4 74 209 224 36 54 37 54 21 52 29 35 17 31 7 6 8 +chr1 133049697 133049797 Eif2d_window5 111 295 309 41 65 43 69 29 71 37 51 23 34 16 8 10 +chr1 133049747 133049847 Eif2d_window6 115 285 297 38 51 43 64 26 72 35 42 21 35 17 8 7 +chr1 133049797 133049897 Eif2d_window7 62 197 217 25 33 34 50 22 51 24 29 16 26 11 5 1 +chr1 133049847 133049947 Eif2d_window8 28 105 113 17 19 25 30 20 34 13 21 11 19 4 2 0 +chr1 133049897 133049997 Eif2d_window9 12 35 63 10 12 13 22 10 25 9 12 8 17 2 6 0 +chr1 133049947 133050047 Eif2d_window10 10 23 39 8 12 10 19 6 15 5 9 5 10 2 5 0 +chr1 133049997 133050097 Eif2d_window11 4 16 37 7 11 7 11 6 13 1 6 5 6 1 3 0 +chr1 133050047 133050147 Eif2d_window12 1 10 21 3 7 5 9 2 10 3 4 3 6 2 0 2 +chr1 133050097 133050197 Eif2d_window13 1 6 13 1 6 6 7 3 7 7 2 2 5 2 0 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined.o.coverage Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,233 @@ +chr15 95484290 95485433 Dbx2 29 170 +chr15 95484290 95484390 Dbx2_window1 1 3 +chr15 95484315 95484415 Dbx2_window2 1 4 +chr15 95484340 95484440 Dbx2_window3 1 4 +chr15 95484365 95484465 Dbx2_window4 0 5 +chr15 95484390 95484490 Dbx2_window5 0 4 +chr15 95484415 95484515 Dbx2_window6 0 6 +chr15 95484440 95484540 Dbx2_window7 0 9 +chr15 95484465 95484565 Dbx2_window8 1 10 +chr15 95484490 95484590 Dbx2_window9 1 10 +chr15 95484515 95484615 Dbx2_window10 1 14 +chr15 95484540 95484640 Dbx2_window11 1 14 +chr15 95484565 95484665 Dbx2_window12 1 16 +chr15 95484590 95484690 Dbx2_window13 1 18 +chr15 95484615 95484715 Dbx2_window14 1 21 +chr15 95484640 95484740 Dbx2_window15 0 24 +chr15 95484665 95484765 Dbx2_window16 0 26 +chr15 95484690 95484790 Dbx2_window17 1 29 +chr15 95484715 95484815 Dbx2_window18 2 31 +chr15 95484740 95484840 Dbx2_window19 2 36 +chr15 95484765 95484865 Dbx2_window20 2 36 +chr15 95484790 95484890 Dbx2_window21 2 35 +chr15 95484815 95484915 Dbx2_window22 4 42 +chr15 95484840 95484940 Dbx2_window23 7 43 +chr15 95484865 95484965 Dbx2_window24 11 46 +chr15 95484890 95484990 Dbx2_window25 13 43 +chr15 95484915 95485015 Dbx2_window26 15 40 +chr15 95484940 95485040 Dbx2_window27 17 48 +chr15 95484965 95485065 Dbx2_window28 17 40 +chr15 95484990 95485090 Dbx2_window29 15 39 +chr15 95485015 95485115 Dbx2_window30 12 41 +chr15 95485040 95485140 Dbx2_window31 5 35 +chr15 95485065 95485165 Dbx2_window32 3 28 +chr15 95485090 95485190 Dbx2_window33 3 31 +chr15 95485115 95485215 Dbx2_window34 4 33 +chr15 95485140 95485240 Dbx2_window35 3 31 +chr15 95485165 95485265 Dbx2_window36 3 34 +chr15 95485190 95485290 Dbx2_window37 6 35 +chr15 95485215 95485315 Dbx2_window38 6 33 +chr15 95485240 95485340 Dbx2_window39 5 31 +chr15 95485265 95485365 Dbx2_window40 5 27 +chr15 95485290 95485390 Dbx2_window41 4 19 +chr15 95485315 95485415 Dbx2_window42 3 14 +chr15 95485340 95485440 Dbx2_window43 1 12 +chr10 20444676 20445116 Pde7b 72 177 +chr10 20444676 20444776 Pde7b_window1 21 34 +chr10 20444701 20444801 Pde7b_window2 22 65 +chr10 20444726 20444826 Pde7b_window3 27 90 +chr10 20444751 20444851 Pde7b_window4 49 126 +chr10 20444776 20444876 Pde7b_window5 57 145 +chr10 20444801 20444901 Pde7b_window6 57 146 +chr10 20444826 20444926 Pde7b_window7 50 139 +chr10 20444851 20444951 Pde7b_window8 43 116 +chr10 20444876 20444976 Pde7b_window9 33 72 +chr10 20444901 20445001 Pde7b_window10 21 53 +chr10 20444926 20445026 Pde7b_window11 15 38 +chr10 20444951 20445051 Pde7b_window12 7 14 +chr10 20444976 20445076 Pde7b_window13 7 11 +chr10 20445001 20445101 Pde7b_window14 7 8 +chr10 20445026 20445126 Pde7b_window15 4 7 +chr18 58715130 58715849 Slc27a6 36 166 +chr18 58715130 58715230 Slc27a6_window1 1 16 +chr18 58715155 58715255 Slc27a6_window2 1 19 +chr18 58715180 58715280 Slc27a6_window3 1 24 +chr18 58715205 58715305 Slc27a6_window4 6 31 +chr18 58715230 58715330 Slc27a6_window5 7 36 +chr18 58715255 58715355 Slc27a6_window6 8 42 +chr18 58715280 58715380 Slc27a6_window7 10 50 +chr18 58715305 58715405 Slc27a6_window8 11 57 +chr18 58715330 58715430 Slc27a6_window9 11 71 +chr18 58715355 58715455 Slc27a6_window10 13 74 +chr18 58715380 58715480 Slc27a6_window11 14 75 +chr18 58715405 58715505 Slc27a6_window12 14 78 +chr18 58715430 58715530 Slc27a6_window13 13 70 +chr18 58715455 58715555 Slc27a6_window14 11 69 +chr18 58715480 58715580 Slc27a6_window15 16 65 +chr18 58715505 58715605 Slc27a6_window16 16 52 +chr18 58715530 58715630 Slc27a6_window17 12 46 +chr18 58715555 58715655 Slc27a6_window18 8 32 +chr18 58715580 58715680 Slc27a6_window19 8 32 +chr18 58715605 58715705 Slc27a6_window20 9 35 +chr18 58715630 58715730 Slc27a6_window21 6 27 +chr18 58715655 58715755 Slc27a6_window22 5 24 +chr18 58715680 58715780 Slc27a6_window23 5 15 +chr18 58715705 58715805 Slc27a6_window24 5 13 +chr18 58715730 58715830 Slc27a6_window25 6 9 +chr18 58715755 58715855 Slc27a6_window26 5 8 +chr2 32816762 32817713 Rpl12 58 243 +chr2 32816762 32816862 Rpl12_window1 0 8 +chr2 32816787 32816887 Rpl12_window2 0 9 +chr2 32816812 32816912 Rpl12_window3 3 14 +chr2 32816837 32816937 Rpl12_window4 8 20 +chr2 32816862 32816962 Rpl12_window5 10 32 +chr2 32816887 32816987 Rpl12_window6 11 34 +chr2 32816912 32817012 Rpl12_window7 11 33 +chr2 32816937 32817037 Rpl12_window8 13 39 +chr2 32816962 32817062 Rpl12_window9 12 44 +chr2 32816987 32817087 Rpl12_window10 9 58 +chr2 32817012 32817112 Rpl12_window11 15 67 +chr2 32817037 32817137 Rpl12_window12 17 67 +chr2 32817062 32817162 Rpl12_window13 23 88 +chr2 32817087 32817187 Rpl12_window14 27 97 +chr2 32817112 32817212 Rpl12_window15 33 101 +chr2 32817137 32817237 Rpl12_window16 32 107 +chr2 32817162 32817262 Rpl12_window17 27 96 +chr2 32817187 32817287 Rpl12_window18 25 83 +chr2 32817212 32817312 Rpl12_window19 17 71 +chr2 32817237 32817337 Rpl12_window20 9 60 +chr2 32817262 32817362 Rpl12_window21 5 54 +chr2 32817287 32817387 Rpl12_window22 3 46 +chr2 32817312 32817412 Rpl12_window23 4 40 +chr2 32817337 32817437 Rpl12_window24 5 41 +chr2 32817362 32817462 Rpl12_window25 7 40 +chr2 32817387 32817487 Rpl12_window26 6 41 +chr2 32817412 32817512 Rpl12_window27 6 37 +chr2 32817437 32817537 Rpl12_window28 7 32 +chr2 32817462 32817562 Rpl12_window29 6 27 +chr2 32817487 32817587 Rpl12_window30 6 19 +chr2 32817512 32817612 Rpl12_window31 2 15 +chr2 32817537 32817637 Rpl12_window32 1 11 +chr2 32817562 32817662 Rpl12_window33 1 11 +chr2 32817587 32817687 Rpl12_window34 3 12 +chr2 32817612 32817712 Rpl12_window35 2 14 +chr2 32817637 32817737 Rpl12_window36 2 15 +chr9 106331200 106332399 Rpl29 94 304 +chr9 106331200 106331300 Rpl29_window1 4 11 +chr9 106331225 106331325 Rpl29_window2 4 13 +chr9 106331250 106331350 Rpl29_window3 5 15 +chr9 106331275 106331375 Rpl29_window4 6 17 +chr9 106331300 106331400 Rpl29_window5 6 17 +chr9 106331325 106331425 Rpl29_window6 7 19 +chr9 106331350 106331450 Rpl29_window7 8 18 +chr9 106331375 106331475 Rpl29_window8 10 18 +chr9 106331400 106331500 Rpl29_window9 12 21 +chr9 106331425 106331525 Rpl29_window10 14 24 +chr9 106331450 106331550 Rpl29_window11 15 22 +chr9 106331475 106331575 Rpl29_window12 16 31 +chr9 106331500 106331600 Rpl29_window13 14 34 +chr9 106331525 106331625 Rpl29_window14 16 40 +chr9 106331550 106331650 Rpl29_window15 27 73 +chr9 106331575 106331675 Rpl29_window16 24 75 +chr9 106331600 106331700 Rpl29_window17 32 96 +chr9 106331625 106331725 Rpl29_window18 41 114 +chr9 106331650 106331750 Rpl29_window19 42 120 +chr9 106331675 106331775 Rpl29_window20 48 127 +chr9 106331700 106331800 Rpl29_window21 36 130 +chr9 106331725 106331825 Rpl29_window22 35 116 +chr9 106331750 106331850 Rpl29_window23 32 119 +chr9 106331775 106331875 Rpl29_window24 27 90 +chr9 106331800 106331900 Rpl29_window25 14 74 +chr9 106331825 106331925 Rpl29_window26 12 64 +chr9 106331850 106331950 Rpl29_window27 8 62 +chr9 106331875 106331975 Rpl29_window28 8 56 +chr9 106331900 106332000 Rpl29_window29 9 41 +chr9 106331925 106332025 Rpl29_window30 6 28 +chr9 106331950 106332050 Rpl29_window31 8 29 +chr9 106331975 106332075 Rpl29_window32 8 30 +chr9 106332000 106332100 Rpl29_window33 6 24 +chr9 106332025 106332125 Rpl29_window34 9 22 +chr9 106332050 106332150 Rpl29_window35 9 23 +chr9 106332075 106332175 Rpl29_window36 6 22 +chr9 106332100 106332200 Rpl29_window37 5 19 +chr9 106332125 106332225 Rpl29_window38 3 15 +chr9 106332150 106332250 Rpl29_window39 1 18 +chr9 106332175 106332275 Rpl29_window40 1 15 +chr9 106332200 106332300 Rpl29_window41 0 9 +chr9 106332225 106332325 Rpl29_window42 0 11 +chr9 106332250 106332350 Rpl29_window43 3 12 +chr9 106332275 106332375 Rpl29_window44 3 7 +chr9 106332300 106332400 Rpl29_window45 3 8 +chr2 153116826 153117777 Kif3b 74 211 +chr2 153116826 153116926 Kif3b_window1 3 13 +chr2 153116851 153116951 Kif3b_window2 2 11 +chr2 153116876 153116976 Kif3b_window3 3 10 +chr2 153116901 153117001 Kif3b_window4 10 18 +chr2 153116926 153117026 Kif3b_window5 14 19 +chr2 153116951 153117051 Kif3b_window6 15 37 +chr2 153116976 153117076 Kif3b_window7 23 49 +chr2 153117001 153117101 Kif3b_window8 24 66 +chr2 153117026 153117126 Kif3b_window9 24 96 +chr2 153117051 153117151 Kif3b_window10 38 104 +chr2 153117076 153117176 Kif3b_window11 38 113 +chr2 153117101 153117201 Kif3b_window12 45 112 +chr2 153117126 153117226 Kif3b_window13 41 98 +chr2 153117151 153117251 Kif3b_window14 35 76 +chr2 153117176 153117276 Kif3b_window15 36 54 +chr2 153117201 153117301 Kif3b_window16 20 40 +chr2 153117226 153117326 Kif3b_window17 10 30 +chr2 153117251 153117351 Kif3b_window18 5 22 +chr2 153117276 153117376 Kif3b_window19 5 18 +chr2 153117301 153117401 Kif3b_window20 5 18 +chr2 153117326 153117426 Kif3b_window21 4 23 +chr2 153117351 153117451 Kif3b_window22 3 28 +chr2 153117376 153117476 Kif3b_window23 4 34 +chr2 153117401 153117501 Kif3b_window24 3 32 +chr2 153117426 153117526 Kif3b_window25 3 30 +chr2 153117451 153117551 Kif3b_window26 2 28 +chr2 153117476 153117576 Kif3b_window27 6 26 +chr2 153117501 153117601 Kif3b_window28 6 23 +chr2 153117526 153117626 Kif3b_window29 7 17 +chr2 153117551 153117651 Kif3b_window30 5 12 +chr2 153117576 153117676 Kif3b_window31 5 13 +chr2 153117601 153117701 Kif3b_window32 6 13 +chr2 153117626 153117726 Kif3b_window33 4 13 +chr2 153117651 153117751 Kif3b_window34 2 11 +chr2 153117676 153117776 Kif3b_window35 2 11 +chr2 153117701 153117801 Kif3b_window36 1 11 +chr1 133049497 133050192 Eif2d 146 406 +chr1 133049497 133049597 Eif2d_window1 1 15 +chr1 133049522 133049622 Eif2d_window2 1 22 +chr1 133049547 133049647 Eif2d_window3 3 31 +chr1 133049572 133049672 Eif2d_window4 8 61 +chr1 133049597 133049697 Eif2d_window5 37 112 +chr1 133049622 133049722 Eif2d_window6 53 151 +chr1 133049647 133049747 Eif2d_window7 74 209 +chr1 133049672 133049772 Eif2d_window8 92 242 +chr1 133049697 133049797 Eif2d_window9 111 295 +chr1 133049722 133049822 Eif2d_window10 128 306 +chr1 133049747 133049847 Eif2d_window11 115 285 +chr1 133049772 133049872 Eif2d_window12 92 241 +chr1 133049797 133049897 Eif2d_window13 62 197 +chr1 133049822 133049922 Eif2d_window14 50 136 +chr1 133049847 133049947 Eif2d_window15 28 105 +chr1 133049872 133049972 Eif2d_window16 11 39 +chr1 133049897 133049997 Eif2d_window17 12 35 +chr1 133049922 133050022 Eif2d_window18 11 28 +chr1 133049947 133050047 Eif2d_window19 10 23 +chr1 133049972 133050072 Eif2d_window20 8 28 +chr1 133049997 133050097 Eif2d_window21 4 16 +chr1 133050022 133050122 Eif2d_window22 5 13 +chr1 133050047 133050147 Eif2d_window23 1 10 +chr1 133050072 133050172 Eif2d_window24 1 8 +chr1 133050097 133050197 Eif2d_window25 1 6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_684.dat Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +BJ-JQ1-2h.trim.sort.nuc.uniq.rmdup.filter.bam 1920
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_686.dat Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +BJ-JQ1-1h.trim.sort.nuc.uniq.rmdup.filter.bam 2047
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_688.dat Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +BJ-DMSO-6h.trim.sort.nuc.uniq.rmdup.filter.bam 615
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_690.dat Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +BJ-DMSO-2h.trim.sort.nuc.uniq.rmdup.filter.bam 1130
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_692.dat Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +BJ-DMSO-1h.trim.sort.nuc.uniq.rmdup.filter.bam 789
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_list Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +dataset_692.dat,dataset_684.dat,dataset_688.dat,dataset_686.dat,dataset_690.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_list_ordered Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +dataset_692.dat,dataset_684.dat,dataset_688.dat,dataset_686.dat,dataset_690.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ext_peak Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,6 @@ +chr10 20442676 20447116 Pde7b +chr15 95482290 95487433 Dbx2 +chr18 58713130 58717849 Slc27a6 +chr2 32814762 32819713 Rpl12 +chr2 153114826 153119777 Kif3b +chr9 106329200 106334399 Rpl29
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lib_sizes.txt Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,16 @@ +15003106 +71588566 +61590166 +24168007 +27558173 +34581324 +24494912 +31303036 +30945942 +23828468 +26987526 +14576615 +20647247 +28129346 +13608142 +21186210
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9.chrom.sizes.txt Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,35 @@ +chr1 197195432 +chr2 181748087 +chrX 166650296 +chr3 159599783 +chr4 155630120 +chr5 152537259 +chr7 152524553 +chr6 149517037 +chr8 131738871 +chr10 129993255 +chr14 125194864 +chr9 124076172 +chr11 121843856 +chr12 121257530 +chr13 120284312 +chr15 103494974 +chr16 98319150 +chr17 95272651 +chr18 90772031 +chr19 61342430 +chrY_random 58682461 +chrY 15902555 +chrUn_random 5900358 +chrX_random 1785075 +chr1_random 1231697 +chr8_random 849593 +chr17_random 628739 +chr9_random 449403 +chr13_random 400311 +chr7_random 362490 +chr5_random 357350 +chr4_random 160594 +chr3_random 41899 +chrM 16299 +chr16_random 3994
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qPCR_regions.bed Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,13 @@ +chr15 95484590 95485290 Dbx2_region1 +chr10 20444726 20444826 Pde7b_region1 +chr10 20444876 20445026 Pde7b_region2 +chr18 58715230 58715730 Slc27a6_region1 +chr2 32816812 32817112 Rpl12_region1 +chr2 32817162 32817712 Rpl12_region2 +chr9 106331200 106331700 Rpl29_region1 +chr9 106331750 106332250 Rpl29_region2 +chr2 153116926 153117176 Kif3b_region1 +chr2 153117226 153117426 Kif3b_region2 +chr2 153117476 153117626 Kif3b_region3 +chr2 153117726 153117826 Kif3b_region4 +chr1 133049697 133049847 Eif2d_region1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qPCR_windows.bed Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,233 @@ +chr15 95484290 95485433 Dbx2 +chr15 95484290 95484390 Dbx2_window1 +chr15 95484315 95484415 Dbx2_window2 +chr15 95484340 95484440 Dbx2_window3 +chr15 95484365 95484465 Dbx2_window4 +chr15 95484390 95484490 Dbx2_window5 +chr15 95484415 95484515 Dbx2_window6 +chr15 95484440 95484540 Dbx2_window7 +chr15 95484465 95484565 Dbx2_window8 +chr15 95484490 95484590 Dbx2_window9 +chr15 95484515 95484615 Dbx2_window10 +chr15 95484540 95484640 Dbx2_window11 +chr15 95484565 95484665 Dbx2_window12 +chr15 95484590 95484690 Dbx2_window13 +chr15 95484615 95484715 Dbx2_window14 +chr15 95484640 95484740 Dbx2_window15 +chr15 95484665 95484765 Dbx2_window16 +chr15 95484690 95484790 Dbx2_window17 +chr15 95484715 95484815 Dbx2_window18 +chr15 95484740 95484840 Dbx2_window19 +chr15 95484765 95484865 Dbx2_window20 +chr15 95484790 95484890 Dbx2_window21 +chr15 95484815 95484915 Dbx2_window22 +chr15 95484840 95484940 Dbx2_window23 +chr15 95484865 95484965 Dbx2_window24 +chr15 95484890 95484990 Dbx2_window25 +chr15 95484915 95485015 Dbx2_window26 +chr15 95484940 95485040 Dbx2_window27 +chr15 95484965 95485065 Dbx2_window28 +chr15 95484990 95485090 Dbx2_window29 +chr15 95485015 95485115 Dbx2_window30 +chr15 95485040 95485140 Dbx2_window31 +chr15 95485065 95485165 Dbx2_window32 +chr15 95485090 95485190 Dbx2_window33 +chr15 95485115 95485215 Dbx2_window34 +chr15 95485140 95485240 Dbx2_window35 +chr15 95485165 95485265 Dbx2_window36 +chr15 95485190 95485290 Dbx2_window37 +chr15 95485215 95485315 Dbx2_window38 +chr15 95485240 95485340 Dbx2_window39 +chr15 95485265 95485365 Dbx2_window40 +chr15 95485290 95485390 Dbx2_window41 +chr15 95485315 95485415 Dbx2_window42 +chr15 95485340 95485440 Dbx2_window43 +chr10 20444676 20445116 Pde7b +chr10 20444676 20444776 Pde7b_window1 +chr10 20444701 20444801 Pde7b_window2 +chr10 20444726 20444826 Pde7b_window3 +chr10 20444751 20444851 Pde7b_window4 +chr10 20444776 20444876 Pde7b_window5 +chr10 20444801 20444901 Pde7b_window6 +chr10 20444826 20444926 Pde7b_window7 +chr10 20444851 20444951 Pde7b_window8 +chr10 20444876 20444976 Pde7b_window9 +chr10 20444901 20445001 Pde7b_window10 +chr10 20444926 20445026 Pde7b_window11 +chr10 20444951 20445051 Pde7b_window12 +chr10 20444976 20445076 Pde7b_window13 +chr10 20445001 20445101 Pde7b_window14 +chr10 20445026 20445126 Pde7b_window15 +chr18 58715130 58715849 Slc27a6 +chr18 58715130 58715230 Slc27a6_window1 +chr18 58715155 58715255 Slc27a6_window2 +chr18 58715180 58715280 Slc27a6_window3 +chr18 58715205 58715305 Slc27a6_window4 +chr18 58715230 58715330 Slc27a6_window5 +chr18 58715255 58715355 Slc27a6_window6 +chr18 58715280 58715380 Slc27a6_window7 +chr18 58715305 58715405 Slc27a6_window8 +chr18 58715330 58715430 Slc27a6_window9 +chr18 58715355 58715455 Slc27a6_window10 +chr18 58715380 58715480 Slc27a6_window11 +chr18 58715405 58715505 Slc27a6_window12 +chr18 58715430 58715530 Slc27a6_window13 +chr18 58715455 58715555 Slc27a6_window14 +chr18 58715480 58715580 Slc27a6_window15 +chr18 58715505 58715605 Slc27a6_window16 +chr18 58715530 58715630 Slc27a6_window17 +chr18 58715555 58715655 Slc27a6_window18 +chr18 58715580 58715680 Slc27a6_window19 +chr18 58715605 58715705 Slc27a6_window20 +chr18 58715630 58715730 Slc27a6_window21 +chr18 58715655 58715755 Slc27a6_window22 +chr18 58715680 58715780 Slc27a6_window23 +chr18 58715705 58715805 Slc27a6_window24 +chr18 58715730 58715830 Slc27a6_window25 +chr18 58715755 58715855 Slc27a6_window26 +chr2 32816762 32817713 Rpl12 +chr2 32816762 32816862 Rpl12_window1 +chr2 32816787 32816887 Rpl12_window2 +chr2 32816812 32816912 Rpl12_window3 +chr2 32816837 32816937 Rpl12_window4 +chr2 32816862 32816962 Rpl12_window5 +chr2 32816887 32816987 Rpl12_window6 +chr2 32816912 32817012 Rpl12_window7 +chr2 32816937 32817037 Rpl12_window8 +chr2 32816962 32817062 Rpl12_window9 +chr2 32816987 32817087 Rpl12_window10 +chr2 32817012 32817112 Rpl12_window11 +chr2 32817037 32817137 Rpl12_window12 +chr2 32817062 32817162 Rpl12_window13 +chr2 32817087 32817187 Rpl12_window14 +chr2 32817112 32817212 Rpl12_window15 +chr2 32817137 32817237 Rpl12_window16 +chr2 32817162 32817262 Rpl12_window17 +chr2 32817187 32817287 Rpl12_window18 +chr2 32817212 32817312 Rpl12_window19 +chr2 32817237 32817337 Rpl12_window20 +chr2 32817262 32817362 Rpl12_window21 +chr2 32817287 32817387 Rpl12_window22 +chr2 32817312 32817412 Rpl12_window23 +chr2 32817337 32817437 Rpl12_window24 +chr2 32817362 32817462 Rpl12_window25 +chr2 32817387 32817487 Rpl12_window26 +chr2 32817412 32817512 Rpl12_window27 +chr2 32817437 32817537 Rpl12_window28 +chr2 32817462 32817562 Rpl12_window29 +chr2 32817487 32817587 Rpl12_window30 +chr2 32817512 32817612 Rpl12_window31 +chr2 32817537 32817637 Rpl12_window32 +chr2 32817562 32817662 Rpl12_window33 +chr2 32817587 32817687 Rpl12_window34 +chr2 32817612 32817712 Rpl12_window35 +chr2 32817637 32817737 Rpl12_window36 +chr9 106331200 106332399 Rpl29 +chr9 106331200 106331300 Rpl29_window1 +chr9 106331225 106331325 Rpl29_window2 +chr9 106331250 106331350 Rpl29_window3 +chr9 106331275 106331375 Rpl29_window4 +chr9 106331300 106331400 Rpl29_window5 +chr9 106331325 106331425 Rpl29_window6 +chr9 106331350 106331450 Rpl29_window7 +chr9 106331375 106331475 Rpl29_window8 +chr9 106331400 106331500 Rpl29_window9 +chr9 106331425 106331525 Rpl29_window10 +chr9 106331450 106331550 Rpl29_window11 +chr9 106331475 106331575 Rpl29_window12 +chr9 106331500 106331600 Rpl29_window13 +chr9 106331525 106331625 Rpl29_window14 +chr9 106331550 106331650 Rpl29_window15 +chr9 106331575 106331675 Rpl29_window16 +chr9 106331600 106331700 Rpl29_window17 +chr9 106331625 106331725 Rpl29_window18 +chr9 106331650 106331750 Rpl29_window19 +chr9 106331675 106331775 Rpl29_window20 +chr9 106331700 106331800 Rpl29_window21 +chr9 106331725 106331825 Rpl29_window22 +chr9 106331750 106331850 Rpl29_window23 +chr9 106331775 106331875 Rpl29_window24 +chr9 106331800 106331900 Rpl29_window25 +chr9 106331825 106331925 Rpl29_window26 +chr9 106331850 106331950 Rpl29_window27 +chr9 106331875 106331975 Rpl29_window28 +chr9 106331900 106332000 Rpl29_window29 +chr9 106331925 106332025 Rpl29_window30 +chr9 106331950 106332050 Rpl29_window31 +chr9 106331975 106332075 Rpl29_window32 +chr9 106332000 106332100 Rpl29_window33 +chr9 106332025 106332125 Rpl29_window34 +chr9 106332050 106332150 Rpl29_window35 +chr9 106332075 106332175 Rpl29_window36 +chr9 106332100 106332200 Rpl29_window37 +chr9 106332125 106332225 Rpl29_window38 +chr9 106332150 106332250 Rpl29_window39 +chr9 106332175 106332275 Rpl29_window40 +chr9 106332200 106332300 Rpl29_window41 +chr9 106332225 106332325 Rpl29_window42 +chr9 106332250 106332350 Rpl29_window43 +chr9 106332275 106332375 Rpl29_window44 +chr9 106332300 106332400 Rpl29_window45 +chr2 153116826 153117777 Kif3b +chr2 153116826 153116926 Kif3b_window1 +chr2 153116851 153116951 Kif3b_window2 +chr2 153116876 153116976 Kif3b_window3 +chr2 153116901 153117001 Kif3b_window4 +chr2 153116926 153117026 Kif3b_window5 +chr2 153116951 153117051 Kif3b_window6 +chr2 153116976 153117076 Kif3b_window7 +chr2 153117001 153117101 Kif3b_window8 +chr2 153117026 153117126 Kif3b_window9 +chr2 153117051 153117151 Kif3b_window10 +chr2 153117076 153117176 Kif3b_window11 +chr2 153117101 153117201 Kif3b_window12 +chr2 153117126 153117226 Kif3b_window13 +chr2 153117151 153117251 Kif3b_window14 +chr2 153117176 153117276 Kif3b_window15 +chr2 153117201 153117301 Kif3b_window16 +chr2 153117226 153117326 Kif3b_window17 +chr2 153117251 153117351 Kif3b_window18 +chr2 153117276 153117376 Kif3b_window19 +chr2 153117301 153117401 Kif3b_window20 +chr2 153117326 153117426 Kif3b_window21 +chr2 153117351 153117451 Kif3b_window22 +chr2 153117376 153117476 Kif3b_window23 +chr2 153117401 153117501 Kif3b_window24 +chr2 153117426 153117526 Kif3b_window25 +chr2 153117451 153117551 Kif3b_window26 +chr2 153117476 153117576 Kif3b_window27 +chr2 153117501 153117601 Kif3b_window28 +chr2 153117526 153117626 Kif3b_window29 +chr2 153117551 153117651 Kif3b_window30 +chr2 153117576 153117676 Kif3b_window31 +chr2 153117601 153117701 Kif3b_window32 +chr2 153117626 153117726 Kif3b_window33 +chr2 153117651 153117751 Kif3b_window34 +chr2 153117676 153117776 Kif3b_window35 +chr2 153117701 153117801 Kif3b_window36 +chr1 133049497 133050192 Eif2d +chr1 133049497 133049597 Eif2d_window1 +chr1 133049522 133049622 Eif2d_window2 +chr1 133049547 133049647 Eif2d_window3 +chr1 133049572 133049672 Eif2d_window4 +chr1 133049597 133049697 Eif2d_window5 +chr1 133049622 133049722 Eif2d_window6 +chr1 133049647 133049747 Eif2d_window7 +chr1 133049672 133049772 Eif2d_window8 +chr1 133049697 133049797 Eif2d_window9 +chr1 133049722 133049822 Eif2d_window10 +chr1 133049747 133049847 Eif2d_window11 +chr1 133049772 133049872 Eif2d_window12 +chr1 133049797 133049897 Eif2d_window13 +chr1 133049822 133049922 Eif2d_window14 +chr1 133049847 133049947 Eif2d_window15 +chr1 133049872 133049972 Eif2d_window16 +chr1 133049897 133049997 Eif2d_window17 +chr1 133049922 133050022 Eif2d_window18 +chr1 133049947 133050047 Eif2d_window19 +chr1 133049972 133050072 Eif2d_window20 +chr1 133049997 133050097 Eif2d_window21 +chr1 133050022 133050122 Eif2d_window22 +chr1 133050047 133050147 Eif2d_window23 +chr1 133050072 133050172 Eif2d_window24 +chr1 133050097 133050197 Eif2d_window25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_counts_ordered.txt Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,5 @@ +789 +1130 +615 +2047 +1920
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,6 @@ +chr15 95484290 95485433 Dbx2 +chr10 20444676 20445116 Pde7b +chr18 58715130 58715849 Slc27a6 +chr2 32816762 32817713 Rpl12 +chr9 106331200 106332399 Rpl29 +chr2 153116826 153117777 Kif3b
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.readcounts.txt Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,1 @@ +test.bam 681
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,5 @@ +<tool_dependency> + <package name="r-base" version="3.4.2"></package> + <package name="samtools" version="1.3"></package> + <package name="bedtools" version="2.27.0.0"></package> +</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/window_coverage.bash Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,67 @@ +#!/bin/bash + +#Requires bam files and bed file containing coordinates of peaks of interest +#Determines regions within peaks where included fragement coverage best correlates +#with total read count under peak. Exports regions as bed file. + +#required arguements: +#($1): series of bam files +#($2): file names of bam files +#($3): window bed file +#($4): percent of window fragments must cover, default is 0.9 +#($5): output coverage file +#($6): output spanning fragment coverage file + +#Usage: ATAC_qPCR_regions.bash bam_series name_list qPCR_windows.bed 0.9 combined.o.bed.coverage combined.f9.bed.coverage + +bam_series=$1 +name_list=$2 +qPCR_windows=$3 +percent_overlap=${4:-0.9} +combined_o=$5 +combined_f9=$6 + +COUNTER=0 +echo $bam_series |tr , '\n' > bam_series.txt +echo $name_list | tr , '\n' > name_list.txt +paste name_list.txt bam_series.txt > bam_name_list.txt +sort -k1 bam_name_list.txt > sorted_bam_name_list.txt +cut -f 2 sorted_bam_name_list.txt > sorted_bam_list.txt + +cat sorted_bam_list.txt | while read file +do + +#create bed file of fragments for each bam file + +samtools sort -n -o - $file | samtools fixmate - - | bamToBed -i - -bedpe | cut -f 1,2,6 > "${file}".includeinsert.bed + +#determine window coverage for each bam file +#combined_o: Total reads in peak/window +#combined_f9: Spanning reads in window + +if [ $COUNTER -eq 0 ] +then +coverageBed -a $qPCR_windows -b $file | cut -f 1,2,3,4,5 > $combined_o +coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 1,2,3,4,5 > $combined_f9 + +else +coverageBed -a $qPCR_windows -b $file | cut -f 5 > temp.o.bed.coverage +coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 5 > temp.f9.bed.coverage +paste $combined_o temp.o.bed.coverage > combined.temp.o.bed.coverage +mv combined.temp.o.bed.coverage $combined_o +paste $combined_f9 temp.f9.bed.coverage > combined.temp.f9.bed.coverage +mv combined.temp.f9.bed.coverage $combined_f9 + +rm temp.o.bed.coverage +rm temp.f9.bed.coverage + +fi + +rm "${file}.includeinsert.bed" + +let COUNTER=COUNTER+1 + +done + + +rm *.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/window_coverage.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,38 @@ +<tool id="window_coverage" name="Calculate window coverage" version="0.1.0"> + <description> Determines spanning and total read coverage for overlapping windows spanning peaks of interest. </description> + <requirements> + <requirement type="package" version="1.3">samtools</requirement> + <requirement type="package" version="2.27.0.0">bedtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + #set input_list = '","'.join( [str( $input.name ) for $input in $input1 ] ) + $__tool_directory__/./window_coverage.bash "$input1" "$input_list" "$input2" "$input3" "$output1" "$output2" + ]]></command> + <inputs> + <param type="data" name="input1" format="bam" multiple="true" label="Filtered Bam Files"/> + <param type="data" name="input2" format="bed" label="qPCR Window Bed File"/> + <param type="float" name="input3" value="0.9" label="Coverage Cutoff"/> + </inputs> + <outputs> + <data name="output1" format="bed" label="Coverage Bed File"/> + <data name="output2" format="bed" label="Spanning Fragment Coverage Bed File" /> + </outputs> + <tests> + <test> + <param name="input1" value="Ch1-1.pe.q10.sort.bam.rmdup.filter.bam,Ch13-1.pe.q10.sort.rmdup.filter.bam"/> + <param name="input2" value="qPCR_windows.bed" /> + <param name="input3" value="0.9" /> + <output name="output1" file="combined.o.coverage"/> + <output name="output2" file="combined.f9.coverage"/> + </test> + </tests> + <help><![CDATA[ + This tools takes a series of bam files and a bed file of overlapping windows spanning peaks of interest and determines the read coverage and spanning fragment coverage for each window. + ]]></help> + <citations> + <citation type="doi">doi:10.1038/nmeth.4663</citation> + </citations> +</tool>