Mercurial > repos > artbio > small_rna_maps
changeset 12:d33263e6e812 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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--- a/small_rna_maps.r Tue Mar 06 06:11:55 2018 -0500 +++ b/small_rna_maps.r Sat Apr 07 06:14:50 2018 -0400 @@ -1,6 +1,6 @@ ## Setup R error handling to go to stderr options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) options(warn = -1) library(RColorBrewer) library(lattice) @@ -11,37 +11,39 @@ option_list <- list( - make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"), - make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"), - make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"), - make_option("--first_plot_method", type = "character", help="How additional data should be plotted"), - make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"), - make_option("--global", type = "character", help="data should be plotted as global size distribution"), - make_option("--output_pdf", type = "character", help="path to the pdf file with plots") - ) - + make_option(c("-i", "--ymin"), type="double", help="set min ylimit. e.g. '-100.0'"), + make_option(c("-a", "--ymax"), type="double", help="set max ylimit. e.g. '100.0'"), + make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"), + make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"), + make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"), + make_option("--first_plot_method", type = "character", help="How additional data should be plotted"), + make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"), + make_option("--global", type = "character", help="data should be plotted as global size distribution"), + make_option("--output_pdf", type = "character", help="path to the pdf file with plots") +) + parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) args = parse_args(parser) - + # data frames implementation ## first table Table = read.delim(args$first_dataframe, header=T, row.names=NULL) if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") { - Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) + Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) } n_samples=length(unique(Table$Dataset)) samples = unique(Table$Dataset) if (args$normalization != "") { - norm_factors = as.numeric(unlist(strsplit(args$normalization, " "))) + norm_factors = as.numeric(unlist(strsplit(args$normalization, " "))) } else { - norm_factors = rep(1, n_samples) + norm_factors = rep(1, n_samples) } if (args$first_plot_method == "Counts" | args$first_plot_method == "Size" | args$first_plot_method == "Coverage") { - i = 1 - for (sample in samples) { - Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i] - i = i + 1 - } + i = 1 + for (sample in samples) { + Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i] + i = i + 1 + } } genes=unique(Table$Chromosome) per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x)) @@ -49,198 +51,202 @@ n_genes=length(per_gene_readmap) # second table if (args$extra_plot_method != '') { - ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL) - if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') { - ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) + ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL) + if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') { + ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) + } + if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") { + i = 1 + for (sample in samples) { + ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i] + i = i + 1 } - if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") { - i = 1 - for (sample in samples) { - ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i] - i = i + 1 - } - } - per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x)) + } + per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x)) } ## functions globalbc = function(df, global="", ...) { - if (global == "yes") { - bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), - data = df, origin = 0, - horizontal=FALSE, - col=c("darkblue"), - scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), - xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85), - ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85), - main=title_first_method[[args$first_plot_method]], - layout = c(2, 6), newpage=T, - as.table=TRUE, - aspect=0.5, - strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"), - ... - ) - } else { - bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), - data = df, origin = 0, - horizontal=FALSE, - group=Polarity, - stack=TRUE, - col=c('red', 'blue'), - scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), - xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85), - ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85), - main=title_first_method[[args$first_plot_method]], - layout = c(2, 6), newpage=T, - as.table=TRUE, - aspect=0.5, - strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"), - ... - ) - } - return(bc) + if (global == "yes") { + bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), + data = df, origin = 0, + horizontal=FALSE, + col=c("darkblue"), + scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), + xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85), + ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85), + main=title_first_method[[args$first_plot_method]], + layout = c(2, 6), newpage=T, + as.table=TRUE, + aspect=0.5, + strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"), + ... + ) + } else { + bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), + data = df, origin = 0, + horizontal=FALSE, + group=Polarity, + stack=TRUE, + col=c('red', 'blue'), + scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), + xlab=list(label=bottom_first_method[[args$first_plot_method]], cex=.85), + ylab=list(label=legend_first_method[[args$first_plot_method]], cex=.85), + main=title_first_method[[args$first_plot_method]], + layout = c(2, 6), newpage=T, + as.table=TRUE, + aspect=0.5, + strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue"), + ... + ) + } + return(bc) } plot_unit = function(df, method=args$first_plot_method, ...) { - if (method == 'Counts') { - p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)), - data=df, - type='h', - lwd=1.5, - scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), - xlab=NULL, main=NULL, ylab=NULL, - as.table=T, - origin = 0, - horizontal=FALSE, - group=Polarity, - col=c("red","blue"), - par.strip.text = list(cex=0.7), - ...) - } else if (method != "Size") { - p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)), - data=df, - type='p', - pch=19, - cex=0.35, - scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), - xlab=NULL, main=NULL, ylab=NULL, - as.table=T, - origin = 0, - horizontal=FALSE, - group=Polarity, - col=c("red","blue"), - par.strip.text = list(cex=0.7), - ...) - } else { - p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0, - horizontal=FALSE, - group=Polarity, - stack=TRUE, - col=c('red', 'blue'), - scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=0.5)), - xlab = NULL, - ylab = NULL, - main = NULL, - as.table=TRUE, - par.strip.text = list(cex=0.6), - ...) - } - combineLimits(p) + if (exists('ymin', where=args)){ + min=args$ymin + }else{ + min='' + } + if ((exists('ymax', where=args))){ + max=args$ymax + }else{ + max='' + } + ylimits=c(min,max) + if (method == 'Counts') { + p = xyplot(Counts~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)), + data=df, + type='h', + lwd=1.5, + scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), + xlab=NULL, main=NULL, ylab=NULL, ylim=ylimits, + as.table=T, + origin = 0, + horizontal=FALSE, + group=Polarity, + col=c("red","blue"), + par.strip.text = list(cex=0.7), + ...) + p=combineLimits(p) + } else if (method != "Size") { + p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)), + data=df, + type='p', + pch=19, + cex=0.35, + scales= list(relation="free", x=list(rot=0, cex=0.7, tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)), + xlab=NULL, main=NULL, ylab=NULL, ylim=ylimits, + as.table=T, + origin = 0, + horizontal=FALSE, + group=Polarity, + col=c("red","blue"), + par.strip.text = list(cex=0.7), + ...) + } else { + p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0, + horizontal=FALSE, + group=Polarity, + stack=TRUE, + col=c('red', 'blue'), + scales=list(y=list(rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=c(1,0))), + xlab = NULL, + ylab = NULL, + main = NULL, + as.table=TRUE, + par.strip.text = list(cex=0.6), + ...) + p=combineLimits(p) + } + return(p) } + ## function parameters #par.settings.firstplot = list(layout.heights=list(top.padding=11, bottom.padding = -14)) #par.settings.secondplot=list(layout.heights=list(top.padding=11, bottom.padding = -15), strip.background=list(col=c("lavender","deepskyblue"))) -par.settings.firstplot = list(layout.heights=list(top.padding=-2, bottom.padding=-2)) -par.settings.secondplot=list(layout.heights=list(top.padding=-1, bottom.padding=-1), strip.background=list(col=c("lavender","deepskyblue"))) -par.settings.single_plot=list(strip.background = list(col = c("lightblue", "lightgreen"))) +par.settings.firstplot = list(layout.heights=list(top.padding=-2, bottom.padding=-2),strip.background=list(col=c("lightblue","lightgreen"))) +par.settings.secondplot=list(layout.heights=list(top.padding=-1, bottom.padding=-1),strip.background=list(col=c("lightblue","lightgreen"))) title_first_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions") title_extra_method = list(Counts="Read Counts", Coverage="Coverage depths", Median="Median sizes", Mean="Mean sizes", Size="Size Distributions") legend_first_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count") -legend_extra_method =list(Counts="Read count", Coverage="Coveragedepth", Median="Median size", Mean="Mean size", Size="Read count") +legend_extra_method =list(Counts="Read count", Coverage="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count") bottom_first_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads") bottom_extra_method =list(Counts="Coordinates (nbre of bases)",Coverage="Coordinates (nbre of bases)", Median="Coordinates (nbre of bases)", Mean="Coordinates (nbre of bases)", Size="Sizes of reads") ## Plotting Functions double_plot <- function(...) { - page_height = 15 - rows_per_page = 10 - graph_heights=c(40,30,40,30,40,30,40,30,40,30,10) - if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 2.3*n_samples +2.5} - pdf(file=args$output_pdf, paper="special", height=page_height, width=page_width) - for (i in seq(1,n_genes,rows_per_page/2)) { - start=i - end=i+rows_per_page/2-1 - if (end>n_genes) {end=n_genes} - if (end-start+1 < 5) {graph_heights=c(rep(c(40,30),end-start+1),10,rep(c(40,30),5-(end-start+1)))} - first_plot.list = lapply(per_gene_readmap[start:end], function(x) plot_unit(x, strip=FALSE, par.settings=par.settings.firstplot)) - second_plot.list = lapply(per_gene_size[start:end], function(x) plot_unit(x, method=args$extra_plot_method, par.settings=par.settings.secondplot)) - plot.list=rbind(second_plot.list, first_plot.list) - args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 11)), - top=textGrob(paste(title_first_method[[args$first_plot_method]], "and", title_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, just="top"), - left=textGrob(paste(legend_first_method[[args$first_plot_method]], "/", legend_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just=0.675*(end-start-(2.2*(4/2.7))),vjust=2, rot=90), - sub=textGrob(paste(bottom_first_method[[args$first_plot_method]], "/", bottom_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just="bottom", vjust=2) - ) - ) - do.call(grid.arrange, args_list) - } - devname=dev.off() + page_height = 15 + rows_per_page = 10 + graph_heights=c(40,30,40,30,40,30,40,30,40,30,10) + page_width=8.2677 * n_samples / 2 + pdf(file=args$output_pdf, paper="special", height=page_height, width=page_width) + for (i in seq(1,n_genes,rows_per_page/2)) { + start=i + end=i+rows_per_page/2-1 + if (end>n_genes) {end=n_genes} + if (end-start+1 < 5) {graph_heights=c(rep(c(40,30),end-start+1),10,rep(c(40,30),5-(end-start+1)))} + first_plot.list = lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings=par.settings.secondplot), strip.left=strip.custom(par.strip.text = list(cex=0.5))))) + second_plot.list = lapply(per_gene_size[start:end], function(x) update(useOuterStrips(plot_unit(x, method=args$extra_plot_method, par.settings=par.settings.firstplot), strip.left=strip.custom(par.strip.text = list(cex=0.5)), strip=FALSE))) + plot.list=rbind(first_plot.list, second_plot.list) + args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 11)), + top=textGrob(paste(title_first_method[[args$first_plot_method]], "and", title_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, just="top"), + left=textGrob(paste(legend_first_method[[args$first_plot_method]], "/", legend_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), vjust=0, hjust=0, x=1, y=(-0.38/4)*(end-start-(3.28/0.38)), rot=90), + sub=textGrob(paste(bottom_first_method[[args$first_plot_method]], "/", bottom_extra_method[[args$extra_plot_method]]), gp=gpar(cex=1), just="bottom", vjust=2) + ) + ) + do.call(grid.arrange, args_list) + } + devname=dev.off() } single_plot <- function(...) { - width = 8.2677 * n_samples / 2 - rows_per_page=8 - graph_heights=c(rep(40,8),10) - pdf(file=args$output_pdf, paper="special", height=15, width=width) - for (i in seq(1,n_genes,rows_per_page)) { - start=i - end=i+rows_per_page-1 - if (end>n_genes) {end=n_genes} - if (end-start+1 < 8) {graph_heights=c(rep(c(40),end-start+1),10,rep(c(40),8-(end-start+1)))} - first_plot.list = lapply(per_gene_readmap[start:end], function(x) plot_unit(x, par.settings=par.settings.firstplot)) - plot.list=rbind(first_plot.list) - args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 9)), - top=textGrob(title_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, just="top"), - left=textGrob(legend_first_method[[args$first_plot_method]], gp=gpar(cex=1), just=(6.4/7)*(end-start-(6.2*(7/6.4))),vjust=2, rot=90), - sub=textGrob(bottom_first_method[[args$first_plot_method]], gp=gpar(cex=1), just="bottom", vjust=2) - ) - ) - do.call(grid.arrange, args_list) - } - devname=dev.off() + width = 8.2677 * n_samples / 2 + rows_per_page=8 + graph_heights=c(rep(40,8),10) + pdf(file=args$output_pdf, paper="special", height=15, width=width) + for (i in seq(1,n_genes,rows_per_page)) { + start=i + end=i+rows_per_page-1 + if (end>n_genes) {end=n_genes} + if (end-start+1 < 8) {graph_heights=c(rep(c(40),end-start+1),10,rep(c(40),8-(end-start+1)))} + first_plot.list = lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings=par.settings.firstplot),strip.left=strip.custom(par.strip.text = list(cex=0.5))))) + plot.list=rbind(first_plot.list) + args_list=c(plot.list, list( nrow=rows_per_page+1, ncol=1, heights=unit(graph_heights, rep("mm", 9)), + top=textGrob(title_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, just="top"), + left=textGrob(legend_first_method[[args$first_plot_method]], gp=gpar(cex=1), vjust=0, hjust=0, x=1, y=(-0.41/7)*(end-start-(6.23/0.41)), rot=90), + sub=textGrob(bottom_first_method[[args$first_plot_method]], gp=gpar(cex=1), just="bottom", vjust=2) + ) + ) + do.call(grid.arrange, args_list) + } + devname=dev.off() } # main if (args$extra_plot_method != '') { double_plot() } if (args$extra_plot_method == '' & !exists('global', where=args)) { - single_plot() + single_plot() } if (exists('global', where=args)) { - pdf(file=args$output, paper="special", height=11.69) - Table <- within(Table, Counts[Polarity=="R"] <- abs(Counts[Polarity=="R"])) # retropedalage - library(reshape2) - ml = melt(Table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size")) - if (args$global == "nomerge") { - castml = dcast(ml, Dataset+Polarity+Size ~ variable, function(x) sum(x)) - castml <- within(castml, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) - bc = globalbc(castml, global="no") - } else { - castml = dcast(ml, Dataset+Size ~ variable, function(x) sum(x)) - bc = globalbc(castml, global="yes") - } - plot(bc) - devname=dev.off() + pdf(file=args$output, paper="special", height=11.69) + Table <- within(Table, Counts[Polarity=="R"] <- abs(Counts[Polarity=="R"])) # retropedalage + library(reshape2) + ml = melt(Table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size")) + if (args$global == "nomerge") { + castml = dcast(ml, Dataset+Polarity+Size ~ variable, function(x) sum(x)) + castml <- within(castml, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) + bc = globalbc(castml, global="no") + } else { + castml = dcast(ml, Dataset+Size ~ variable, function(x) sum(x)) + bc = globalbc(castml, global="yes") + } + plot(bc) + devname=dev.off() } - - - - - - - - -
--- a/small_rna_maps.xml Tue Mar 06 06:11:55 2018 -0500 +++ b/small_rna_maps.xml Sat Apr 07 06:14:50 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="2.4.3"> +<tool id="small_rna_maps" name="small_rna_maps" version="2.5.0"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement> @@ -13,35 +13,65 @@ <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ - #for $file in $inputs - samtools index '$file' && - #end for - python '$__tool_directory__'/small_rna_maps.py - --inputs - #for $file in $inputs - '$file' - #end for - --sample_names - #for $sample in $inputs - '$sample.name' - #end for + #if $inputs_cond.normalize == "no": + #for $file in $inputs_cond.inputs + samtools index '$file'; + #end for + python '$__tool_directory__'/small_rna_maps.py + --inputs + #for $file in $inputs_cond.inputs + '$file' + #end for + --sample_names + #for $sample in $inputs_cond.inputs + '$sample.name' + #end for + #else if $inputs_cond.normalize == "yes": + #for $file in $inputs_cond.series + samtools index '$file.inputs'; + #end for + python '$__tool_directory__'/small_rna_maps.py + --inputs + #for $file in $inputs_cond.series + '$file.inputs' + #end for + --sample_names + #for $sample in $inputs_cond.series + '$sample.inputs.name' + #end for + #end if --minsize $minsize --maxsize $maxsize --cluster $cluster #if str($plots_options.plots_options_selector ) == "two_plot": --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' - --outputs '$output_tab' '$extra_output_tab' && + --outputs '$output_tab' '$extra_output_tab'; #elif str($plots_options.plots_options_selector ) == "global": --plot_methods 'Size' - --outputs '$output_tab' && + --outputs '$output_tab'; #else: --plot_methods '${plots_options.first_plot}' - --outputs '$output_tab' && + --outputs '$output_tab' ; #end if Rscript '$__tool_directory__'/small_rna_maps.r --first_dataframe '$output_tab' --extra_dataframe '$extra_output_tab' - --normalization '$normalization' + --normalization + #if $inputs_cond.normalize == "no": + '' + #else if $inputs_cond.normalize == "yes": + #set $norm = "" + #for $file in $inputs_cond.series + #set $norm += str($file.normalization)+' ' + #end for + #set $norm = $norm[:-1] + '$norm' + #end if + #if $ylimits_cond.ylimits == "no": + --ymin '' --ymax '' + #else: + --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}' + #end if #if str($plots_options.plots_options_selector ) == "two_plot": --first_plot_method '${plots_options.first_plot}' --extra_plot_method '${plots_options.extra_plot}' @@ -56,15 +86,25 @@ --output_pdf '$output_pdf' ]]></command> <inputs> - <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> - <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" - help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> + <conditional name="inputs_cond"> + <param name="normalize" type="boolean" label="Will there be normalization?" truevalue="yes" falsevalue="no" checked="false"/> + <when value="no"> + <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> + </when> + <when value="yes"> + <repeat name="series" title="Normalization factors" min="1"> + <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" /> + <param name="normalization" type="float" label="Enter size/normalization factors." + help="e.g. '0.75' '1.23'" value="1.0"/> + </repeat> + </when> + </conditional> <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" value="0" help="default value: 0" /> <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" value="10000" help="default value: 10000" /> - <param name="cluster" type="integer" label="aggregation distance in nucleotides" - value="0" help="if not 0, sets the distance (in nt) below which data are clustered to a single median position" /> + <param name="cluster" type="integer" label="Aggregation distance in nucleotides" + value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" /> <conditional name="plots_options"> <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> <option value="one_plot">Just one plot per chromosome</option> @@ -72,14 +112,14 @@ <option value="global">Global read size distributions of aligned reads</option> </param> <when value="two_plot"> - <param name="first_plot" type="select" display="radio" label="Select the type of the first plot"> + <param name="first_plot" type="select" display="radio" label="Select the type of the top plot"> <option value="Counts">Counts</option> <option value="Coverage">Coverage</option> <option value="Mean">Mean Sizes</option> <option value="Median">Median Sizes</option> <option value="Size">Size Distributions</option> </param> - <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot"> + <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot"> <option value="Counts">Counts</option> <option value="Coverage">Coverage</option> <option value="Mean">Mean Sizes</option> @@ -88,7 +128,7 @@ </param> </when> <when value="one_plot"> - <param name="first_plot" type="select" display="radio" label="select the type of the first plot"> + <param name="first_plot" type="select" display="radio" label="select the type of plot"> <option value="Counts">Counts</option> <option value="Coverage">Coverage</option> <option value="Mean">Mean Sizes</option> @@ -104,6 +144,16 @@ </param> </when> </conditional> + <conditional name="ylimits_cond"> + <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?" + help="This limit won't be applied to size distribution plots"/> + <when value="yes"> + <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/> + <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/> + </when> + <when value="no"> + </when> + </conditional> </inputs> <outputs> @@ -116,15 +166,100 @@ <tests> <test> + <param name="inputs" value="input1.bam" ftype="bam"/> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="ylimits" value="yes" /> + <param name="ymin" value="-5" /> + <param name="ymax" value="5" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Counts" /> + <output file="input1_counts_yminneg5_5.tab" name="output_tab" /> + <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> + </test> + <test> + <param name="inputs" value="input1.bam" ftype="bam"/> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="5" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Coverage" /> + <output file="input1_coverage_cluster5.tab" name="output_tab" /> + <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" /> + </test> + <test> + <param name="inputs" value="input1.bam" ftype="bam"/> + <param name="minsize" value="20" /> + <param name="maxsize" value="30" /> + <param name="cluster" value="0" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Size" /> + <output file="input1_min20_max30_size.tab" name="output_tab" /> + <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> + </test> + <test> + <param name="inputs" value="input1.bam" ftype="bam"/> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Mean" /> + <output file="input1_mean.tab" name="output_tab" /> + <output file="input1__single_plot_mean.pdf" name="output_pdf" /> + </test> + <test> + <param name="inputs" value="input1.bam" ftype="bam"/> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Median" /> + <output file="input1_median.tab" name="output_tab" /> + <output file="input1_single_plot_median.pdf" name="output_pdf" /> + </test> + <test> + <param name="normalize" value="yes" /> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input2.bam" ftype="bam" /> + <param name="normalization" value="2.0" /> + </repeat> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="plots_options_selector" value="one_plot" /> + <param name="first_plot" value="Counts" /> + <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" /> + <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> + </test> + <test> <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> <param name="minsize" value="0" /> - <param name="cluster" value="5" /> <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> + <param name="ylimits" value="yes" /> + <param name="ymin" value="-5" /> + <param name="ymax" value="5" /> + <param name="plots_options_selector" value="two_plot" /> + <param name="first_plot" value="Counts" /> + <param name="extra_plot" value="Size" /> + <output file="input1_input2_counts.tab" name="output_tab" /> + <output file="input1_input2_size.tab" name="extra_output_tab" /> + <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> + </test> + <test> + <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam"/> + <param name="minsize" value="0" /> + <param name="maxsize" value="10000" /> + <param name="cluster" value="0" /> <param name="plots_options_selector" value="one_plot" /> - <param name="normalization" value="1 1" /> - <param name="first_plot" value="Counts" /> - <output file="count_cluster_5.tab" name="output_tab" /> - <output file="count_cluster_5.pdf" name="output_pdf" /> + <param name="first_plot" value="Coverage" /> + <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" /> + <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" /> </test> <test> <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> @@ -150,223 +285,33 @@ <output file="size.tab" name="output_tab" /> <output file="global_merge.pdf" name="output_pdf" /> </test> - <test> - <param name="inputs" value="input1.bam" ftype="bam"/> - <param name="minsize" value="20" /> - <param name="maxsize" value="30" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="global" /> - <param name="mergestrands" value="merge" /> - <param name="first_plot" value="Size" /> - <param name="normalization" value="1 1" /> - <output file="size20-30.tab" name="output_tab" /> - <output file="global_merge_20-30.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Mean" /> - <param name="normalization" value="1 1" /> - <output file="count.tab" name="output_tab" /> - <output file="mean.tab" name="extra_output_tab" /> - <output file="count-mean.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/> - <param name="minsize" value="20" /> - <param name="maxsize" value="30" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Mean" /> - <param name="normalization" value="1 1" /> - <output file="count20-30.tab" name="output_tab" /> - <output file="mean20-30.tab" name="extra_output_tab" /> - <output file="count-mean-20-30.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Mean" /> - <param name="normalization" value="1 1" /> - <output file="doubled_count.tab" name="output_tab" /> - <output file="doubled_mean.tab" name="extra_output_tab" /> - <output file="doubled_count-mean.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Median" /> - <param name="normalization" value="1 1" /> - <output file="count.tab" name="output_tab" /> - <output file="median.tab" name="extra_output_tab" /> - <output file="count-median.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Coverage" /> - <param name="normalization" value="1 1" /> - <output file="count.tab" name="output_tab" /> - <output file="coverage.tab" name="extra_output_tab" /> - <output file="count-coverage.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Size" /> - <param name="normalization" value="1 1" /> - <output file="count.tab" name="output_tab" /> - <output file="size.tab" name="extra_output_tab" /> - <output file="count-size.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Size" /> - <param name="extra_plot" value="Counts" /> - <param name="normalization" value="1 1" /> - <output file="size.tab" name="output_tab" /> - <output file="count.tab" name="extra_output_tab" /> - <output file="size-count.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Size" /> - <param name="extra_plot" value="Counts" /> - <param name="normalization" value="1 0.75" /> - <output file="size.tab" name="output_tab" /> - <output file="count.tab" name="extra_output_tab" /> - <output file="size-count_normed.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input_single_chr.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Coverage" /> - <param name="normalization" value="1 1" /> - <output file="count_1_chr.tab" name="output_tab" /> - <output file="coverage_1_chr.tab" name="extra_output_tab" /> - <output file="counts_coverage_1.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input_5_chr.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="two_plot" /> - <param name="first_plot" value="Counts" /> - <param name="extra_plot" value="Coverage" /> - <param name="normalization" value="1 1" /> - <output file="count_5_chr.tab" name="output_tab" /> - <output file="coverage_5_chr.tab" name="extra_output_tab" /> - <output file="counts_coverage_5.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input_single_chr.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="one_plot" /> - <param name="first_plot" value="Counts" /> - <param name="normalization" value="1 1" /> - <output file="count_1_chr.tab" name="output_tab" /> - <output file="count_1.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="cluster" value="0" /> - <param name="maxsize" value="10000" /> - <param name="plots_options_selector" value="one_plot" /> - <param name="normalization" value="1 1" /> - <param name="first_plot" value="Counts" /> - <output file="count.tab" name="output_tab" /> - <output file="count.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="one_plot" /> - <param name="first_plot" value="Size" /> - <param name="normalization" value="1 1" /> - <output file="size.tab" name="output_tab" /> - <output file="size.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="one_plot" /> - <param name="first_plot" value="Coverage" /> - <param name="normalization" value="1 1" /> - <output file="coverage.tab" name="output_tab" /> - <output file="coverage.pdf" name="output_pdf" /> - </test> - <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> - <param name="minsize" value="0" /> - <param name="maxsize" value="10000" /> - <param name="cluster" value="0" /> - <param name="plots_options_selector" value="one_plot" /> - <param name="first_plot" value="Coverage" /> - <param name="normalization" value="1 0.2" /> - <output file="coverage.tab" name="output_tab" /> - <output file="coverage_normed.pdf" name="output_pdf" /> - </test> </tests> - - <help> **What it does** -Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5) -size read distribution along chromosome references. +Plots mapping statistics of an alignment along the reference chromosomes : -Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads -whose 5' end map to a given coordinate in a chromosome reference. + - counts + - mean sizes + - median sizes + - coverage depth + - size distribution + +Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads +in each position of a chromosome reference. Coverage depths are computed from the input bam alignment files using the python pysam module. -The variables mentioned above (1-5) can be plotted either separately or in all possible -pairwise combinations. +The metrics mentioned above can be plotted either separately: + +.. image:: one_plot.png -For comparison purpose, values from bam alignment files can be normalized by a size factor -before plotting. If the normalization field is leaved blank, default normalization of 1 -is assumed. +Or in all possible pairwise combinations: + +.. image:: two_plot.png + +For comparison purposes, values from bam alignment files can be normalized by a size factor +before plotting. **Inputs** @@ -374,16 +319,11 @@ - single-read - sorted - - mapping to the same reference - -Optionally, a space-separated list of normalization/size factors may be added before plotting. -This list maps to the selected bam alignments from bottom to top. + - mapped to the same reference **Output** -A pdf file generated by the R package lattice - -One or two dataframes used to plot data +A pdf file generated by the R package lattice and one or two dataframes used to plot the data. </help>
--- a/test-data/count.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,617 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input1.bam FBtr0070001 72 1 F 1 -input1.bam FBtr0070001 72 7 F 6 -input1.bam FBtr0070001 72 8 F 3 -input1.bam FBtr0070001 72 11 F 2 -input1.bam FBtr0070001 72 16 F 1 -input1.bam FBtr0070001 72 17 F 1 -input1.bam FBtr0070001 72 18 F 1 -input1.bam FBtr0070001 72 27 F 2 -input1.bam FBtr0070001 72 30 F 1 -input1.bam FBtr0070001 72 31 F 11 -input1.bam FBtr0070001 72 32 F 27 -input1.bam FBtr0070001 72 34 F 1 -input1.bam FBtr0070001 72 72 F 0 -input1.bam FBtr0070533 72 1 F 1 -input1.bam FBtr0070533 72 12 F 2 -input1.bam FBtr0070533 72 15 F 1 -input1.bam FBtr0070533 72 19 F 5 -input1.bam FBtr0070533 72 20 F 1 -input1.bam FBtr0070533 72 21 F 1 -input1.bam FBtr0070533 72 22 F 1 -input1.bam FBtr0070533 72 25 F 1 -input1.bam FBtr0070533 72 26 F 1 -input1.bam FBtr0070533 72 28 F 1 -input1.bam FBtr0070533 72 32 F 4 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FBtr0079820 74 1 F 0 -input2.bam FBtr0079820 74 39 F 1 -input2.bam FBtr0079820 74 52 F 1 -input2.bam FBtr0079820 74 53 F 28 -input2.bam FBtr0079820 74 54 F 26 -input2.bam FBtr0079820 74 55 F 10 -input2.bam FBtr0079820 74 56 F 2 -input2.bam FBtr0079820 74 57 F 6 -input2.bam FBtr0079820 74 58 F 5 -input2.bam FBtr0079820 74 59 F 11 -input2.bam FBtr0079820 74 60 F 19 -input2.bam FBtr0079820 74 74 F 0 -input2.bam FBtr0080609 72 1 F 0 -input2.bam FBtr0080609 72 20 F 1 -input2.bam FBtr0080609 72 21 F 2 -input2.bam FBtr0080609 72 22 F 1 -input2.bam FBtr0080609 72 33 F 1 -input2.bam FBtr0080609 72 39 F 1 -input2.bam FBtr0080609 72 52 F 1 -input2.bam FBtr0080609 72 53 F 1 -input2.bam FBtr0080609 72 72 F 0 -input2.bam FBtr0080644 72 1 F 0 -input2.bam FBtr0080644 72 57 F 1 -input2.bam FBtr0080644 72 58 F 7 -input2.bam FBtr0080644 72 72 F 0 -input2.bam FBtr0080646 72 1 F 0 -input2.bam FBtr0080646 72 51 F 1 -input2.bam FBtr0080646 72 57 F 2 -input2.bam FBtr0080646 72 58 F 9 -input2.bam FBtr0080646 72 72 F 0 -input2.bam FBtr0080647 72 1 F 1 -input2.bam FBtr0080647 72 57 F 4 -input2.bam FBtr0080647 72 58 F 7 -input2.bam FBtr0080647 72 72 F 0 -input2.bam FBtr0080660 72 1 F 0 -input2.bam FBtr0080660 72 58 F 11 -input2.bam FBtr0080660 72 72 F 0 -input2.bam FBtr0080663 71 1 F 2 -input2.bam FBtr0080663 71 11 F 1 -input2.bam FBtr0080663 71 12 F 4 -input2.bam FBtr0080663 71 13 F 4 -input2.bam FBtr0080663 71 14 F 22 -input2.bam FBtr0080663 71 15 F 14 -input2.bam FBtr0080663 71 16 F 5 -input2.bam FBtr0080663 71 17 F 12 -input2.bam FBtr0080663 71 18 F 5 -input2.bam FBtr0080663 71 19 F 6 -input2.bam FBtr0080663 71 20 F 6 -input2.bam FBtr0080663 71 21 F 13 -input2.bam FBtr0080663 71 22 F 3 -input2.bam FBtr0080663 71 31 F 1 -input2.bam FBtr0080663 71 50 F 2 -input2.bam FBtr0080663 71 51 F 1 -input2.bam FBtr0080663 71 52 F 2 -input2.bam FBtr0080663 71 57 F 3 -input2.bam FBtr0080663 71 71 F 0 -input2.bam FBtr0080664 71 1 F 1 -input2.bam FBtr0080664 71 3 F 2 -input2.bam FBtr0080664 71 10 F 1 -input2.bam FBtr0080664 71 11 F 2 -input2.bam FBtr0080664 71 12 F 3 -input2.bam FBtr0080664 71 13 F 11 -input2.bam FBtr0080664 71 14 F 11 -input2.bam FBtr0080664 71 15 F 17 -input2.bam FBtr0080664 71 16 F 15 -input2.bam FBtr0080664 71 17 F 13 -input2.bam FBtr0080664 71 18 F 10 -input2.bam FBtr0080664 71 19 F 8 -input2.bam FBtr0080664 71 20 F 1 -input2.bam FBtr0080664 71 21 F 15 -input2.bam FBtr0080664 71 22 F 6 -input2.bam FBtr0080664 71 24 F 1 -input2.bam FBtr0080664 71 30 F 1 -input2.bam FBtr0080664 71 31 F 3 -input2.bam FBtr0080664 71 32 F 39 -input2.bam FBtr0080664 71 33 F 4 -input2.bam FBtr0080664 71 34 F 37 -input2.bam FBtr0080664 71 35 F 135 -input2.bam FBtr0080664 71 36 F 8 -input2.bam FBtr0080664 71 37 F 25 -input2.bam FBtr0080664 71 38 F 8 -input2.bam FBtr0080664 71 39 F 1 -input2.bam FBtr0080664 71 42 F 1 -input2.bam FBtr0080664 71 47 F 1 -input2.bam FBtr0080664 71 50 F 2 -input2.bam FBtr0080664 71 52 F 1 -input2.bam FBtr0080664 71 53 F 1 -input2.bam FBtr0080664 71 56 F 1 -input2.bam FBtr0080664 71 57 F 2 -input2.bam FBtr0080664 71 62 R 1 -input2.bam FBtr0080664 71 71 F 0 -input2.bam FBtr0080664 71 71 R 1
--- a/test-data/count20-30.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,350 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input2.bam FBtr0070001 72 1 F 0 -input2.bam FBtr0070001 72 13 F 1 -input2.bam FBtr0070001 72 19 F 1 -input2.bam FBtr0070001 72 28 F 1 -input2.bam FBtr0070001 72 32 F 3 -input2.bam FBtr0070001 72 53 F 1 -input2.bam FBtr0070001 72 72 F 0 -input2.bam FBtr0070533 72 1 F 0 -input2.bam FBtr0070533 72 16 F 1 -input2.bam FBtr0070533 72 19 F 1 -input2.bam FBtr0070533 72 20 F 1 -input2.bam FBtr0070533 72 21 F 2 -input2.bam FBtr0070533 72 22 F 10 -input2.bam FBtr0070533 72 72 F 0 -input2.bam FBtr0070603 72 1 F 0 -input2.bam FBtr0070603 72 17 F 4 -input2.bam FBtr0070603 72 19 F 2 -input2.bam FBtr0070603 72 20 F 1 -input2.bam FBtr0070603 72 22 F 9 -input2.bam FBtr0070603 72 27 F 1 -input2.bam FBtr0070603 72 28 F 2 -input2.bam FBtr0070603 72 30 F 1 -input2.bam FBtr0070603 72 31 F 1 -input2.bam FBtr0070603 72 34 F 2 -input2.bam FBtr0070603 72 35 F 1 -input2.bam FBtr0070603 72 37 F 1 -input2.bam FBtr0070603 72 41 F 1 -input2.bam FBtr0070603 72 51 F 2 -input2.bam FBtr0070603 72 72 F 0 -input2.bam FBtr0070604 72 1 F 0 -input2.bam FBtr0070604 72 31 F 1 -input2.bam FBtr0070604 72 32 F 5 -input2.bam FBtr0070604 72 53 F 2 -input2.bam FBtr0070604 72 72 F 0 -input2.bam FBtr0070911 73 1 F 0 -input2.bam FBtr0070911 73 32 F 1 -input2.bam FBtr0070911 73 73 F 0 -input2.bam FBtr0078490 72 1 F 3 -input2.bam FBtr0078490 72 13 F 1 -input2.bam FBtr0078490 72 20 F 1 -input2.bam FBtr0078490 72 30 F 1 -input2.bam FBtr0078490 72 72 F 0 -input2.bam FBtr0078580 72 1 F 3 -input2.bam FBtr0078580 72 11 F 1 -input2.bam FBtr0078580 72 13 F 1 -input2.bam FBtr0078580 72 15 F 2 -input2.bam FBtr0078580 72 16 F 3 -input2.bam FBtr0078580 72 17 F 2 -input2.bam FBtr0078580 72 18 F 9 -input2.bam FBtr0078580 72 19 F 19 -input2.bam FBtr0078580 72 20 F 19 -input2.bam FBtr0078580 72 21 F 39 -input2.bam FBtr0078580 72 25 F 1 -input2.bam FBtr0078580 72 26 F 1 -input2.bam FBtr0078580 72 28 F 2 -input2.bam FBtr0078580 72 29 F 1 -input2.bam FBtr0078580 72 40 F 1 -input2.bam FBtr0078580 72 72 F 0 -input2.bam FBtr0078790 73 1 F 0 -input2.bam FBtr0078790 73 42 F 1 -input2.bam FBtr0078790 73 51 F 1 -input2.bam FBtr0078790 73 52 F 2 -input2.bam FBtr0078790 73 73 F 0 -input2.bam FBtr0079064 72 1 F 0 -input2.bam FBtr0079064 72 72 F 0 -input2.bam FBtr0079090 72 1 F 0 -input2.bam FBtr0079090 72 16 F 1 -input2.bam FBtr0079090 72 72 F 0 -input2.bam FBtr0079338 73 1 F 0 -input2.bam FBtr0079338 73 41 F 2 -input2.bam FBtr0079338 73 42 F 1 -input2.bam FBtr0079338 73 73 F 0 -input2.bam FBtr0079528 71 1 F 0 -input2.bam FBtr0079528 71 3 F 1 -input2.bam FBtr0079528 71 10 F 4 -input2.bam FBtr0079528 71 11 F 3 -input2.bam FBtr0079528 71 13 F 2 -input2.bam FBtr0079528 71 14 F 2 -input2.bam FBtr0079528 71 15 F 1 -input2.bam FBtr0079528 71 18 F 3 -input2.bam FBtr0079528 71 19 F 1 -input2.bam FBtr0079528 71 30 F 1 -input2.bam FBtr0079528 71 31 F 1 -input2.bam FBtr0079528 71 32 F 7 -input2.bam FBtr0079528 71 36 F 2 -input2.bam FBtr0079528 71 37 F 3 -input2.bam FBtr0079528 71 38 F 3 -input2.bam FBtr0079528 71 71 F 0 -input2.bam FBtr0079596 73 1 F 0 -input2.bam FBtr0079596 73 3 F 3 -input2.bam FBtr0079596 73 4 F 3 -input2.bam FBtr0079596 73 5 F 9 -input2.bam FBtr0079596 73 9 F 1 -input2.bam FBtr0079596 73 11 F 18 -input2.bam FBtr0079596 73 12 F 41 -input2.bam FBtr0079596 73 13 F 36 -input2.bam FBtr0079596 73 14 F 4 -input2.bam FBtr0079596 73 22 F 1 -input2.bam FBtr0079596 73 53 F 2 -input2.bam FBtr0079596 73 59 R 1 -input2.bam FBtr0079596 73 73 F 0 -input2.bam FBtr0079677 72 1 F 0 -input2.bam FBtr0079677 72 15 F 1 -input2.bam FBtr0079677 72 72 F 0 -input2.bam FBtr0079690 72 1 F 0 -input2.bam FBtr0079690 72 15 F 1 -input2.bam FBtr0079690 72 17 F 1 -input2.bam FBtr0079690 72 19 F 1 -input2.bam FBtr0079690 72 72 F 0 -input2.bam FBtr0079692 73 1 F 0 -input2.bam FBtr0079692 73 12 F 1 -input2.bam FBtr0079692 73 15 F 1 -input2.bam FBtr0079692 73 73 F 0 -input2.bam FBtr0079693 72 1 F 0 -input2.bam FBtr0079693 72 17 F 1 -input2.bam FBtr0079693 72 52 F 1 -input2.bam FBtr0079693 72 72 F 0 -input2.bam FBtr0079694 72 1 F 0 -input2.bam FBtr0079694 72 72 F 0 -input2.bam FBtr0079702 72 1 F 0 -input2.bam FBtr0079702 72 72 F 0 -input2.bam FBtr0079728 72 1 F 0 -input2.bam FBtr0079728 72 72 F 0 -input2.bam FBtr0079729 72 1 F 0 -input2.bam FBtr0079729 72 72 F 0 -input2.bam FBtr0079752 72 1 F 0 -input2.bam FBtr0079752 72 49 F 1 -input2.bam FBtr0079752 72 72 F 0 -input2.bam FBtr0079820 74 1 F 0 -input2.bam FBtr0079820 74 52 F 1 -input2.bam FBtr0079820 74 53 F 24 -input2.bam FBtr0079820 74 54 F 6 -input2.bam FBtr0079820 74 55 F 1 -input2.bam FBtr0079820 74 74 F 0 -input2.bam FBtr0080609 72 1 F 0 -input2.bam FBtr0080609 72 21 F 1 -input2.bam FBtr0080609 72 22 F 1 -input2.bam FBtr0080609 72 33 F 1 -input2.bam FBtr0080609 72 72 F 0 -input2.bam FBtr0080644 72 1 F 0 -input2.bam FBtr0080644 72 72 F 0 -input2.bam FBtr0080646 72 1 F 0 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FBtr0080664 71 33 F 1 -input2.bam FBtr0080664 71 36 F 4 -input2.bam FBtr0080664 71 37 F 2 -input2.bam FBtr0080664 71 38 F 2 -input2.bam FBtr0080664 71 42 F 1 -input2.bam FBtr0080664 71 62 R 1 -input2.bam FBtr0080664 71 71 F 0 -input2.bam FBtr0080664 71 71 R 1 -input1.bam FBtr0070001 72 1 F 0 -input1.bam FBtr0070001 72 7 F 5 -input1.bam FBtr0070001 72 8 F 3 -input1.bam FBtr0070001 72 11 F 2 -input1.bam FBtr0070001 72 17 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 0 -input1.bam FBtr0070533 72 19 F 5 -input1.bam FBtr0070533 72 20 F 1 -input1.bam FBtr0070533 72 22 F 1 -input1.bam FBtr0070533 72 28 F 1 -input1.bam FBtr0070533 72 32 F 3 -input1.bam FBtr0070533 72 72 F 0 -input1.bam FBtr0070603 72 1 F 0 -input1.bam FBtr0070603 72 3 F 1 -input1.bam FBtr0070603 72 4 F 1 -input1.bam FBtr0070603 72 12 F 1 -input1.bam FBtr0070603 72 13 F 1 -input1.bam FBtr0070603 72 15 F 1 -input1.bam FBtr0070603 72 16 F 1 -input1.bam FBtr0070603 72 17 F 3 -input1.bam FBtr0070603 72 19 F 8 -input1.bam FBtr0070603 72 20 F 2 -input1.bam FBtr0070603 72 21 F 1 -input1.bam FBtr0070603 72 22 F 2 -input1.bam FBtr0070603 72 24 F 1 -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 2 -input1.bam FBtr0070603 72 42 F 1 -input1.bam FBtr0070603 72 72 F 0 -input1.bam FBtr0070604 72 1 F 0 -input1.bam FBtr0070604 72 18 F 1 -input1.bam FBtr0070604 72 31 F 9 -input1.bam FBtr0070604 72 32 F 24 -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 73 F 0 -input1.bam FBtr0078490 72 1 F 0 -input1.bam FBtr0078490 72 28 F 1 -input1.bam FBtr0078490 72 72 F 0 -input1.bam FBtr0078580 72 1 F 417 -input1.bam FBtr0078580 72 3 F 3 -input1.bam FBtr0078580 72 4 F 4 -input1.bam FBtr0078580 72 5 F 4 -input1.bam FBtr0078580 72 6 F 2 -input1.bam FBtr0078580 72 7 F 1 -input1.bam FBtr0078580 72 11 F 1 -input1.bam FBtr0078580 72 12 F 2 -input1.bam FBtr0078580 72 16 F 1 -input1.bam FBtr0078580 72 19 F 1 -input1.bam FBtr0078580 72 20 F 2 -input1.bam FBtr0078580 72 21 F 4 -input1.bam FBtr0078580 72 25 F 2 -input1.bam FBtr0078580 72 72 F 0 -input1.bam FBtr0078790 73 1 F 0 -input1.bam FBtr0078790 73 33 F 1 -input1.bam FBtr0078790 73 42 F 2 -input1.bam FBtr0078790 73 44 F 1 -input1.bam FBtr0078790 73 52 F 1 -input1.bam FBtr0078790 73 73 F 0 -input1.bam FBtr0079064 72 1 F 0 -input1.bam FBtr0079064 72 3 F 1 -input1.bam FBtr0079064 72 72 F 0 -input1.bam FBtr0079090 72 1 F 1 -input1.bam FBtr0079090 72 26 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 42 F 8 -input1.bam FBtr0079338 73 43 F 1 -input1.bam FBtr0079338 73 73 F 0 -input1.bam FBtr0079528 71 1 F 10 -input1.bam FBtr0079528 71 3 F 54 -input1.bam FBtr0079528 71 4 F 2 -input1.bam FBtr0079528 71 8 F 2 -input1.bam FBtr0079528 71 10 F 1 -input1.bam FBtr0079528 71 11 F 1 -input1.bam FBtr0079528 71 18 F 3 -input1.bam FBtr0079528 71 36 F 1 -input1.bam FBtr0079528 71 71 F 0 -input1.bam FBtr0079596 73 1 F 0 -input1.bam FBtr0079596 73 3 F 11 -input1.bam FBtr0079596 73 4 F 30 -input1.bam FBtr0079596 73 13 F 1 -input1.bam FBtr0079596 73 53 F 1 -input1.bam FBtr0079596 73 54 F 1 -input1.bam FBtr0079596 73 73 F 0 -input1.bam FBtr0079677 72 1 F 1 -input1.bam FBtr0079677 72 72 F 0 -input1.bam FBtr0079690 72 1 F 0 -input1.bam FBtr0079690 72 27 F 1 -input1.bam FBtr0079690 72 72 F 0 -input1.bam FBtr0079692 73 1 F 1 -input1.bam FBtr0079692 73 32 F 1 -input1.bam FBtr0079692 73 73 F 0 -input1.bam FBtr0079693 72 1 F 1 -input1.bam FBtr0079693 72 25 F 1 -input1.bam FBtr0079693 72 72 F 0 -input1.bam FBtr0079694 72 1 F 3 -input1.bam FBtr0079694 72 72 F 0 -input1.bam FBtr0079702 72 1 F 0 -input1.bam FBtr0079702 72 72 F 0 -input1.bam FBtr0079728 72 1 F 0 -input1.bam FBtr0079728 72 8 F 1 -input1.bam FBtr0079728 72 19 F 1 -input1.bam FBtr0079728 72 72 F 0 -input1.bam FBtr0079729 72 1 F 0 -input1.bam FBtr0079729 72 13 F 1 -input1.bam FBtr0079729 72 72 F 0 -input1.bam FBtr0079752 72 1 F 1 -input1.bam FBtr0079752 72 7 F 1 -input1.bam FBtr0079752 72 52 F 1 -input1.bam FBtr0079752 72 72 F 0 -input1.bam FBtr0079820 74 1 F 0 -input1.bam FBtr0079820 74 45 F 1 -input1.bam FBtr0079820 74 49 F 1 -input1.bam FBtr0079820 74 51 F 1 -input1.bam FBtr0079820 74 74 F 0 -input1.bam FBtr0080609 72 1 F 3 -input1.bam FBtr0080609 72 3 F 2 -input1.bam FBtr0080609 72 4 F 10 -input1.bam FBtr0080609 72 12 F 1 -input1.bam FBtr0080609 72 16 F 1 -input1.bam FBtr0080609 72 17 F 1 -input1.bam FBtr0080609 72 19 F 1 -input1.bam FBtr0080609 72 20 F 1 -input1.bam FBtr0080609 72 42 F 1 -input1.bam FBtr0080609 72 72 F 0 -input1.bam FBtr0080644 72 1 F 1 -input1.bam FBtr0080644 72 4 F 1 -input1.bam FBtr0080644 72 72 F 0 -input1.bam FBtr0080646 72 1 F 0 -input1.bam FBtr0080646 72 6 F 1 -input1.bam FBtr0080646 72 7 F 1 -input1.bam FBtr0080646 72 72 F 0 -input1.bam FBtr0080647 72 1 F 0 -input1.bam FBtr0080647 72 6 F 1 -input1.bam FBtr0080647 72 8 F 1 -input1.bam FBtr0080647 72 72 F 0 -input1.bam FBtr0080660 72 1 F 0 -input1.bam FBtr0080660 72 4 F 4 -input1.bam FBtr0080660 72 7 F 2 -input1.bam FBtr0080660 72 72 F 0 -input1.bam FBtr0080663 71 1 F 6 -input1.bam FBtr0080663 71 3 F 56 -input1.bam FBtr0080663 71 4 F 4 -input1.bam FBtr0080663 71 8 F 2 -input1.bam FBtr0080663 71 51 F 1 -input1.bam FBtr0080663 71 71 F 0 -input1.bam FBtr0080664 71 1 F 6 -input1.bam FBtr0080664 71 3 F 56 -input1.bam FBtr0080664 71 4 F 4 -input1.bam FBtr0080664 71 6 F 1 -input1.bam FBtr0080664 71 7 F 1 -input1.bam FBtr0080664 71 8 F 3 -input1.bam FBtr0080664 71 9 F 1 -input1.bam FBtr0080664 71 12 F 1 -input1.bam FBtr0080664 71 13 F 2 -input1.bam FBtr0080664 71 33 F 1 -input1.bam FBtr0080664 71 36 F 1 -input1.bam FBtr0080664 71 71 F 0
--- a/test-data/count_1_chr.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input_single_chr.bam 1 80 1 F 1 -input_single_chr.bam 1 80 80 F 0
--- a/test-data/count_5_chr.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input_5_chr.bam 1 80 1 F 1 -input_5_chr.bam 1 80 80 F 0 -input_5_chr.bam 2 80 1 F 1 -input_5_chr.bam 2 80 80 F 0 -input_5_chr.bam 3 80 1 F 1 -input_5_chr.bam 3 80 80 F 0 -input_5_chr.bam 4 80 1 F 1 -input_5_chr.bam 4 80 80 F 0 -input_5_chr.bam 5 80 1 F 1 -input_5_chr.bam 5 80 80 F 0
--- a/test-data/count_cluster_5.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,265 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input1.bam FBtr0070001 72 1 F 1 -input1.bam FBtr0070001 72 12 F 14 -input1.bam FBtr0070001 72 30 F 42 -input1.bam FBtr0070001 72 72 F 0 -input1.bam FBtr0070533 72 1 F 1 -input1.bam FBtr0070533 72 25 F 23 -input1.bam FBtr0070533 72 72 F 0 -input1.bam FBtr0070603 72 1 F 0 -input1.bam FBtr0070603 72 21 F 68 -input1.bam FBtr0070603 72 53 F 2 -input1.bam FBtr0070603 72 72 F 0 -input1.bam FBtr0070604 72 1 F 1 -input1.bam FBtr0070604 72 20 F 2 -input1.bam FBtr0070604 72 31 F 36 -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 15 F 4 -input1.bam FBtr0078490 72 26 F 3 -input1.bam FBtr0078490 72 38 F 1 -input1.bam FBtr0078490 72 72 F 0 -input1.bam FBtr0078580 72 1 F 0 -input1.bam FBtr0078580 72 16 F 1102 -input1.bam FBtr0078580 72 52 F 2 -input1.bam FBtr0078580 72 72 F 0 -input1.bam FBtr0078790 73 1 F 1 -input1.bam FBtr0078790 73 17 F 2 -input1.bam FBtr0078790 73 33 F 1 -input1.bam FBtr0078790 73 47 F 9 -input1.bam FBtr0078790 73 69 R 1 -input1.bam FBtr0078790 73 73 F 0 -input1.bam FBtr0079064 72 1 F 0 -input1.bam FBtr0079064 72 2 F 2 -input1.bam FBtr0079064 72 33 F 1 -input1.bam FBtr0079064 72 52 F 1 -input1.bam FBtr0079064 72 72 F 0 -input1.bam FBtr0079090 72 1 F 2 -input1.bam FBtr0079090 72 26 F 1 -input1.bam FBtr0079090 72 33 F 1 -input1.bam FBtr0079090 72 53 F 1 -input1.bam FBtr0079090 72 56 R 1 -input1.bam FBtr0079090 72 72 F 0 -input1.bam FBtr0079338 73 1 F 0 -input1.bam FBtr0079338 73 14 F 5 -input1.bam FBtr0079338 73 25 F 1 -input1.bam FBtr0079338 73 44 F 10 -input1.bam FBtr0079338 73 73 F 0 -input1.bam FBtr0079528 71 1 F 0 -input1.bam FBtr0079528 71 9 F 97 -input1.bam FBtr0079528 71 28 F 1 -input1.bam FBtr0079528 71 36 F 3 -input1.bam FBtr0079528 71 51 F 5 -input1.bam FBtr0079528 71 71 F 0 -input1.bam FBtr0079596 73 1 F 0 -input1.bam FBtr0079596 73 10 F 148 -input1.bam FBtr0079596 73 53 F 4 -input1.bam FBtr0079596 73 73 F 0 -input1.bam FBtr0079677 72 1 F 0 -input1.bam FBtr0079677 72 3 F 2 -input1.bam FBtr0079677 72 52 F 2 -input1.bam FBtr0079677 72 72 F 0 -input1.bam FBtr0079690 72 1 F 1 -input1.bam FBtr0079690 72 24 F 2 -input1.bam FBtr0079690 72 33 F 2 -input1.bam FBtr0079690 72 72 F 0 -input1.bam FBtr0079692 73 1 F 3 -input1.bam FBtr0079692 73 18 F 1 -input1.bam FBtr0079692 73 25 F 1 -input1.bam FBtr0079692 73 32 F 1 -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 54 F 2 -input1.bam FBtr0079729 72 72 F 0 -input1.bam FBtr0079752 72 1 F 2 -input1.bam FBtr0079752 72 9 F 2 -input1.bam FBtr0079752 72 33 F 2 -input1.bam FBtr0079752 72 52 F 2 -input1.bam FBtr0079752 72 72 F 0 -input1.bam FBtr0079820 74 1 F 0 -input1.bam FBtr0079820 74 50 F 13 -input1.bam FBtr0079820 74 74 F 0 -input1.bam FBtr0080609 72 1 F 0 -input1.bam FBtr0080609 72 10 F 60 -input1.bam FBtr0080609 72 42 F 1 -input1.bam FBtr0080609 72 51 F 2 -input1.bam FBtr0080609 72 72 F 0 -input1.bam FBtr0080644 72 1 F 0 -input1.bam FBtr0080644 72 6 F 6 -input1.bam FBtr0080644 72 72 F 0 -input1.bam FBtr0080646 72 1 F 0 -input1.bam FBtr0080646 72 4 F 3 -input1.bam FBtr0080646 72 72 F 0 -input1.bam FBtr0080647 72 1 F 0 -input1.bam FBtr0080647 72 6 F 10 -input1.bam FBtr0080647 72 72 F 0 -input1.bam FBtr0080660 72 1 F 0 -input1.bam FBtr0080660 72 4 F 7 -input1.bam FBtr0080660 72 72 F 0 -input1.bam FBtr0080663 71 1 F 0 -input1.bam FBtr0080663 71 9 F 102 -input1.bam FBtr0080663 71 26 F 1 -input1.bam FBtr0080663 71 32 F 2 -input1.bam FBtr0080663 71 50 F 10 -input1.bam FBtr0080663 71 71 F 0 -input1.bam FBtr0080664 71 1 F 0 -input1.bam FBtr0080664 71 11 F 108 -input1.bam FBtr0080664 71 33 F 9 -input1.bam FBtr0080664 71 53 F 11 -input1.bam FBtr0080664 71 71 F 0 -input2.bam FBtr0070001 72 1 F 1 -input2.bam FBtr0070001 72 15 F 4 -input2.bam FBtr0070001 72 30 F 4 -input2.bam FBtr0070001 72 55 F 15 -input2.bam FBtr0070001 72 72 F 0 -input2.bam FBtr0070533 72 1 F 0 -input2.bam FBtr0070533 72 21 F 44 -input2.bam FBtr0070533 72 39 F 1 -input2.bam FBtr0070533 72 72 F 0 -input2.bam FBtr0070603 72 1 F 0 -input2.bam FBtr0070603 72 26 F 57 -input2.bam FBtr0070603 72 52 F 4 -input2.bam FBtr0070603 72 72 F 0 -input2.bam FBtr0070604 72 1 F 0 -input2.bam FBtr0070604 72 2 F 1 -input2.bam FBtr0070604 72 31 F 6 -input2.bam FBtr0070604 72 40 F 1 -input2.bam FBtr0070604 72 55 F 47 -input2.bam FBtr0070604 72 72 F 0 -input2.bam FBtr0070911 73 1 F 0 -input2.bam FBtr0070911 73 11 F 1 -input2.bam FBtr0070911 73 32 F 1 -input2.bam FBtr0070911 73 48 F 1 -input2.bam FBtr0070911 73 73 F 0 -input2.bam FBtr0078490 72 1 F 3 -input2.bam FBtr0078490 72 13 F 6 -input2.bam FBtr0078490 72 20 F 1 -input2.bam FBtr0078490 72 30 F 1 -input2.bam FBtr0078490 72 39 F 3 -input2.bam FBtr0078490 72 72 F 0 -input2.bam FBtr0078580 72 1 F 146 -input2.bam FBtr0078580 72 21 F 215 -input2.bam FBtr0078580 72 41 F 6 -input2.bam FBtr0078580 72 52 F 3 -input2.bam FBtr0078580 72 72 F 0 -input2.bam FBtr0078790 73 1 F 0 -input2.bam FBtr0078790 73 17 F 1 -input2.bam FBtr0078790 73 47 F 9 -input2.bam FBtr0078790 73 73 F 0 -input2.bam FBtr0079064 72 1 F 3 -input2.bam FBtr0079064 72 52 F 2 -input2.bam FBtr0079064 72 72 F 0 -input2.bam FBtr0079090 72 1 F 1 -input2.bam FBtr0079090 72 18 F 2 -input2.bam FBtr0079090 72 34 F 2 -input2.bam FBtr0079090 72 52 F 2 -input2.bam FBtr0079090 72 72 F 0 -input2.bam FBtr0079338 73 1 F 0 -input2.bam FBtr0079338 73 15 F 19 -input2.bam FBtr0079338 73 40 F 4 -input2.bam FBtr0079338 73 73 F 0 -input2.bam FBtr0079528 71 1 F 0 -input2.bam FBtr0079528 71 2 F 3 -input2.bam FBtr0079528 71 16 F 114 -input2.bam FBtr0079528 71 43 F 248 -input2.bam FBtr0079528 71 71 F 0 -input2.bam FBtr0079596 73 1 F 0 -input2.bam FBtr0079596 73 11 F 311 -input2.bam FBtr0079596 73 42 F 1 -input2.bam FBtr0079596 73 53 F 3 -input2.bam FBtr0079596 73 59 R 1 -input2.bam FBtr0079596 73 73 F 0 -input2.bam FBtr0079677 72 1 F 2 -input2.bam FBtr0079677 72 15 F 1 -input2.bam FBtr0079677 72 24 F 1 -input2.bam FBtr0079677 72 43 F 1 -input2.bam FBtr0079677 72 53 F 2 -input2.bam FBtr0079677 72 72 F 0 -input2.bam FBtr0079690 72 1 F 1 -input2.bam FBtr0079690 72 18 F 4 -input2.bam FBtr0079690 72 72 F 0 -input2.bam FBtr0079692 73 1 F 0 -input2.bam FBtr0079692 73 8 F 4 -input2.bam FBtr0079692 73 73 F 0 -input2.bam FBtr0079693 72 1 F 3 -input2.bam FBtr0079693 72 18 F 3 -input2.bam FBtr0079693 72 45 F 1 -input2.bam FBtr0079693 72 53 F 2 -input2.bam FBtr0079693 72 72 F 0 -input2.bam FBtr0079694 72 1 F 2 -input2.bam FBtr0079694 72 17 F 3 -input2.bam FBtr0079694 72 52 F 1 -input2.bam FBtr0079694 72 72 F 0 -input2.bam FBtr0079702 72 1 F 2 -input2.bam FBtr0079702 72 52 F 2 -input2.bam FBtr0079702 72 72 F 0 -input2.bam FBtr0079728 72 1 F 3 -input2.bam FBtr0079728 72 20 F 1 -input2.bam FBtr0079728 72 52 F 2 -input2.bam FBtr0079728 72 72 F 0 -input2.bam FBtr0079729 72 1 F 1 -input2.bam FBtr0079729 72 19 F 1 -input2.bam FBtr0079729 72 33 F 1 -input2.bam FBtr0079729 72 53 F 1 -input2.bam FBtr0079729 72 72 F 0 -input2.bam FBtr0079752 72 1 F 0 -input2.bam FBtr0079752 72 50 F 2 -input2.bam FBtr0079752 72 72 F 0 -input2.bam FBtr0079820 74 1 F 0 -input2.bam FBtr0079820 74 39 F 1 -input2.bam FBtr0079820 74 56 F 108 -input2.bam FBtr0079820 74 74 F 0 -input2.bam FBtr0080609 72 1 F 0 -input2.bam FBtr0080609 72 21 F 4 -input2.bam FBtr0080609 72 33 F 1 -input2.bam FBtr0080609 72 39 F 1 -input2.bam FBtr0080609 72 52 F 2 -input2.bam FBtr0080609 72 72 F 0 -input2.bam FBtr0080644 72 1 F 0 -input2.bam FBtr0080644 72 57 F 8 -input2.bam FBtr0080644 72 72 F 0 -input2.bam FBtr0080646 72 1 F 0 -input2.bam FBtr0080646 72 51 F 1 -input2.bam FBtr0080646 72 57 F 11 -input2.bam FBtr0080646 72 72 F 0 -input2.bam FBtr0080647 72 1 F 1 -input2.bam FBtr0080647 72 57 F 11 -input2.bam FBtr0080647 72 72 F 0 -input2.bam FBtr0080660 72 1 F 0 -input2.bam FBtr0080660 72 58 F 11 -input2.bam FBtr0080660 72 72 F 0 -input2.bam FBtr0080663 71 1 F 2 -input2.bam FBtr0080663 71 16 F 95 -input2.bam FBtr0080663 71 31 F 1 -input2.bam FBtr0080663 71 53 F 8 -input2.bam FBtr0080663 71 71 F 0 -input2.bam FBtr0080664 71 1 F 0 -input2.bam FBtr0080664 71 2 F 3 -input2.bam FBtr0080664 71 17 F 114 -input2.bam FBtr0080664 71 43 F 270 -input2.bam FBtr0080664 71 62 R 1 -input2.bam FBtr0080664 71 71 F 0 -input2.bam FBtr0080664 71 71 R 1
--- a/test-data/count_single_chr.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input_single_chr.bam Anopheles_C_Virus|KU169878 8919 1 F 0 -input_single_chr.bam Anopheles_C_Virus|KU169878 8919 749 R 1 -input_single_chr.bam Anopheles_C_Virus|KU169878 8919 8919 F 0
--- a/test-data/coverage.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3109 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Coverage -input1.bam FBtr0070001 72 1 F 1 -input1.bam FBtr0070001 72 2 F 1 -input1.bam FBtr0070001 72 3 F 1 -input1.bam FBtr0070001 72 4 F 1 -input1.bam FBtr0070001 72 5 F 1 -input1.bam FBtr0070001 72 6 F 1 -input1.bam FBtr0070001 72 7 F 7 -input1.bam FBtr0070001 72 8 F 10 -input1.bam FBtr0070001 72 9 F 10 -input1.bam FBtr0070001 72 10 F 10 -input1.bam FBtr0070001 72 11 F 12 -input1.bam FBtr0070001 72 12 F 12 -input1.bam FBtr0070001 72 13 F 12 -input1.bam FBtr0070001 72 14 F 12 -input1.bam FBtr0070001 72 15 F 12 -input1.bam FBtr0070001 72 16 F 13 -input1.bam FBtr0070001 72 17 F 14 -input1.bam FBtr0070001 72 18 F 14 -input1.bam FBtr0070001 72 19 F 14 -input1.bam FBtr0070001 72 20 F 14 -input1.bam FBtr0070001 72 21 F 14 -input1.bam FBtr0070001 72 22 F 14 -input1.bam FBtr0070001 72 23 F 13 -input1.bam FBtr0070001 72 24 F 13 -input1.bam FBtr0070001 72 25 F 13 -input1.bam FBtr0070001 72 26 F 13 -input1.bam FBtr0070001 72 27 F 14 -input1.bam FBtr0070001 72 28 F 11 -input1.bam FBtr0070001 72 29 F 8 -input1.bam FBtr0070001 72 30 F 9 -input1.bam FBtr0070001 72 31 F 18 -input1.bam FBtr0070001 72 32 F 44 -input1.bam FBtr0070001 72 33 F 44 -input1.bam FBtr0070001 72 34 F 44 -input1.bam FBtr0070001 72 35 F 43 -input1.bam FBtr0070001 72 36 F 43 -input1.bam FBtr0070001 72 37 F 43 -input1.bam FBtr0070001 72 38 F 43 -input1.bam FBtr0070001 72 39 F 43 -input1.bam FBtr0070001 72 40 F 42 -input1.bam FBtr0070001 72 41 F 42 -input1.bam FBtr0070001 72 42 F 42 -input1.bam FBtr0070001 72 43 F 42 -input1.bam FBtr0070001 72 44 F 42 -input1.bam FBtr0070001 72 45 F 42 -input1.bam FBtr0070001 72 46 F 42 -input1.bam FBtr0070001 72 47 F 42 -input1.bam FBtr0070001 72 48 F 42 -input1.bam FBtr0070001 72 49 F 42 -input1.bam FBtr0070001 72 50 F 41 -input1.bam FBtr0070001 72 51 F 40 -input1.bam FBtr0070001 72 52 F 40 -input1.bam FBtr0070001 72 53 F 39 -input1.bam FBtr0070001 72 72 F 0 -input1.bam FBtr0070533 72 1 F 1 -input1.bam FBtr0070533 72 2 F 1 -input1.bam FBtr0070533 72 3 F 1 -input1.bam FBtr0070533 72 4 F 1 -input1.bam FBtr0070533 72 5 F 1 -input1.bam FBtr0070533 72 6 F 1 -input1.bam FBtr0070533 72 7 F 1 -input1.bam FBtr0070533 72 8 F 1 -input1.bam FBtr0070533 72 9 F 1 -input1.bam FBtr0070533 72 10 F 1 -input1.bam FBtr0070533 72 11 F 1 -input1.bam FBtr0070533 72 12 F 3 -input1.bam FBtr0070533 72 13 F 3 -input1.bam FBtr0070533 72 14 F 3 -input1.bam FBtr0070533 72 15 F 4 -input1.bam FBtr0070533 72 16 F 3 -input1.bam FBtr0070533 72 17 F 3 -input1.bam FBtr0070533 72 18 F 3 -input1.bam FBtr0070533 72 19 F 8 -input1.bam FBtr0070533 72 20 F 9 -input1.bam FBtr0070533 72 21 F 10 -input1.bam FBtr0070533 72 22 F 11 -input1.bam FBtr0070533 72 23 F 11 -input1.bam FBtr0070533 72 24 F 11 -input1.bam FBtr0070533 72 25 F 12 -input1.bam FBtr0070533 72 26 F 13 -input1.bam FBtr0070533 72 27 F 13 -input1.bam FBtr0070533 72 28 F 14 -input1.bam FBtr0070533 72 29 F 14 -input1.bam FBtr0070533 72 30 F 11 -input1.bam FBtr0070533 72 31 F 11 -input1.bam FBtr0070533 72 32 F 15 -input1.bam FBtr0070533 72 33 F 15 -input1.bam FBtr0070533 72 34 F 15 -input1.bam FBtr0070533 72 35 F 16 -input1.bam FBtr0070533 72 36 F 16 -input1.bam FBtr0070533 72 37 F 18 -input1.bam FBtr0070533 72 38 F 20 -input1.bam FBtr0070533 72 39 F 19 -input1.bam FBtr0070533 72 40 F 17 -input1.bam FBtr0070533 72 41 F 15 -input1.bam FBtr0070533 72 42 F 11 -input1.bam FBtr0070533 72 43 F 10 -input1.bam FBtr0070533 72 44 F 10 -input1.bam FBtr0070533 72 45 F 10 -input1.bam FBtr0070533 72 46 F 10 -input1.bam FBtr0070533 72 47 F 10 -input1.bam FBtr0070533 72 48 F 10 -input1.bam FBtr0070533 72 49 F 10 -input1.bam FBtr0070533 72 50 F 9 -input1.bam FBtr0070533 72 51 F 9 -input1.bam FBtr0070533 72 52 F 8 -input1.bam FBtr0070533 72 53 F 7 -input1.bam FBtr0070533 72 54 F 4 -input1.bam FBtr0070533 72 55 F 4 -input1.bam FBtr0070533 72 72 F 0 -input1.bam FBtr0070603 72 1 F 2 -input1.bam FBtr0070603 72 2 F 2 -input1.bam FBtr0070603 72 3 F 3 -input1.bam FBtr0070603 72 4 F 4 -input1.bam FBtr0070603 72 5 F 4 -input1.bam FBtr0070603 72 6 F 5 -input1.bam FBtr0070603 72 7 F 12 -input1.bam FBtr0070603 72 8 F 16 -input1.bam FBtr0070603 72 9 F 23 -input1.bam FBtr0070603 72 10 F 23 -input1.bam FBtr0070603 72 11 F 23 -input1.bam FBtr0070603 72 12 F 25 -input1.bam FBtr0070603 72 13 F 26 -input1.bam FBtr0070603 72 14 F 26 -input1.bam FBtr0070603 72 15 F 28 -input1.bam FBtr0070603 72 16 F 29 -input1.bam FBtr0070603 72 17 F 32 -input1.bam FBtr0070603 72 18 F 33 -input1.bam FBtr0070603 72 19 F 41 -input1.bam FBtr0070603 72 20 F 44 -input1.bam FBtr0070603 72 21 F 45 -input1.bam FBtr0070603 72 22 F 48 -input1.bam FBtr0070603 72 23 F 48 -input1.bam FBtr0070603 72 24 F 30 -input1.bam FBtr0070603 72 25 F 30 -input1.bam FBtr0070603 72 26 F 36 -input1.bam FBtr0070603 72 27 F 39 -input1.bam FBtr0070603 72 28 F 39 -input1.bam FBtr0070603 72 29 F 38 -input1.bam FBtr0070603 72 30 F 38 -input1.bam FBtr0070603 72 31 F 38 -input1.bam FBtr0070603 72 32 F 38 -input1.bam FBtr0070603 72 33 F 37 -input1.bam FBtr0070603 72 34 F 39 -input1.bam FBtr0070603 72 35 F 35 -input1.bam FBtr0070603 72 36 F 34 -input1.bam FBtr0070603 72 37 F 34 -input1.bam FBtr0070603 72 38 F 35 -input1.bam FBtr0070603 72 39 F 34 -input1.bam FBtr0070603 72 40 F 33 -input1.bam FBtr0070603 72 41 F 32 -input1.bam FBtr0070603 72 42 F 21 -input1.bam FBtr0070603 72 43 F 21 -input1.bam FBtr0070603 72 44 F 20 -input1.bam FBtr0070603 72 45 F 18 -input1.bam FBtr0070603 72 46 F 16 -input1.bam FBtr0070603 72 47 F 16 -input1.bam FBtr0070603 72 48 F 15 -input1.bam FBtr0070603 72 49 F 15 -input1.bam FBtr0070603 72 50 F 14 -input1.bam FBtr0070603 72 51 F 14 -input1.bam FBtr0070603 72 52 F 10 -input1.bam FBtr0070603 72 53 F 6 -input1.bam FBtr0070603 72 54 F 3 -input1.bam FBtr0070603 72 55 F 3 -input1.bam FBtr0070603 72 56 F 3 -input1.bam FBtr0070603 72 57 F 3 -input1.bam FBtr0070603 72 58 F 3 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--- a/test-data/coverage_1_chr.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Coverage -input_single_chr.bam 1 80 1 F 1 -input_single_chr.bam 1 80 2 F 1 -input_single_chr.bam 1 80 3 F 1 -input_single_chr.bam 1 80 4 F 1 -input_single_chr.bam 1 80 5 F 1 -input_single_chr.bam 1 80 6 F 1 -input_single_chr.bam 1 80 7 F 1 -input_single_chr.bam 1 80 8 F 1 -input_single_chr.bam 1 80 9 F 1 -input_single_chr.bam 1 80 10 F 1 -input_single_chr.bam 1 80 11 F 1 -input_single_chr.bam 1 80 12 F 1 -input_single_chr.bam 1 80 13 F 1 -input_single_chr.bam 1 80 14 F 1 -input_single_chr.bam 1 80 15 F 1 -input_single_chr.bam 1 80 16 F 1 -input_single_chr.bam 1 80 17 F 1 -input_single_chr.bam 1 80 18 F 1 -input_single_chr.bam 1 80 19 F 1 -input_single_chr.bam 1 80 20 F 1 -input_single_chr.bam 1 80 21 F 1 -input_single_chr.bam 1 80 22 F 1 -input_single_chr.bam 1 80 23 F 1 -input_single_chr.bam 1 80 24 F 1 -input_single_chr.bam 1 80 25 F 1 -input_single_chr.bam 1 80 26 F 1 -input_single_chr.bam 1 80 27 F 1 -input_single_chr.bam 1 80 28 F 1 -input_single_chr.bam 1 80 29 F 1 -input_single_chr.bam 1 80 30 F 1 -input_single_chr.bam 1 80 31 F 1 -input_single_chr.bam 1 80 32 F 1 -input_single_chr.bam 1 80 33 F 1 -input_single_chr.bam 1 80 34 F 1 -input_single_chr.bam 1 80 35 F 1 -input_single_chr.bam 1 80 36 F 1 -input_single_chr.bam 1 80 37 F 1 -input_single_chr.bam 1 80 38 F 1 -input_single_chr.bam 1 80 39 F 1 -input_single_chr.bam 1 80 40 F 1 -input_single_chr.bam 1 80 41 F 1 -input_single_chr.bam 1 80 42 F 1 -input_single_chr.bam 1 80 43 F 1 -input_single_chr.bam 1 80 44 F 1 -input_single_chr.bam 1 80 45 F 1 -input_single_chr.bam 1 80 46 F 1 -input_single_chr.bam 1 80 47 F 1 -input_single_chr.bam 1 80 48 F 1 -input_single_chr.bam 1 80 49 F 1 -input_single_chr.bam 1 80 50 F 1 -input_single_chr.bam 1 80 51 F 1 -input_single_chr.bam 1 80 52 F 1 -input_single_chr.bam 1 80 53 F 1 -input_single_chr.bam 1 80 54 F 1 -input_single_chr.bam 1 80 55 F 1 -input_single_chr.bam 1 80 56 F 1 -input_single_chr.bam 1 80 57 F 1 -input_single_chr.bam 1 80 58 F 1 -input_single_chr.bam 1 80 59 F 1 -input_single_chr.bam 1 80 60 F 1 -input_single_chr.bam 1 80 61 F 1 -input_single_chr.bam 1 80 62 F 1 -input_single_chr.bam 1 80 63 F 1 -input_single_chr.bam 1 80 64 F 1 -input_single_chr.bam 1 80 65 F 1 -input_single_chr.bam 1 80 66 F 1 -input_single_chr.bam 1 80 67 F 1 -input_single_chr.bam 1 80 68 F 1 -input_single_chr.bam 1 80 69 F 1 -input_single_chr.bam 1 80 70 F 1 -input_single_chr.bam 1 80 71 F 1 -input_single_chr.bam 1 80 72 F 1 -input_single_chr.bam 1 80 73 F 1 -input_single_chr.bam 1 80 74 F 1 -input_single_chr.bam 1 80 75 F 1 -input_single_chr.bam 1 80 76 F 1 -input_single_chr.bam 1 80 77 F 1 -input_single_chr.bam 1 80 78 F 1 -input_single_chr.bam 1 80 79 F 1 -input_single_chr.bam 1 80 80 F 1
--- a/test-data/coverage_5_chr.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,401 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Coverage -input_5_chr.bam 1 80 1 F 1 -input_5_chr.bam 1 80 2 F 1 -input_5_chr.bam 1 80 3 F 1 -input_5_chr.bam 1 80 4 F 1 -input_5_chr.bam 1 80 5 F 1 -input_5_chr.bam 1 80 6 F 1 -input_5_chr.bam 1 80 7 F 1 -input_5_chr.bam 1 80 8 F 1 -input_5_chr.bam 1 80 9 F 1 -input_5_chr.bam 1 80 10 F 1 -input_5_chr.bam 1 80 11 F 1 -input_5_chr.bam 1 80 12 F 1 -input_5_chr.bam 1 80 13 F 1 -input_5_chr.bam 1 80 14 F 1 -input_5_chr.bam 1 80 15 F 1 -input_5_chr.bam 1 80 16 F 1 -input_5_chr.bam 1 80 17 F 1 -input_5_chr.bam 1 80 18 F 1 -input_5_chr.bam 1 80 19 F 1 -input_5_chr.bam 1 80 20 F 1 -input_5_chr.bam 1 80 21 F 1 -input_5_chr.bam 1 80 22 F 1 -input_5_chr.bam 1 80 23 F 1 -input_5_chr.bam 1 80 24 F 1 -input_5_chr.bam 1 80 25 F 1 -input_5_chr.bam 1 80 26 F 1 -input_5_chr.bam 1 80 27 F 1 -input_5_chr.bam 1 80 28 F 1 -input_5_chr.bam 1 80 29 F 1 -input_5_chr.bam 1 80 30 F 1 -input_5_chr.bam 1 80 31 F 1 -input_5_chr.bam 1 80 32 F 1 -input_5_chr.bam 1 80 33 F 1 -input_5_chr.bam 1 80 34 F 1 -input_5_chr.bam 1 80 35 F 1 -input_5_chr.bam 1 80 36 F 1 -input_5_chr.bam 1 80 37 F 1 -input_5_chr.bam 1 80 38 F 1 -input_5_chr.bam 1 80 39 F 1 -input_5_chr.bam 1 80 40 F 1 -input_5_chr.bam 1 80 41 F 1 -input_5_chr.bam 1 80 42 F 1 -input_5_chr.bam 1 80 43 F 1 -input_5_chr.bam 1 80 44 F 1 -input_5_chr.bam 1 80 45 F 1 -input_5_chr.bam 1 80 46 F 1 -input_5_chr.bam 1 80 47 F 1 -input_5_chr.bam 1 80 48 F 1 -input_5_chr.bam 1 80 49 F 1 -input_5_chr.bam 1 80 50 F 1 -input_5_chr.bam 1 80 51 F 1 -input_5_chr.bam 1 80 52 F 1 -input_5_chr.bam 1 80 53 F 1 -input_5_chr.bam 1 80 54 F 1 -input_5_chr.bam 1 80 55 F 1 -input_5_chr.bam 1 80 56 F 1 -input_5_chr.bam 1 80 57 F 1 -input_5_chr.bam 1 80 58 F 1 -input_5_chr.bam 1 80 59 F 1 -input_5_chr.bam 1 80 60 F 1 -input_5_chr.bam 1 80 61 F 1 -input_5_chr.bam 1 80 62 F 1 -input_5_chr.bam 1 80 63 F 1 -input_5_chr.bam 1 80 64 F 1 -input_5_chr.bam 1 80 65 F 1 -input_5_chr.bam 1 80 66 F 1 -input_5_chr.bam 1 80 67 F 1 -input_5_chr.bam 1 80 68 F 1 -input_5_chr.bam 1 80 69 F 1 -input_5_chr.bam 1 80 70 F 1 -input_5_chr.bam 1 80 71 F 1 -input_5_chr.bam 1 80 72 F 1 -input_5_chr.bam 1 80 73 F 1 -input_5_chr.bam 1 80 74 F 1 -input_5_chr.bam 1 80 75 F 1 -input_5_chr.bam 1 80 76 F 1 -input_5_chr.bam 1 80 77 F 1 -input_5_chr.bam 1 80 78 F 1 -input_5_chr.bam 1 80 79 F 1 -input_5_chr.bam 1 80 80 F 1 -input_5_chr.bam 2 80 1 F 1 -input_5_chr.bam 2 80 2 F 1 -input_5_chr.bam 2 80 3 F 1 -input_5_chr.bam 2 80 4 F 1 -input_5_chr.bam 2 80 5 F 1 -input_5_chr.bam 2 80 6 F 1 -input_5_chr.bam 2 80 7 F 1 -input_5_chr.bam 2 80 8 F 1 -input_5_chr.bam 2 80 9 F 1 -input_5_chr.bam 2 80 10 F 1 -input_5_chr.bam 2 80 11 F 1 -input_5_chr.bam 2 80 12 F 1 -input_5_chr.bam 2 80 13 F 1 -input_5_chr.bam 2 80 14 F 1 -input_5_chr.bam 2 80 15 F 1 -input_5_chr.bam 2 80 16 F 1 -input_5_chr.bam 2 80 17 F 1 -input_5_chr.bam 2 80 18 F 1 -input_5_chr.bam 2 80 19 F 1 -input_5_chr.bam 2 80 20 F 1 -input_5_chr.bam 2 80 21 F 1 -input_5_chr.bam 2 80 22 F 1 -input_5_chr.bam 2 80 23 F 1 -input_5_chr.bam 2 80 24 F 1 -input_5_chr.bam 2 80 25 F 1 -input_5_chr.bam 2 80 26 F 1 -input_5_chr.bam 2 80 27 F 1 -input_5_chr.bam 2 80 28 F 1 -input_5_chr.bam 2 80 29 F 1 -input_5_chr.bam 2 80 30 F 1 -input_5_chr.bam 2 80 31 F 1 -input_5_chr.bam 2 80 32 F 1 -input_5_chr.bam 2 80 33 F 1 -input_5_chr.bam 2 80 34 F 1 -input_5_chr.bam 2 80 35 F 1 -input_5_chr.bam 2 80 36 F 1 -input_5_chr.bam 2 80 37 F 1 -input_5_chr.bam 2 80 38 F 1 -input_5_chr.bam 2 80 39 F 1 -input_5_chr.bam 2 80 40 F 1 -input_5_chr.bam 2 80 41 F 1 -input_5_chr.bam 2 80 42 F 1 -input_5_chr.bam 2 80 43 F 1 -input_5_chr.bam 2 80 44 F 1 -input_5_chr.bam 2 80 45 F 1 -input_5_chr.bam 2 80 46 F 1 -input_5_chr.bam 2 80 47 F 1 -input_5_chr.bam 2 80 48 F 1 -input_5_chr.bam 2 80 49 F 1 -input_5_chr.bam 2 80 50 F 1 -input_5_chr.bam 2 80 51 F 1 -input_5_chr.bam 2 80 52 F 1 -input_5_chr.bam 2 80 53 F 1 -input_5_chr.bam 2 80 54 F 1 -input_5_chr.bam 2 80 55 F 1 -input_5_chr.bam 2 80 56 F 1 -input_5_chr.bam 2 80 57 F 1 -input_5_chr.bam 2 80 58 F 1 -input_5_chr.bam 2 80 59 F 1 -input_5_chr.bam 2 80 60 F 1 -input_5_chr.bam 2 80 61 F 1 -input_5_chr.bam 2 80 62 F 1 -input_5_chr.bam 2 80 63 F 1 -input_5_chr.bam 2 80 64 F 1 -input_5_chr.bam 2 80 65 F 1 -input_5_chr.bam 2 80 66 F 1 -input_5_chr.bam 2 80 67 F 1 -input_5_chr.bam 2 80 68 F 1 -input_5_chr.bam 2 80 69 F 1 -input_5_chr.bam 2 80 70 F 1 -input_5_chr.bam 2 80 71 F 1 -input_5_chr.bam 2 80 72 F 1 -input_5_chr.bam 2 80 73 F 1 -input_5_chr.bam 2 80 74 F 1 -input_5_chr.bam 2 80 75 F 1 -input_5_chr.bam 2 80 76 F 1 -input_5_chr.bam 2 80 77 F 1 -input_5_chr.bam 2 80 78 F 1 -input_5_chr.bam 2 80 79 F 1 -input_5_chr.bam 2 80 80 F 1 -input_5_chr.bam 3 80 1 F 1 -input_5_chr.bam 3 80 2 F 1 -input_5_chr.bam 3 80 3 F 1 -input_5_chr.bam 3 80 4 F 1 -input_5_chr.bam 3 80 5 F 1 -input_5_chr.bam 3 80 6 F 1 -input_5_chr.bam 3 80 7 F 1 -input_5_chr.bam 3 80 8 F 1 -input_5_chr.bam 3 80 9 F 1 -input_5_chr.bam 3 80 10 F 1 -input_5_chr.bam 3 80 11 F 1 -input_5_chr.bam 3 80 12 F 1 -input_5_chr.bam 3 80 13 F 1 -input_5_chr.bam 3 80 14 F 1 -input_5_chr.bam 3 80 15 F 1 -input_5_chr.bam 3 80 16 F 1 -input_5_chr.bam 3 80 17 F 1 -input_5_chr.bam 3 80 18 F 1 -input_5_chr.bam 3 80 19 F 1 -input_5_chr.bam 3 80 20 F 1 -input_5_chr.bam 3 80 21 F 1 -input_5_chr.bam 3 80 22 F 1 -input_5_chr.bam 3 80 23 F 1 -input_5_chr.bam 3 80 24 F 1 -input_5_chr.bam 3 80 25 F 1 -input_5_chr.bam 3 80 26 F 1 -input_5_chr.bam 3 80 27 F 1 -input_5_chr.bam 3 80 28 F 1 -input_5_chr.bam 3 80 29 F 1 -input_5_chr.bam 3 80 30 F 1 -input_5_chr.bam 3 80 31 F 1 -input_5_chr.bam 3 80 32 F 1 -input_5_chr.bam 3 80 33 F 1 -input_5_chr.bam 3 80 34 F 1 -input_5_chr.bam 3 80 35 F 1 -input_5_chr.bam 3 80 36 F 1 -input_5_chr.bam 3 80 37 F 1 -input_5_chr.bam 3 80 38 F 1 -input_5_chr.bam 3 80 39 F 1 -input_5_chr.bam 3 80 40 F 1 -input_5_chr.bam 3 80 41 F 1 -input_5_chr.bam 3 80 42 F 1 -input_5_chr.bam 3 80 43 F 1 -input_5_chr.bam 3 80 44 F 1 -input_5_chr.bam 3 80 45 F 1 -input_5_chr.bam 3 80 46 F 1 -input_5_chr.bam 3 80 47 F 1 -input_5_chr.bam 3 80 48 F 1 -input_5_chr.bam 3 80 49 F 1 -input_5_chr.bam 3 80 50 F 1 -input_5_chr.bam 3 80 51 F 1 -input_5_chr.bam 3 80 52 F 1 -input_5_chr.bam 3 80 53 F 1 -input_5_chr.bam 3 80 54 F 1 -input_5_chr.bam 3 80 55 F 1 -input_5_chr.bam 3 80 56 F 1 -input_5_chr.bam 3 80 57 F 1 -input_5_chr.bam 3 80 58 F 1 -input_5_chr.bam 3 80 59 F 1 -input_5_chr.bam 3 80 60 F 1 -input_5_chr.bam 3 80 61 F 1 -input_5_chr.bam 3 80 62 F 1 -input_5_chr.bam 3 80 63 F 1 -input_5_chr.bam 3 80 64 F 1 -input_5_chr.bam 3 80 65 F 1 -input_5_chr.bam 3 80 66 F 1 -input_5_chr.bam 3 80 67 F 1 -input_5_chr.bam 3 80 68 F 1 -input_5_chr.bam 3 80 69 F 1 -input_5_chr.bam 3 80 70 F 1 -input_5_chr.bam 3 80 71 F 1 -input_5_chr.bam 3 80 72 F 1 -input_5_chr.bam 3 80 73 F 1 -input_5_chr.bam 3 80 74 F 1 -input_5_chr.bam 3 80 75 F 1 -input_5_chr.bam 3 80 76 F 1 -input_5_chr.bam 3 80 77 F 1 -input_5_chr.bam 3 80 78 F 1 -input_5_chr.bam 3 80 79 F 1 -input_5_chr.bam 3 80 80 F 1 -input_5_chr.bam 4 80 1 F 1 -input_5_chr.bam 4 80 2 F 1 -input_5_chr.bam 4 80 3 F 1 -input_5_chr.bam 4 80 4 F 1 -input_5_chr.bam 4 80 5 F 1 -input_5_chr.bam 4 80 6 F 1 -input_5_chr.bam 4 80 7 F 1 -input_5_chr.bam 4 80 8 F 1 -input_5_chr.bam 4 80 9 F 1 -input_5_chr.bam 4 80 10 F 1 -input_5_chr.bam 4 80 11 F 1 -input_5_chr.bam 4 80 12 F 1 -input_5_chr.bam 4 80 13 F 1 -input_5_chr.bam 4 80 14 F 1 -input_5_chr.bam 4 80 15 F 1 -input_5_chr.bam 4 80 16 F 1 -input_5_chr.bam 4 80 17 F 1 -input_5_chr.bam 4 80 18 F 1 -input_5_chr.bam 4 80 19 F 1 -input_5_chr.bam 4 80 20 F 1 -input_5_chr.bam 4 80 21 F 1 -input_5_chr.bam 4 80 22 F 1 -input_5_chr.bam 4 80 23 F 1 -input_5_chr.bam 4 80 24 F 1 -input_5_chr.bam 4 80 25 F 1 -input_5_chr.bam 4 80 26 F 1 -input_5_chr.bam 4 80 27 F 1 -input_5_chr.bam 4 80 28 F 1 -input_5_chr.bam 4 80 29 F 1 -input_5_chr.bam 4 80 30 F 1 -input_5_chr.bam 4 80 31 F 1 -input_5_chr.bam 4 80 32 F 1 -input_5_chr.bam 4 80 33 F 1 -input_5_chr.bam 4 80 34 F 1 -input_5_chr.bam 4 80 35 F 1 -input_5_chr.bam 4 80 36 F 1 -input_5_chr.bam 4 80 37 F 1 -input_5_chr.bam 4 80 38 F 1 -input_5_chr.bam 4 80 39 F 1 -input_5_chr.bam 4 80 40 F 1 -input_5_chr.bam 4 80 41 F 1 -input_5_chr.bam 4 80 42 F 1 -input_5_chr.bam 4 80 43 F 1 -input_5_chr.bam 4 80 44 F 1 -input_5_chr.bam 4 80 45 F 1 -input_5_chr.bam 4 80 46 F 1 -input_5_chr.bam 4 80 47 F 1 -input_5_chr.bam 4 80 48 F 1 -input_5_chr.bam 4 80 49 F 1 -input_5_chr.bam 4 80 50 F 1 -input_5_chr.bam 4 80 51 F 1 -input_5_chr.bam 4 80 52 F 1 -input_5_chr.bam 4 80 53 F 1 -input_5_chr.bam 4 80 54 F 1 -input_5_chr.bam 4 80 55 F 1 -input_5_chr.bam 4 80 56 F 1 -input_5_chr.bam 4 80 57 F 1 -input_5_chr.bam 4 80 58 F 1 -input_5_chr.bam 4 80 59 F 1 -input_5_chr.bam 4 80 60 F 1 -input_5_chr.bam 4 80 61 F 1 -input_5_chr.bam 4 80 62 F 1 -input_5_chr.bam 4 80 63 F 1 -input_5_chr.bam 4 80 64 F 1 -input_5_chr.bam 4 80 65 F 1 -input_5_chr.bam 4 80 66 F 1 -input_5_chr.bam 4 80 67 F 1 -input_5_chr.bam 4 80 68 F 1 -input_5_chr.bam 4 80 69 F 1 -input_5_chr.bam 4 80 70 F 1 -input_5_chr.bam 4 80 71 F 1 -input_5_chr.bam 4 80 72 F 1 -input_5_chr.bam 4 80 73 F 1 -input_5_chr.bam 4 80 74 F 1 -input_5_chr.bam 4 80 75 F 1 -input_5_chr.bam 4 80 76 F 1 -input_5_chr.bam 4 80 77 F 1 -input_5_chr.bam 4 80 78 F 1 -input_5_chr.bam 4 80 79 F 1 -input_5_chr.bam 4 80 80 F 1 -input_5_chr.bam 5 80 1 F 1 -input_5_chr.bam 5 80 2 F 1 -input_5_chr.bam 5 80 3 F 1 -input_5_chr.bam 5 80 4 F 1 -input_5_chr.bam 5 80 5 F 1 -input_5_chr.bam 5 80 6 F 1 -input_5_chr.bam 5 80 7 F 1 -input_5_chr.bam 5 80 8 F 1 -input_5_chr.bam 5 80 9 F 1 -input_5_chr.bam 5 80 10 F 1 -input_5_chr.bam 5 80 11 F 1 -input_5_chr.bam 5 80 12 F 1 -input_5_chr.bam 5 80 13 F 1 -input_5_chr.bam 5 80 14 F 1 -input_5_chr.bam 5 80 15 F 1 -input_5_chr.bam 5 80 16 F 1 -input_5_chr.bam 5 80 17 F 1 -input_5_chr.bam 5 80 18 F 1 -input_5_chr.bam 5 80 19 F 1 -input_5_chr.bam 5 80 20 F 1 -input_5_chr.bam 5 80 21 F 1 -input_5_chr.bam 5 80 22 F 1 -input_5_chr.bam 5 80 23 F 1 -input_5_chr.bam 5 80 24 F 1 -input_5_chr.bam 5 80 25 F 1 -input_5_chr.bam 5 80 26 F 1 -input_5_chr.bam 5 80 27 F 1 -input_5_chr.bam 5 80 28 F 1 -input_5_chr.bam 5 80 29 F 1 -input_5_chr.bam 5 80 30 F 1 -input_5_chr.bam 5 80 31 F 1 -input_5_chr.bam 5 80 32 F 1 -input_5_chr.bam 5 80 33 F 1 -input_5_chr.bam 5 80 34 F 1 -input_5_chr.bam 5 80 35 F 1 -input_5_chr.bam 5 80 36 F 1 -input_5_chr.bam 5 80 37 F 1 -input_5_chr.bam 5 80 38 F 1 -input_5_chr.bam 5 80 39 F 1 -input_5_chr.bam 5 80 40 F 1 -input_5_chr.bam 5 80 41 F 1 -input_5_chr.bam 5 80 42 F 1 -input_5_chr.bam 5 80 43 F 1 -input_5_chr.bam 5 80 44 F 1 -input_5_chr.bam 5 80 45 F 1 -input_5_chr.bam 5 80 46 F 1 -input_5_chr.bam 5 80 47 F 1 -input_5_chr.bam 5 80 48 F 1 -input_5_chr.bam 5 80 49 F 1 -input_5_chr.bam 5 80 50 F 1 -input_5_chr.bam 5 80 51 F 1 -input_5_chr.bam 5 80 52 F 1 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--- a/test-data/doubled_count.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,599 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Counts -input1.bam_0 FBtr0070001 72 1 F 1 -input1.bam_0 FBtr0070001 72 7 F 6 -input1.bam_0 FBtr0070001 72 8 F 3 -input1.bam_0 FBtr0070001 72 11 F 2 -input1.bam_0 FBtr0070001 72 16 F 1 -input1.bam_0 FBtr0070001 72 17 F 1 -input1.bam_0 FBtr0070001 72 18 F 1 -input1.bam_0 FBtr0070001 72 27 F 2 -input1.bam_0 FBtr0070001 72 30 F 1 -input1.bam_0 FBtr0070001 72 31 F 11 -input1.bam_0 FBtr0070001 72 32 F 27 -input1.bam_0 FBtr0070001 72 34 F 1 -input1.bam_0 FBtr0070001 72 72 F 0 -input1.bam_0 FBtr0070533 72 1 F 1 -input1.bam_0 FBtr0070533 72 12 F 2 -input1.bam_0 FBtr0070533 72 15 F 1 -input1.bam_0 FBtr0070533 72 19 F 5 -input1.bam_0 FBtr0070533 72 20 F 1 -input1.bam_0 FBtr0070533 72 21 F 1 -input1.bam_0 FBtr0070533 72 22 F 1 -input1.bam_0 FBtr0070533 72 25 F 1 -input1.bam_0 FBtr0070533 72 26 F 1 -input1.bam_0 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+input2.bam FBtr0080663 R 23 0 +input2.bam FBtr0080663 R 24 0 +input2.bam FBtr0080664 F 15 165 +input2.bam FBtr0080664 F 16 59 +input2.bam FBtr0080664 F 17 20 +input2.bam FBtr0080664 F 18 75 +input2.bam FBtr0080664 F 19 24 +input2.bam FBtr0080664 F 20 21 +input2.bam FBtr0080664 F 21 8 +input2.bam FBtr0080664 F 22 4 +input2.bam FBtr0080664 F 23 4 +input2.bam FBtr0080664 F 24 0 +input2.bam FBtr0080664 F 25 3 +input2.bam FBtr0080664 F 26 4 +input2.bam FBtr0080664 R 15 0 +input2.bam FBtr0080664 R 16 0 +input2.bam FBtr0080664 R 17 0 +input2.bam FBtr0080664 R 18 0 +input2.bam FBtr0080664 R 19 0 +input2.bam FBtr0080664 R 20 0 +input2.bam FBtr0080664 R 21 0 +input2.bam FBtr0080664 R 22 1 +input2.bam FBtr0080664 R 23 1 +input2.bam FBtr0080664 R 24 0 +input2.bam FBtr0080664 R 25 0 +input2.bam FBtr0080664 R 26 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_cluster5_counts.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,132 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 12 F 14 +input1.bam FBtr0070001 72 30 F 42 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 25 F 23 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 0 +input1.bam FBtr0070603 72 21 F 68 +input1.bam FBtr0070603 72 53 F 2 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 1 +input1.bam FBtr0070604 72 20 F 2 +input1.bam FBtr0070604 72 31 F 36 +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 15 F 4 +input1.bam FBtr0078490 72 26 F 3 +input1.bam FBtr0078490 72 38 F 1 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 0 +input1.bam FBtr0078580 72 16 F 1102 +input1.bam FBtr0078580 72 52 F 2 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 1 +input1.bam FBtr0078790 73 17 F 2 +input1.bam FBtr0078790 73 33 F 1 +input1.bam FBtr0078790 73 47 F 9 +input1.bam FBtr0078790 73 69 R 1 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 0 +input1.bam FBtr0079064 72 2 F 2 +input1.bam FBtr0079064 72 33 F 1 +input1.bam FBtr0079064 72 52 F 1 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 2 +input1.bam FBtr0079090 72 26 F 1 +input1.bam FBtr0079090 72 33 F 1 +input1.bam FBtr0079090 72 53 F 1 +input1.bam FBtr0079090 72 56 R 1 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 14 F 5 +input1.bam FBtr0079338 73 25 F 1 +input1.bam FBtr0079338 73 44 F 10 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 0 +input1.bam FBtr0079528 71 9 F 97 +input1.bam FBtr0079528 71 28 F 1 +input1.bam FBtr0079528 71 36 F 3 +input1.bam FBtr0079528 71 51 F 5 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 0 +input1.bam FBtr0079596 73 10 F 148 +input1.bam FBtr0079596 73 53 F 4 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 0 +input1.bam FBtr0079677 72 3 F 2 +input1.bam FBtr0079677 72 52 F 2 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 1 +input1.bam FBtr0079690 72 24 F 2 +input1.bam FBtr0079690 72 33 F 2 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 3 +input1.bam FBtr0079692 73 18 F 1 +input1.bam FBtr0079692 73 25 F 1 +input1.bam FBtr0079692 73 32 F 1 +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 54 F 2 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 2 +input1.bam FBtr0079752 72 9 F 2 +input1.bam FBtr0079752 72 33 F 2 +input1.bam FBtr0079752 72 52 F 2 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 50 F 13 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 0 +input1.bam FBtr0080609 72 10 F 60 +input1.bam FBtr0080609 72 42 F 1 +input1.bam FBtr0080609 72 51 F 2 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 0 +input1.bam FBtr0080644 72 6 F 6 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 0 +input1.bam FBtr0080646 72 4 F 3 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 0 +input1.bam FBtr0080647 72 6 F 10 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 7 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 0 +input1.bam FBtr0080663 71 9 F 102 +input1.bam FBtr0080663 71 26 F 1 +input1.bam FBtr0080663 71 32 F 2 +input1.bam FBtr0080663 71 50 F 10 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 0 +input1.bam FBtr0080664 71 11 F 108 +input1.bam FBtr0080664 71 33 F 9 +input1.bam FBtr0080664 71 53 F 11 +input1.bam FBtr0080664 71 71 F 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_counts.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,300 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 7 F 6 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 16 F 1 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 18 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 12 F 2 +input1.bam FBtr0070533 72 15 F 1 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 21 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 25 F 1 +input1.bam FBtr0070533 72 26 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 72 32 F 4 +input1.bam FBtr0070533 72 35 F 1 +input1.bam FBtr0070533 72 37 F 2 +input1.bam FBtr0070533 72 38 F 2 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 2 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_counts_yminneg5_5.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,300 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 7 F 6 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 16 F 1 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 18 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 12 F 2 +input1.bam FBtr0070533 72 15 F 1 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 21 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 25 F 1 +input1.bam FBtr0070533 72 26 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 72 32 F 4 +input1.bam FBtr0070533 72 35 F 1 +input1.bam FBtr0070533 72 37 F 2 +input1.bam FBtr0070533 72 38 F 2 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 2 +input1.bam FBtr0070603 72 3 F 1 +input1.bam FBtr0070603 72 4 F 1 +input1.bam FBtr0070603 72 6 F 1 +input1.bam FBtr0070603 72 7 F 7 +input1.bam FBtr0070603 72 8 F 4 +input1.bam FBtr0070603 72 9 F 7 +input1.bam FBtr0070603 72 12 F 2 +input1.bam FBtr0070603 72 13 F 1 +input1.bam FBtr0070603 72 15 F 2 +input1.bam FBtr0070603 72 16 F 2 +input1.bam FBtr0070603 72 17 F 3 +input1.bam FBtr0070603 72 18 F 1 +input1.bam FBtr0070603 72 19 F 9 +input1.bam FBtr0070603 72 20 F 3 +input1.bam FBtr0070603 72 21 F 1 +input1.bam FBtr0070603 72 22 F 3 +input1.bam FBtr0070603 72 24 F 2 +input1.bam FBtr0070603 72 25 F 1 +input1.bam FBtr0070603 72 26 F 6 +input1.bam FBtr0070603 72 27 F 3 +input1.bam FBtr0070603 72 32 F 1 +input1.bam FBtr0070603 72 34 F 3 +input1.bam FBtr0070603 72 38 F 1 +input1.bam FBtr0070603 72 42 F 1 +input1.bam FBtr0070603 72 51 F 1 +input1.bam FBtr0070603 72 56 F 1 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 1 +input1.bam FBtr0070604 72 18 F 1 +input1.bam FBtr0070604 72 22 F 1 +input1.bam FBtr0070604 72 30 F 2 +input1.bam FBtr0070604 72 31 F 10 +input1.bam FBtr0070604 72 32 F 24 +input1.bam FBtr0070604 72 57 F 1 +input1.bam FBtr0070604 72 72 F 0 +input1.bam FBtr0070911 73 1 F 0 +input1.bam FBtr0070911 73 15 F 1 +input1.bam FBtr0070911 73 38 F 1 +input1.bam FBtr0070911 73 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 13 F 2 +input1.bam FBtr0078490 72 17 F 1 +input1.bam FBtr0078490 72 18 F 1 +input1.bam FBtr0078490 72 25 F 1 +input1.bam FBtr0078490 72 28 F 2 +input1.bam FBtr0078490 72 38 F 1 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 1041 +input1.bam FBtr0078580 72 3 F 3 +input1.bam FBtr0078580 72 4 F 4 +input1.bam FBtr0078580 72 5 F 5 +input1.bam FBtr0078580 72 6 F 4 +input1.bam FBtr0078580 72 7 F 1 +input1.bam FBtr0078580 72 8 F 2 +input1.bam FBtr0078580 72 11 F 1 +input1.bam FBtr0078580 72 12 F 13 +input1.bam FBtr0078580 72 14 F 7 +input1.bam FBtr0078580 72 15 F 1 +input1.bam FBtr0078580 72 16 F 4 +input1.bam FBtr0078580 72 17 F 1 +input1.bam FBtr0078580 72 19 F 1 +input1.bam FBtr0078580 72 20 F 2 +input1.bam FBtr0078580 72 21 F 5 +input1.bam FBtr0078580 72 24 F 3 +input1.bam FBtr0078580 72 25 F 2 +input1.bam FBtr0078580 72 29 F 1 +input1.bam FBtr0078580 72 31 F 1 +input1.bam FBtr0078580 72 52 F 2 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 1 +input1.bam FBtr0078790 73 17 F 2 +input1.bam FBtr0078790 73 33 F 1 +input1.bam FBtr0078790 73 42 F 4 +input1.bam FBtr0078790 73 44 F 2 +input1.bam FBtr0078790 73 46 F 1 +input1.bam FBtr0078790 73 47 F 1 +input1.bam FBtr0078790 73 52 F 1 +input1.bam FBtr0078790 73 69 R 1 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 1 +input1.bam FBtr0079064 72 3 F 1 +input1.bam FBtr0079064 72 33 F 1 +input1.bam FBtr0079064 72 52 F 1 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 2 +input1.bam FBtr0079090 72 26 F 1 +input1.bam FBtr0079090 72 33 F 1 +input1.bam FBtr0079090 72 53 F 1 +input1.bam FBtr0079090 72 56 R 1 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 12 F 1 +input1.bam FBtr0079338 73 13 F 2 +input1.bam FBtr0079338 73 14 F 1 +input1.bam FBtr0079338 73 17 F 1 +input1.bam FBtr0079338 73 25 F 1 +input1.bam FBtr0079338 73 42 F 8 +input1.bam FBtr0079338 73 43 F 1 +input1.bam FBtr0079338 73 46 F 1 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 19 +input1.bam FBtr0079528 71 3 F 55 +input1.bam FBtr0079528 71 4 F 2 +input1.bam FBtr0079528 71 8 F 4 +input1.bam FBtr0079528 71 10 F 1 +input1.bam FBtr0079528 71 11 F 2 +input1.bam FBtr0079528 71 13 F 1 +input1.bam FBtr0079528 71 14 F 4 +input1.bam FBtr0079528 71 16 F 1 +input1.bam FBtr0079528 71 17 F 4 +input1.bam FBtr0079528 71 18 F 4 +input1.bam FBtr0079528 71 28 F 1 +input1.bam FBtr0079528 71 35 F 1 +input1.bam FBtr0079528 71 36 F 1 +input1.bam FBtr0079528 71 37 F 1 +input1.bam FBtr0079528 71 51 F 5 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 13 +input1.bam FBtr0079596 73 3 F 13 +input1.bam FBtr0079596 73 4 F 31 +input1.bam FBtr0079596 73 5 F 2 +input1.bam FBtr0079596 73 6 F 11 +input1.bam FBtr0079596 73 8 F 9 +input1.bam FBtr0079596 73 9 F 12 +input1.bam FBtr0079596 73 10 F 3 +input1.bam FBtr0079596 73 11 F 19 +input1.bam FBtr0079596 73 12 F 1 +input1.bam FBtr0079596 73 13 F 20 +input1.bam FBtr0079596 73 14 F 6 +input1.bam FBtr0079596 73 15 F 1 +input1.bam FBtr0079596 73 16 F 3 +input1.bam FBtr0079596 73 17 F 2 +input1.bam FBtr0079596 73 18 F 1 +input1.bam FBtr0079596 73 19 F 1 +input1.bam FBtr0079596 73 53 F 2 +input1.bam FBtr0079596 73 54 F 2 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 1 +input1.bam FBtr0079677 72 5 F 1 +input1.bam FBtr0079677 72 52 F 1 +input1.bam FBtr0079677 72 53 F 1 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 1 +input1.bam FBtr0079690 72 22 F 1 +input1.bam FBtr0079690 72 27 F 1 +input1.bam FBtr0079690 72 33 F 2 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 3 +input1.bam FBtr0079692 73 18 F 1 +input1.bam FBtr0079692 73 25 F 1 +input1.bam FBtr0079692 73 32 F 1 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 5 +input1.bam FBtr0079693 72 25 F 1 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 5 +input1.bam FBtr0079694 72 18 F 1 +input1.bam FBtr0079694 72 52 F 1 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 1 +input1.bam FBtr0079702 72 19 F 2 +input1.bam FBtr0079702 72 56 F 1 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 2 +input1.bam FBtr0079728 72 8 F 1 +input1.bam FBtr0079728 72 19 F 1 +input1.bam FBtr0079728 72 33 F 3 +input1.bam FBtr0079728 72 56 F 1 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 1 +input1.bam FBtr0079729 72 13 F 1 +input1.bam FBtr0079729 72 52 F 1 +input1.bam FBtr0079729 72 57 F 1 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 2 +input1.bam FBtr0079752 72 7 F 1 +input1.bam FBtr0079752 72 12 F 1 +input1.bam FBtr0079752 72 33 F 2 +input1.bam FBtr0079752 72 52 F 2 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 1 +input1.bam FBtr0079820 74 46 F 2 +input1.bam FBtr0079820 74 48 F 1 +input1.bam FBtr0079820 74 49 F 1 +input1.bam FBtr0079820 74 51 F 1 +input1.bam FBtr0079820 74 54 F 4 +input1.bam FBtr0079820 74 55 F 1 +input1.bam FBtr0079820 74 56 F 2 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 13 +input1.bam FBtr0080609 72 3 F 2 +input1.bam FBtr0080609 72 4 F 10 +input1.bam FBtr0080609 72 5 F 2 +input1.bam FBtr0080609 72 7 F 19 +input1.bam FBtr0080609 72 8 F 4 +input1.bam FBtr0080609 72 9 F 3 +input1.bam FBtr0080609 72 12 F 1 +input1.bam FBtr0080609 72 15 F 1 +input1.bam FBtr0080609 72 16 F 1 +input1.bam FBtr0080609 72 17 F 2 +input1.bam FBtr0080609 72 19 F 1 +input1.bam FBtr0080609 72 20 F 1 +input1.bam FBtr0080609 72 42 F 1 +input1.bam FBtr0080609 72 51 F 1 +input1.bam FBtr0080609 72 52 F 1 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 1 +input1.bam FBtr0080644 72 4 F 2 +input1.bam FBtr0080644 72 7 F 1 +input1.bam FBtr0080644 72 12 F 2 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 1 +input1.bam FBtr0080646 72 6 F 1 +input1.bam FBtr0080646 72 7 F 1 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 3 +input1.bam FBtr0080647 72 3 F 1 +input1.bam FBtr0080647 72 6 F 2 +input1.bam FBtr0080647 72 8 F 1 +input1.bam FBtr0080647 72 11 F 2 +input1.bam FBtr0080647 72 12 F 1 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 4 +input1.bam FBtr0080660 72 7 F 3 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 22 +input1.bam FBtr0080663 71 3 F 56 +input1.bam FBtr0080663 71 4 F 4 +input1.bam FBtr0080663 71 7 F 1 +input1.bam FBtr0080663 71 8 F 4 +input1.bam FBtr0080663 71 12 F 2 +input1.bam FBtr0080663 71 14 F 2 +input1.bam FBtr0080663 71 15 F 1 +input1.bam FBtr0080663 71 16 F 3 +input1.bam FBtr0080663 71 17 F 7 +input1.bam FBtr0080663 71 26 F 1 +input1.bam FBtr0080663 71 32 F 2 +input1.bam FBtr0080663 71 50 F 1 +input1.bam FBtr0080663 71 51 F 9 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 16 +input1.bam FBtr0080664 71 3 F 56 +input1.bam FBtr0080664 71 4 F 4 +input1.bam FBtr0080664 71 6 F 1 +input1.bam FBtr0080664 71 7 F 1 +input1.bam FBtr0080664 71 8 F 4 +input1.bam FBtr0080664 71 9 F 1 +input1.bam FBtr0080664 71 11 F 3 +input1.bam FBtr0080664 71 12 F 3 +input1.bam FBtr0080664 71 13 F 2 +input1.bam FBtr0080664 71 14 F 3 +input1.bam FBtr0080664 71 16 F 2 +input1.bam FBtr0080664 71 17 F 10 +input1.bam FBtr0080664 71 18 F 1 +input1.bam FBtr0080664 71 21 F 1 +input1.bam FBtr0080664 71 28 F 2 +input1.bam FBtr0080664 71 32 F 1 +input1.bam FBtr0080664 71 33 F 1 +input1.bam FBtr0080664 71 34 F 1 +input1.bam FBtr0080664 71 35 F 1 +input1.bam FBtr0080664 71 36 F 1 +input1.bam FBtr0080664 71 37 F 1 +input1.bam FBtr0080664 71 38 F 1 +input1.bam FBtr0080664 71 50 F 2 +input1.bam FBtr0080664 71 51 F 7 +input1.bam FBtr0080664 71 52 F 1 +input1.bam FBtr0080664 71 56 F 1 +input1.bam FBtr0080664 71 71 F 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_coverage.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,1603 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Coverage +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 2 F 1 +input1.bam FBtr0070001 72 3 F 1 +input1.bam FBtr0070001 72 4 F 1 +input1.bam FBtr0070001 72 5 F 1 +input1.bam FBtr0070001 72 6 F 1 +input1.bam FBtr0070001 72 7 F 7 +input1.bam FBtr0070001 72 8 F 10 +input1.bam FBtr0070001 72 9 F 10 +input1.bam FBtr0070001 72 10 F 10 +input1.bam FBtr0070001 72 11 F 12 +input1.bam FBtr0070001 72 12 F 12 +input1.bam FBtr0070001 72 13 F 12 +input1.bam FBtr0070001 72 14 F 12 +input1.bam FBtr0070001 72 15 F 12 +input1.bam FBtr0070001 72 16 F 13 +input1.bam FBtr0070001 72 17 F 14 +input1.bam FBtr0070001 72 18 F 14 +input1.bam FBtr0070001 72 19 F 14 +input1.bam FBtr0070001 72 20 F 14 +input1.bam FBtr0070001 72 21 F 14 +input1.bam FBtr0070001 72 22 F 14 +input1.bam FBtr0070001 72 23 F 13 +input1.bam FBtr0070001 72 24 F 13 +input1.bam FBtr0070001 72 25 F 13 +input1.bam FBtr0070001 72 26 F 13 +input1.bam FBtr0070001 72 27 F 14 +input1.bam FBtr0070001 72 28 F 11 +input1.bam FBtr0070001 72 29 F 8 +input1.bam FBtr0070001 72 30 F 9 +input1.bam FBtr0070001 72 31 F 18 +input1.bam FBtr0070001 72 32 F 44 +input1.bam FBtr0070001 72 33 F 44 +input1.bam FBtr0070001 72 34 F 44 +input1.bam FBtr0070001 72 35 F 43 +input1.bam FBtr0070001 72 36 F 43 +input1.bam FBtr0070001 72 37 F 43 +input1.bam FBtr0070001 72 38 F 43 +input1.bam FBtr0070001 72 39 F 43 +input1.bam FBtr0070001 72 40 F 42 +input1.bam FBtr0070001 72 41 F 42 +input1.bam FBtr0070001 72 42 F 42 +input1.bam FBtr0070001 72 43 F 42 +input1.bam FBtr0070001 72 44 F 42 +input1.bam FBtr0070001 72 45 F 42 +input1.bam FBtr0070001 72 46 F 42 +input1.bam FBtr0070001 72 47 F 42 +input1.bam FBtr0070001 72 48 F 42 +input1.bam FBtr0070001 72 49 F 42 +input1.bam FBtr0070001 72 50 F 41 +input1.bam FBtr0070001 72 51 F 40 +input1.bam FBtr0070001 72 52 F 40 +input1.bam FBtr0070001 72 53 F 39 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 2 F 1 +input1.bam FBtr0070533 72 3 F 1 +input1.bam FBtr0070533 72 4 F 1 +input1.bam FBtr0070533 72 5 F 1 +input1.bam FBtr0070533 72 6 F 1 +input1.bam FBtr0070533 72 7 F 1 +input1.bam FBtr0070533 72 8 F 1 +input1.bam FBtr0070533 72 9 F 1 +input1.bam FBtr0070533 72 10 F 1 +input1.bam FBtr0070533 72 11 F 1 +input1.bam FBtr0070533 72 12 F 3 +input1.bam FBtr0070533 72 13 F 3 +input1.bam FBtr0070533 72 14 F 3 +input1.bam FBtr0070533 72 15 F 4 +input1.bam FBtr0070533 72 16 F 3 +input1.bam FBtr0070533 72 17 F 3 +input1.bam FBtr0070533 72 18 F 3 +input1.bam FBtr0070533 72 19 F 8 +input1.bam FBtr0070533 72 20 F 9 +input1.bam FBtr0070533 72 21 F 10 +input1.bam FBtr0070533 72 22 F 11 +input1.bam FBtr0070533 72 23 F 11 +input1.bam FBtr0070533 72 24 F 11 +input1.bam FBtr0070533 72 25 F 12 +input1.bam FBtr0070533 72 26 F 13 +input1.bam FBtr0070533 72 27 F 13 +input1.bam FBtr0070533 72 28 F 14 +input1.bam FBtr0070533 72 29 F 14 +input1.bam FBtr0070533 72 30 F 11 +input1.bam FBtr0070533 72 31 F 11 +input1.bam FBtr0070533 72 32 F 15 +input1.bam FBtr0070533 72 33 F 15 +input1.bam FBtr0070533 72 34 F 15 +input1.bam FBtr0070533 72 35 F 16 +input1.bam FBtr0070533 72 36 F 16 +input1.bam FBtr0070533 72 37 F 18 +input1.bam FBtr0070533 72 38 F 20 +input1.bam FBtr0070533 72 39 F 19 +input1.bam FBtr0070533 72 40 F 17 +input1.bam FBtr0070533 72 41 F 15 +input1.bam FBtr0070533 72 42 F 11 +input1.bam FBtr0070533 72 43 F 10 +input1.bam FBtr0070533 72 44 F 10 +input1.bam FBtr0070533 72 45 F 10 +input1.bam FBtr0070533 72 46 F 10 +input1.bam FBtr0070533 72 47 F 10 +input1.bam FBtr0070533 72 48 F 10 +input1.bam FBtr0070533 72 49 F 10 +input1.bam FBtr0070533 72 50 F 9 +input1.bam FBtr0070533 72 51 F 9 +input1.bam FBtr0070533 72 52 F 8 +input1.bam FBtr0070533 72 53 F 7 +input1.bam FBtr0070533 72 54 F 4 +input1.bam FBtr0070533 72 55 F 4 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 2 +input1.bam FBtr0070603 72 2 F 2 +input1.bam FBtr0070603 72 3 F 3 +input1.bam FBtr0070603 72 4 F 4 +input1.bam FBtr0070603 72 5 F 4 +input1.bam FBtr0070603 72 6 F 5 +input1.bam FBtr0070603 72 7 F 12 +input1.bam FBtr0070603 72 8 F 16 +input1.bam FBtr0070603 72 9 F 23 +input1.bam FBtr0070603 72 10 F 23 +input1.bam FBtr0070603 72 11 F 23 +input1.bam FBtr0070603 72 12 F 25 +input1.bam FBtr0070603 72 13 F 26 +input1.bam FBtr0070603 72 14 F 26 +input1.bam FBtr0070603 72 15 F 28 +input1.bam FBtr0070603 72 16 F 29 +input1.bam FBtr0070603 72 17 F 32 +input1.bam FBtr0070603 72 18 F 33 +input1.bam FBtr0070603 72 19 F 41 +input1.bam FBtr0070603 72 20 F 44 +input1.bam FBtr0070603 72 21 F 45 +input1.bam FBtr0070603 72 22 F 48 +input1.bam FBtr0070603 72 23 F 48 +input1.bam FBtr0070603 72 24 F 30 +input1.bam FBtr0070603 72 25 F 30 +input1.bam FBtr0070603 72 26 F 36 +input1.bam FBtr0070603 72 27 F 39 +input1.bam FBtr0070603 72 28 F 39 +input1.bam FBtr0070603 72 29 F 38 +input1.bam FBtr0070603 72 30 F 38 +input1.bam FBtr0070603 72 31 F 38 +input1.bam FBtr0070603 72 32 F 38 +input1.bam FBtr0070603 72 33 F 37 +input1.bam FBtr0070603 72 34 F 39 +input1.bam FBtr0070603 72 35 F 35 +input1.bam FBtr0070603 72 36 F 34 +input1.bam FBtr0070603 72 37 F 34 +input1.bam FBtr0070603 72 38 F 35 +input1.bam FBtr0070603 72 39 F 34 +input1.bam FBtr0070603 72 40 F 33 +input1.bam FBtr0070603 72 41 F 32 +input1.bam FBtr0070603 72 42 F 21 +input1.bam FBtr0070603 72 43 F 21 +input1.bam FBtr0070603 72 44 F 20 +input1.bam FBtr0070603 72 45 F 18 +input1.bam FBtr0070603 72 46 F 16 +input1.bam FBtr0070603 72 47 F 16 +input1.bam FBtr0070603 72 48 F 15 +input1.bam FBtr0070603 72 49 F 15 +input1.bam FBtr0070603 72 50 F 14 +input1.bam FBtr0070603 72 51 F 14 +input1.bam FBtr0070603 72 52 F 10 +input1.bam FBtr0070603 72 53 F 6 +input1.bam FBtr0070603 72 54 F 3 +input1.bam FBtr0070603 72 55 F 3 +input1.bam FBtr0070603 72 56 F 3 +input1.bam FBtr0070603 72 57 F 3 +input1.bam FBtr0070603 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_coverage_cluster5.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,1603 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Coverage +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 2 F 1 +input1.bam FBtr0070001 72 3 F 1 +input1.bam FBtr0070001 72 4 F 1 +input1.bam FBtr0070001 72 5 F 1 +input1.bam FBtr0070001 72 6 F 1 +input1.bam FBtr0070001 72 7 F 7 +input1.bam FBtr0070001 72 8 F 10 +input1.bam FBtr0070001 72 9 F 10 +input1.bam FBtr0070001 72 10 F 10 +input1.bam FBtr0070001 72 11 F 12 +input1.bam FBtr0070001 72 12 F 12 +input1.bam FBtr0070001 72 13 F 12 +input1.bam FBtr0070001 72 14 F 12 +input1.bam FBtr0070001 72 15 F 12 +input1.bam FBtr0070001 72 16 F 13 +input1.bam FBtr0070001 72 17 F 14 +input1.bam FBtr0070001 72 18 F 14 +input1.bam FBtr0070001 72 19 F 14 +input1.bam FBtr0070001 72 20 F 14 +input1.bam FBtr0070001 72 21 F 14 +input1.bam FBtr0070001 72 22 F 14 +input1.bam FBtr0070001 72 23 F 13 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FBtr0080663 71 25 F 77 +input1.bam FBtr0080663 71 26 F 70 +input1.bam FBtr0080663 71 27 F 34 +input1.bam FBtr0080663 71 28 F 21 +input1.bam FBtr0080663 71 29 F 14 +input1.bam FBtr0080663 71 30 F 14 +input1.bam FBtr0080663 71 31 F 13 +input1.bam FBtr0080663 71 32 F 7 +input1.bam FBtr0080663 71 33 F 4 +input1.bam FBtr0080663 71 34 F 4 +input1.bam FBtr0080663 71 35 F 3 +input1.bam FBtr0080663 71 36 F 3 +input1.bam FBtr0080663 71 37 F 3 +input1.bam FBtr0080663 71 38 F 3 +input1.bam FBtr0080663 71 39 F 3 +input1.bam FBtr0080663 71 40 F 3 +input1.bam FBtr0080663 71 41 F 3 +input1.bam FBtr0080663 71 42 F 3 +input1.bam FBtr0080663 71 43 F 3 +input1.bam FBtr0080663 71 44 F 2 +input1.bam FBtr0080663 71 45 F 2 +input1.bam FBtr0080663 71 46 F 2 +input1.bam FBtr0080663 71 47 F 1 +input1.bam FBtr0080663 71 50 F 1 +input1.bam FBtr0080663 71 51 F 10 +input1.bam FBtr0080663 71 52 F 10 +input1.bam FBtr0080663 71 53 F 10 +input1.bam FBtr0080663 71 54 F 10 +input1.bam FBtr0080663 71 55 F 10 +input1.bam FBtr0080663 71 56 F 10 +input1.bam FBtr0080663 71 57 F 10 +input1.bam FBtr0080663 71 58 F 10 +input1.bam FBtr0080663 71 59 F 10 +input1.bam FBtr0080663 71 60 F 10 +input1.bam FBtr0080663 71 61 F 10 +input1.bam FBtr0080663 71 62 F 10 +input1.bam FBtr0080663 71 63 F 10 +input1.bam FBtr0080663 71 64 F 10 +input1.bam FBtr0080663 71 65 F 10 +input1.bam FBtr0080663 71 66 F 2 +input1.bam FBtr0080663 71 67 F 1 +input1.bam FBtr0080663 71 68 F 1 +input1.bam FBtr0080663 71 69 F 1 +input1.bam FBtr0080663 71 70 F 1 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 16 +input1.bam FBtr0080664 71 2 F 16 +input1.bam FBtr0080664 71 3 F 72 +input1.bam FBtr0080664 71 4 F 76 +input1.bam FBtr0080664 71 5 F 76 +input1.bam FBtr0080664 71 6 F 77 +input1.bam FBtr0080664 71 7 F 78 +input1.bam FBtr0080664 71 8 F 82 +input1.bam FBtr0080664 71 9 F 83 +input1.bam FBtr0080664 71 10 F 83 +input1.bam FBtr0080664 71 11 F 86 +input1.bam FBtr0080664 71 12 F 89 +input1.bam FBtr0080664 71 13 F 91 +input1.bam FBtr0080664 71 14 F 94 +input1.bam FBtr0080664 71 15 F 94 +input1.bam FBtr0080664 71 16 F 95 +input1.bam FBtr0080664 71 17 F 100 +input1.bam FBtr0080664 71 18 F 98 +input1.bam FBtr0080664 71 19 F 97 +input1.bam FBtr0080664 71 20 F 97 +input1.bam FBtr0080664 71 21 F 97 +input1.bam FBtr0080664 71 22 F 97 +input1.bam FBtr0080664 71 23 F 93 +input1.bam FBtr0080664 71 24 F 88 +input1.bam FBtr0080664 71 25 F 88 +input1.bam FBtr0080664 71 26 F 82 +input1.bam FBtr0080664 71 27 F 47 +input1.bam FBtr0080664 71 28 F 33 +input1.bam FBtr0080664 71 29 F 23 +input1.bam FBtr0080664 71 30 F 23 +input1.bam FBtr0080664 71 31 F 20 +input1.bam FBtr0080664 71 32 F 13 +input1.bam FBtr0080664 71 33 F 6 +input1.bam FBtr0080664 71 34 F 7 +input1.bam FBtr0080664 71 35 F 8 +input1.bam FBtr0080664 71 36 F 7 +input1.bam FBtr0080664 71 37 F 8 +input1.bam FBtr0080664 71 38 F 9 +input1.bam FBtr0080664 71 39 F 9 +input1.bam FBtr0080664 71 40 F 9 +input1.bam FBtr0080664 71 41 F 9 +input1.bam FBtr0080664 71 42 F 9 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_input2_counts.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,617 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 7 F 6 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 16 F 1 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 18 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 12 F 2 +input1.bam FBtr0070533 72 15 F 1 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 21 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 25 F 1 +input1.bam FBtr0070533 72 26 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_input2_mean.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,617 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Mean +input1.bam FBtr0070001 72 1 F 17.0 +input1.bam FBtr0070001 72 7 F 20.3 +input1.bam FBtr0070001 72 8 F 21.3 +input1.bam FBtr0070001 72 11 F 20.5 +input1.bam FBtr0070001 72 16 F 19.0 +input1.bam FBtr0070001 72 17 F 23.0 +input1.bam FBtr0070001 72 18 F 16.0 +input1.bam FBtr0070001 72 27 F 23.5 +input1.bam FBtr0070001 72 30 F 23.0 +input1.bam FBtr0070001 72 31 F 23.0 +input1.bam FBtr0070001 72 32 F 22.0 +input1.bam FBtr0070001 72 34 F 20.0 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 15.0 +input1.bam FBtr0070533 72 12 F 18.0 +input1.bam FBtr0070533 72 15 F 15.0 +input1.bam FBtr0070533 72 19 F 21.8 +input1.bam FBtr0070533 72 20 F 23.0 +input1.bam FBtr0070533 72 21 F 18.0 +input1.bam FBtr0070533 72 22 F 20.0 +input1.bam FBtr0070533 72 25 F 17.0 +input1.bam FBtr0070533 72 26 F 16.0 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72 F 0 +input2.bam FBtr0079729 72 1 F 15.0 +input2.bam FBtr0079729 72 19 F 16.0 +input2.bam FBtr0079729 72 33 F 17.0 +input2.bam FBtr0079729 72 53 F 16.0 +input2.bam FBtr0079729 72 72 F 0 +input2.bam FBtr0079752 72 1 F 0 +input2.bam FBtr0079752 72 49 F 24.0 +input2.bam FBtr0079752 72 52 F 17.0 +input2.bam FBtr0079752 72 72 F 0 +input2.bam FBtr0079820 74 1 F 0 +input2.bam FBtr0079820 74 39 F 16.0 +input2.bam FBtr0079820 74 52 F 21.0 +input2.bam FBtr0079820 74 53 F 20.0 +input2.bam FBtr0079820 74 54 F 19.3 +input2.bam FBtr0079820 74 55 F 18.6 +input2.bam FBtr0079820 74 56 F 16.5 +input2.bam FBtr0079820 74 57 F 16.8 +input2.bam FBtr0079820 74 58 F 16.0 +input2.bam FBtr0079820 74 59 F 15.5 +input2.bam FBtr0079820 74 60 F 15.0 +input2.bam FBtr0079820 74 74 F 0 +input2.bam FBtr0080609 72 1 F 0 +input2.bam FBtr0080609 72 20 F 19.0 +input2.bam FBtr0080609 72 21 F 21.0 +input2.bam FBtr0080609 72 22 F 23.0 +input2.bam FBtr0080609 72 33 F 22.0 +input2.bam FBtr0080609 72 39 F 17.0 +input2.bam FBtr0080609 72 52 F 18.0 +input2.bam FBtr0080609 72 53 F 19.0 +input2.bam FBtr0080609 72 72 F 0 +input2.bam FBtr0080644 72 1 F 0 +input2.bam FBtr0080644 72 57 F 15.0 +input2.bam FBtr0080644 72 58 F 15.0 +input2.bam FBtr0080644 72 72 F 0 +input2.bam FBtr0080646 72 1 F 0 +input2.bam FBtr0080646 72 51 F 21.0 +input2.bam FBtr0080646 72 57 F 15.5 +input2.bam FBtr0080646 72 58 F 15.0 +input2.bam FBtr0080646 72 72 F 0 +input2.bam FBtr0080647 72 1 F 18.0 +input2.bam FBtr0080647 72 57 F 15.5 +input2.bam FBtr0080647 72 58 F 15.0 +input2.bam FBtr0080647 72 72 F 0 +input2.bam FBtr0080660 72 1 F 0 +input2.bam FBtr0080660 72 58 F 15.0 +input2.bam FBtr0080660 72 72 F 0 +input2.bam FBtr0080663 71 1 F 22.0 +input2.bam FBtr0080663 71 11 F 21.0 +input2.bam FBtr0080663 71 12 F 20.5 +input2.bam FBtr0080663 71 13 F 19.8 +input2.bam FBtr0080663 71 14 F 18.6 +input2.bam FBtr0080663 71 15 F 17.9 +input2.bam FBtr0080663 71 16 F 17.0 +input2.bam FBtr0080663 71 17 F 16.0 +input2.bam FBtr0080663 71 18 F 18.2 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_input2_norm_1_2_counts.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,617 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 1 +input1.bam FBtr0070001 72 7 F 6 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 16 F 1 +input1.bam FBtr0070001 72 17 F 1 +input1.bam FBtr0070001 72 18 F 1 +input1.bam FBtr0070001 72 27 F 2 +input1.bam FBtr0070001 72 30 F 1 +input1.bam FBtr0070001 72 31 F 11 +input1.bam FBtr0070001 72 32 F 27 +input1.bam FBtr0070001 72 34 F 1 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 1 +input1.bam FBtr0070533 72 12 F 2 +input1.bam FBtr0070533 72 15 F 1 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 21 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 25 F 1 +input1.bam FBtr0070533 72 26 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 72 32 F 4 +input1.bam FBtr0070533 72 35 F 1 +input1.bam FBtr0070533 72 37 F 2 +input1.bam FBtr0070533 72 38 F 2 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 2 +input1.bam FBtr0070603 72 3 F 1 +input1.bam FBtr0070603 72 4 F 1 +input1.bam FBtr0070603 72 6 F 1 +input1.bam FBtr0070603 72 7 F 7 +input1.bam FBtr0070603 72 8 F 4 +input1.bam FBtr0070603 72 9 F 7 +input1.bam FBtr0070603 72 12 F 2 +input1.bam FBtr0070603 72 13 F 1 +input1.bam FBtr0070603 72 15 F 2 +input1.bam FBtr0070603 72 16 F 2 +input1.bam FBtr0070603 72 17 F 3 +input1.bam FBtr0070603 72 18 F 1 +input1.bam FBtr0070603 72 19 F 9 +input1.bam FBtr0070603 72 20 F 3 +input1.bam FBtr0070603 72 21 F 1 +input1.bam FBtr0070603 72 22 F 3 +input1.bam FBtr0070603 72 24 F 2 +input1.bam FBtr0070603 72 25 F 1 +input1.bam FBtr0070603 72 26 F 6 +input1.bam FBtr0070603 72 27 F 3 +input1.bam FBtr0070603 72 32 F 1 +input1.bam FBtr0070603 72 34 F 3 +input1.bam FBtr0070603 72 38 F 1 +input1.bam FBtr0070603 72 42 F 1 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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 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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 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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 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+input2.bam FBtr0079820 R 21 0 +input2.bam FBtr0079820 R 22 0 +input2.bam FBtr0080609 F 17 2 +input2.bam FBtr0080609 F 18 1 +input2.bam FBtr0080609 F 19 2 +input2.bam FBtr0080609 F 20 0 +input2.bam FBtr0080609 F 21 0 +input2.bam FBtr0080609 F 22 1 +input2.bam FBtr0080609 F 23 1 +input2.bam FBtr0080609 F 24 0 +input2.bam FBtr0080609 F 25 1 +input2.bam FBtr0080609 R 17 0 +input2.bam FBtr0080609 R 18 0 +input2.bam FBtr0080609 R 19 0 +input2.bam FBtr0080609 R 20 0 +input2.bam FBtr0080609 R 21 0 +input2.bam FBtr0080609 R 22 0 +input2.bam FBtr0080609 R 23 0 +input2.bam FBtr0080609 R 24 0 +input2.bam FBtr0080609 R 25 0 +input2.bam FBtr0080644 F 15 8 +input2.bam FBtr0080644 R 15 0 +input2.bam FBtr0080646 F 15 10 +input2.bam FBtr0080646 F 16 1 +input2.bam FBtr0080646 F 17 0 +input2.bam FBtr0080646 F 18 0 +input2.bam FBtr0080646 F 19 0 +input2.bam FBtr0080646 F 20 0 +input2.bam FBtr0080646 F 21 1 +input2.bam FBtr0080646 R 15 0 +input2.bam FBtr0080646 R 16 0 +input2.bam FBtr0080646 R 17 0 +input2.bam FBtr0080646 R 18 0 +input2.bam FBtr0080646 R 19 0 +input2.bam FBtr0080646 R 20 0 +input2.bam FBtr0080646 R 21 0 +input2.bam FBtr0080647 F 15 9 +input2.bam FBtr0080647 F 16 2 +input2.bam FBtr0080647 F 17 0 +input2.bam FBtr0080647 F 18 1 +input2.bam FBtr0080647 R 15 0 +input2.bam FBtr0080647 R 16 0 +input2.bam FBtr0080647 R 17 0 +input2.bam FBtr0080647 R 18 0 +input2.bam FBtr0080660 F 15 11 +input2.bam FBtr0080660 R 15 0 +input2.bam FBtr0080663 F 15 26 +input2.bam FBtr0080663 F 16 14 +input2.bam FBtr0080663 F 17 14 +input2.bam FBtr0080663 F 18 26 +input2.bam FBtr0080663 F 19 9 +input2.bam FBtr0080663 F 20 7 +input2.bam FBtr0080663 F 21 4 +input2.bam FBtr0080663 F 22 5 +input2.bam FBtr0080663 F 23 0 +input2.bam FBtr0080663 F 24 1 +input2.bam FBtr0080663 R 15 0 +input2.bam FBtr0080663 R 16 0 +input2.bam FBtr0080663 R 17 0 +input2.bam FBtr0080663 R 18 0 +input2.bam FBtr0080663 R 19 0 +input2.bam FBtr0080663 R 20 0 +input2.bam FBtr0080663 R 21 0 +input2.bam FBtr0080663 R 22 0 +input2.bam FBtr0080663 R 23 0 +input2.bam FBtr0080663 R 24 0 +input2.bam FBtr0080664 F 15 165 +input2.bam FBtr0080664 F 16 59 +input2.bam FBtr0080664 F 17 20 +input2.bam FBtr0080664 F 18 75 +input2.bam FBtr0080664 F 19 24 +input2.bam FBtr0080664 F 20 21 +input2.bam FBtr0080664 F 21 8 +input2.bam FBtr0080664 F 22 4 +input2.bam FBtr0080664 F 23 4 +input2.bam FBtr0080664 F 24 0 +input2.bam FBtr0080664 F 25 3 +input2.bam FBtr0080664 F 26 4 +input2.bam FBtr0080664 R 15 0 +input2.bam FBtr0080664 R 16 0 +input2.bam FBtr0080664 R 17 0 +input2.bam FBtr0080664 R 18 0 +input2.bam FBtr0080664 R 19 0 +input2.bam FBtr0080664 R 20 0 +input2.bam FBtr0080664 R 21 0 +input2.bam FBtr0080664 R 22 1 +input2.bam FBtr0080664 R 23 1 +input2.bam FBtr0080664 R 24 0 +input2.bam FBtr0080664 R 25 0 +input2.bam FBtr0080664 R 26 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_mean.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,300 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Mean +input1.bam FBtr0070001 72 1 F 17.0 +input1.bam FBtr0070001 72 7 F 20.3 +input1.bam FBtr0070001 72 8 F 21.3 +input1.bam FBtr0070001 72 11 F 20.5 +input1.bam FBtr0070001 72 16 F 19.0 +input1.bam FBtr0070001 72 17 F 23.0 +input1.bam FBtr0070001 72 18 F 16.0 +input1.bam FBtr0070001 72 27 F 23.5 +input1.bam FBtr0070001 72 30 F 23.0 +input1.bam FBtr0070001 72 31 F 23.0 +input1.bam FBtr0070001 72 32 F 22.0 +input1.bam FBtr0070001 72 34 F 20.0 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 15.0 +input1.bam FBtr0070533 72 12 F 18.0 +input1.bam FBtr0070533 72 15 F 15.0 +input1.bam FBtr0070533 72 19 F 21.8 +input1.bam FBtr0070533 72 20 F 23.0 +input1.bam FBtr0070533 72 21 F 18.0 +input1.bam FBtr0070533 72 22 F 20.0 +input1.bam FBtr0070533 72 25 F 17.0 +input1.bam FBtr0070533 72 26 F 16.0 +input1.bam FBtr0070533 72 28 F 25.0 +input1.bam FBtr0070533 72 32 F 20.5 +input1.bam FBtr0070533 72 35 F 19.0 +input1.bam FBtr0070533 72 37 F 19.0 +input1.bam FBtr0070533 72 38 F 18.0 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 16.5 +input1.bam FBtr0070603 72 3 F 21.0 +input1.bam FBtr0070603 72 4 F 20.0 +input1.bam FBtr0070603 72 6 F 18.0 +input1.bam FBtr0070603 72 7 F 17.1 +input1.bam FBtr0070603 72 8 F 16.0 +input1.bam FBtr0070603 72 9 F 15.0 +input1.bam FBtr0070603 72 12 F 20.0 +input1.bam FBtr0070603 72 13 F 22.0 +input1.bam FBtr0070603 72 15 F 18.5 +input1.bam FBtr0070603 72 16 F 20.5 +input1.bam FBtr0070603 72 17 F 24.0 +input1.bam FBtr0070603 72 18 F 16.0 +input1.bam FBtr0070603 72 19 F 22.6 +input1.bam FBtr0070603 72 20 F 21.0 +input1.bam FBtr0070603 72 21 F 25.0 +input1.bam FBtr0070603 72 22 F 20.7 +input1.bam FBtr0070603 72 24 F 19.5 +input1.bam FBtr0070603 72 25 F 23.0 +input1.bam FBtr0070603 72 26 F 25.8 +input1.bam FBtr0070603 72 27 F 26.3 +input1.bam FBtr0070603 72 32 F 20.0 +input1.bam FBtr0070603 72 34 F 19.3 +input1.bam FBtr0070603 72 38 F 18.0 +input1.bam FBtr0070603 72 42 F 21.0 +input1.bam FBtr0070603 72 51 F 18.0 +input1.bam FBtr0070603 72 56 F 16.0 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 15.0 +input1.bam FBtr0070604 72 18 F 23.0 +input1.bam FBtr0070604 72 22 F 19.0 +input1.bam FBtr0070604 72 30 F 18.0 +input1.bam FBtr0070604 72 31 F 22.6 +input1.bam FBtr0070604 72 32 F 22.0 +input1.bam FBtr0070604 72 57 F 15.0 +input1.bam FBtr0070604 72 72 F 0 +input1.bam FBtr0070911 73 1 F 0 +input1.bam FBtr0070911 73 15 F 21.0 +input1.bam FBtr0070911 73 38 F 15.0 +input1.bam FBtr0070911 73 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 13 F 16.0 +input1.bam FBtr0078490 72 17 F 16.0 +input1.bam FBtr0078490 72 18 F 15.0 +input1.bam FBtr0078490 72 25 F 15.0 +input1.bam FBtr0078490 72 28 F 19.0 +input1.bam FBtr0078490 72 38 F 18.0 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 18.9 +input1.bam FBtr0078580 72 3 F 22.0 +input1.bam FBtr0078580 72 4 F 25.3 +input1.bam FBtr0078580 72 5 F 21.0 +input1.bam FBtr0078580 72 6 F 19.0 +input1.bam FBtr0078580 72 7 F 22.0 +input1.bam FBtr0078580 72 8 F 18.0 +input1.bam FBtr0078580 72 11 F 23.0 +input1.bam FBtr0078580 72 12 F 18.0 +input1.bam FBtr0078580 72 14 F 15.3 +input1.bam FBtr0078580 72 15 F 16.0 +input1.bam FBtr0078580 72 16 F 19.0 +input1.bam FBtr0078580 72 17 F 17.0 +input1.bam FBtr0078580 72 19 F 24.0 +input1.bam FBtr0078580 72 20 F 21.0 +input1.bam FBtr0078580 72 21 F 19.4 +input1.bam FBtr0078580 72 24 F 17.0 +input1.bam FBtr0078580 72 25 F 27.5 +input1.bam FBtr0078580 72 29 F 17.0 +input1.bam FBtr0078580 72 31 F 17.0 +input1.bam FBtr0078580 72 52 F 16.0 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 19.0 +input1.bam FBtr0078790 73 17 F 16.0 +input1.bam FBtr0078790 73 33 F 23.0 +input1.bam FBtr0078790 73 42 F 18.5 +input1.bam FBtr0078790 73 44 F 19.5 +input1.bam FBtr0078790 73 46 F 17.0 +input1.bam FBtr0078790 73 47 F 18.0 +input1.bam FBtr0078790 73 52 F 20.0 +input1.bam FBtr0078790 73 69 R 15.0 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 15.0 +input1.bam FBtr0079064 72 3 F 21.0 +input1.bam FBtr0079064 72 33 F 15.0 +input1.bam FBtr0079064 72 52 F 17.0 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 21.5 +input1.bam FBtr0079090 72 26 F 24.0 +input1.bam FBtr0079090 72 33 F 16.0 +input1.bam FBtr0079090 72 53 F 18.0 +input1.bam FBtr0079090 72 56 R 21.0 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 12 F 17.0 +input1.bam FBtr0079338 73 13 F 17.5 +input1.bam FBtr0079338 73 14 F 15.0 +input1.bam FBtr0079338 73 17 F 15.0 +input1.bam FBtr0079338 73 25 F 16.0 +input1.bam FBtr0079338 73 42 F 21.8 +input1.bam FBtr0079338 73 43 F 21.0 +input1.bam FBtr0079338 73 46 F 18.0 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 20.8 +input1.bam FBtr0079528 71 3 F 23.6 +input1.bam FBtr0079528 71 4 F 24.0 +input1.bam FBtr0079528 71 8 F 20.3 +input1.bam FBtr0079528 71 10 F 21.0 +input1.bam FBtr0079528 71 11 F 19.0 +input1.bam FBtr0079528 71 13 F 16.0 +input1.bam FBtr0079528 71 14 F 18.5 +input1.bam FBtr0079528 71 16 F 15.0 +input1.bam FBtr0079528 71 17 F 15.3 +input1.bam FBtr0079528 71 18 F 19.8 +input1.bam FBtr0079528 71 28 F 16.0 +input1.bam FBtr0079528 71 35 F 15.0 +input1.bam FBtr0079528 71 36 F 20.0 +input1.bam FBtr0079528 71 37 F 18.0 +input1.bam FBtr0079528 71 51 F 15.0 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 16.2 +input1.bam FBtr0079596 73 3 F 21.8 +input1.bam FBtr0079596 73 4 F 21.5 +input1.bam FBtr0079596 73 5 F 18.5 +input1.bam FBtr0079596 73 6 F 17.5 +input1.bam FBtr0079596 73 8 F 16.6 +input1.bam FBtr0079596 73 9 F 16.1 +input1.bam FBtr0079596 73 10 F 15.3 +input1.bam FBtr0079596 73 11 F 15.2 +input1.bam FBtr0079596 73 12 F 17.0 +input1.bam FBtr0079596 73 13 F 16.1 +input1.bam FBtr0079596 73 14 F 15.0 +input1.bam FBtr0079596 73 15 F 18.0 +input1.bam FBtr0079596 73 16 F 16.7 +input1.bam FBtr0079596 73 17 F 16.0 +input1.bam FBtr0079596 73 18 F 15.0 +input1.bam FBtr0079596 73 19 F 15.0 +input1.bam FBtr0079596 73 53 F 18.5 +input1.bam FBtr0079596 73 54 F 19.5 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 23.0 +input1.bam FBtr0079677 72 5 F 19.0 +input1.bam FBtr0079677 72 52 F 19.0 +input1.bam FBtr0079677 72 53 F 18.0 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 15.0 +input1.bam FBtr0079690 72 22 F 15.0 +input1.bam FBtr0079690 72 27 F 25.0 +input1.bam FBtr0079690 72 33 F 16.0 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 19.3 +input1.bam FBtr0079692 73 18 F 18.0 +input1.bam FBtr0079692 73 25 F 17.0 +input1.bam FBtr0079692 73 32 F 20.0 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 17.2 +input1.bam FBtr0079693 72 25 F 23.0 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 20.4 +input1.bam FBtr0079694 72 18 F 19.0 +input1.bam FBtr0079694 72 52 F 17.0 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 15.0 +input1.bam FBtr0079702 72 19 F 18.0 +input1.bam FBtr0079702 72 56 F 15.0 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 16.0 +input1.bam FBtr0079728 72 8 F 20.0 +input1.bam FBtr0079728 72 19 F 24.0 +input1.bam FBtr0079728 72 33 F 15.7 +input1.bam FBtr0079728 72 56 F 15.0 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 15.0 +input1.bam FBtr0079729 72 13 F 22.0 +input1.bam FBtr0079729 72 52 F 18.0 +input1.bam FBtr0079729 72 57 F 16.0 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 19.5 +input1.bam FBtr0079752 72 7 F 20.0 +input1.bam FBtr0079752 72 12 F 16.0 +input1.bam FBtr0079752 72 33 F 16.0 +input1.bam FBtr0079752 72 52 F 19.5 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 20.0 +input1.bam FBtr0079820 74 46 F 17.0 +input1.bam FBtr0079820 74 48 F 18.0 +input1.bam FBtr0079820 74 49 F 24.0 +input1.bam FBtr0079820 74 51 F 20.0 +input1.bam FBtr0079820 74 54 F 17.0 +input1.bam FBtr0079820 74 55 F 18.0 +input1.bam FBtr0079820 74 56 F 18.5 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 18.8 +input1.bam FBtr0080609 72 3 F 21.0 +input1.bam FBtr0080609 72 4 F 20.0 +input1.bam FBtr0080609 72 5 F 19.0 +input1.bam FBtr0080609 72 7 F 17.1 +input1.bam FBtr0080609 72 8 F 16.0 +input1.bam FBtr0080609 72 9 F 15.0 +input1.bam FBtr0080609 72 12 F 23.0 +input1.bam FBtr0080609 72 15 F 19.0 +input1.bam FBtr0080609 72 16 F 23.0 +input1.bam FBtr0080609 72 17 F 20.5 +input1.bam FBtr0080609 72 19 F 26.0 +input1.bam FBtr0080609 72 20 F 25.0 +input1.bam FBtr0080609 72 42 F 21.0 +input1.bam FBtr0080609 72 51 F 18.0 +input1.bam FBtr0080609 72 52 F 15.0 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 27.0 +input1.bam FBtr0080644 72 4 F 20.5 +input1.bam FBtr0080644 72 7 F 16.0 +input1.bam FBtr0080644 72 12 F 16.0 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 16.0 +input1.bam FBtr0080646 72 6 F 22.0 +input1.bam FBtr0080646 72 7 F 21.0 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 16.3 +input1.bam FBtr0080647 72 3 F 16.0 +input1.bam FBtr0080647 72 6 F 19.0 +input1.bam FBtr0080647 72 8 F 20.0 +input1.bam FBtr0080647 72 11 F 17.0 +input1.bam FBtr0080647 72 12 F 16.0 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 24.0 +input1.bam FBtr0080660 72 7 F 19.3 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 18.8 +input1.bam FBtr0080663 71 3 F 23.7 +input1.bam FBtr0080663 71 4 F 23.3 +input1.bam FBtr0080663 71 7 F 16.0 +input1.bam FBtr0080663 71 8 F 19.3 +input1.bam FBtr0080663 71 12 F 16.0 +input1.bam FBtr0080663 71 14 F 19.0 +input1.bam FBtr0080663 71 15 F 17.0 +input1.bam FBtr0080663 71 16 F 15.7 +input1.bam FBtr0080663 71 17 F 15.6 +input1.bam FBtr0080663 71 26 F 18.0 +input1.bam FBtr0080663 71 32 F 15.5 +input1.bam FBtr0080663 71 50 F 17.0 +input1.bam FBtr0080663 71 51 F 15.6 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 19.5 +input1.bam FBtr0080664 71 3 F 23.8 +input1.bam FBtr0080664 71 4 F 23.5 +input1.bam FBtr0080664 71 6 F 23.0 +input1.bam FBtr0080664 71 7 F 21.0 +input1.bam FBtr0080664 71 8 F 20.5 +input1.bam FBtr0080664 71 9 F 20.0 +input1.bam FBtr0080664 71 11 F 16.7 +input1.bam FBtr0080664 71 12 F 18.0 +input1.bam FBtr0080664 71 13 F 20.0 +input1.bam FBtr0080664 71 14 F 18.3 +input1.bam FBtr0080664 71 16 F 15.0 +input1.bam FBtr0080664 71 17 F 15.8 +input1.bam FBtr0080664 71 18 F 15.0 +input1.bam FBtr0080664 71 21 F 15.0 +input1.bam FBtr0080664 71 28 F 16.0 +input1.bam FBtr0080664 71 32 F 15.0 +input1.bam FBtr0080664 71 33 F 20.0 +input1.bam FBtr0080664 71 34 F 16.0 +input1.bam FBtr0080664 71 35 F 15.0 +input1.bam FBtr0080664 71 36 F 21.0 +input1.bam FBtr0080664 71 37 F 18.0 +input1.bam FBtr0080664 71 38 F 15.0 +input1.bam FBtr0080664 71 50 F 16.0 +input1.bam FBtr0080664 71 51 F 15.0 +input1.bam FBtr0080664 71 52 F 15.0 +input1.bam FBtr0080664 71 56 F 16.0 +input1.bam FBtr0080664 71 71 F 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_median.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,300 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Median +input1.bam FBtr0070001 72 1 F 17.0 +input1.bam FBtr0070001 72 7 F 21.0 +input1.bam FBtr0070001 72 8 F 21.0 +input1.bam FBtr0070001 72 11 F 20.5 +input1.bam FBtr0070001 72 16 F 19.0 +input1.bam FBtr0070001 72 17 F 23.0 +input1.bam FBtr0070001 72 18 F 16.0 +input1.bam FBtr0070001 72 27 F 23.5 +input1.bam FBtr0070001 72 30 F 23.0 +input1.bam FBtr0070001 72 31 F 23.0 +input1.bam FBtr0070001 72 32 F 22.0 +input1.bam FBtr0070001 72 34 F 20.0 +input1.bam FBtr0070001 72 72 F 0 +input1.bam FBtr0070533 72 1 F 15.0 +input1.bam FBtr0070533 72 12 F 18.0 +input1.bam FBtr0070533 72 15 F 15.0 +input1.bam FBtr0070533 72 19 F 22.0 +input1.bam FBtr0070533 72 20 F 23.0 +input1.bam FBtr0070533 72 21 F 18.0 +input1.bam FBtr0070533 72 22 F 20.0 +input1.bam FBtr0070533 72 25 F 17.0 +input1.bam FBtr0070533 72 26 F 16.0 +input1.bam FBtr0070533 72 28 F 25.0 +input1.bam FBtr0070533 72 32 F 21.0 +input1.bam FBtr0070533 72 35 F 19.0 +input1.bam FBtr0070533 72 37 F 19.0 +input1.bam FBtr0070533 72 38 F 18.0 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 16.5 +input1.bam FBtr0070603 72 3 F 21.0 +input1.bam FBtr0070603 72 4 F 20.0 +input1.bam FBtr0070603 72 6 F 18.0 +input1.bam FBtr0070603 72 7 F 17.0 +input1.bam FBtr0070603 72 8 F 16.0 +input1.bam FBtr0070603 72 9 F 15.0 +input1.bam FBtr0070603 72 12 F 20.0 +input1.bam FBtr0070603 72 13 F 22.0 +input1.bam FBtr0070603 72 15 F 18.5 +input1.bam FBtr0070603 72 16 F 20.5 +input1.bam FBtr0070603 72 17 F 25.0 +input1.bam FBtr0070603 72 18 F 16.0 +input1.bam FBtr0070603 72 19 F 23.0 +input1.bam FBtr0070603 72 20 F 22.0 +input1.bam FBtr0070603 72 21 F 25.0 +input1.bam FBtr0070603 72 22 F 20.0 +input1.bam FBtr0070603 72 24 F 19.5 +input1.bam FBtr0070603 72 25 F 23.0 +input1.bam FBtr0070603 72 26 F 26.0 +input1.bam FBtr0070603 72 27 F 26.0 +input1.bam FBtr0070603 72 32 F 20.0 +input1.bam FBtr0070603 72 34 F 20.0 +input1.bam FBtr0070603 72 38 F 18.0 +input1.bam FBtr0070603 72 42 F 21.0 +input1.bam FBtr0070603 72 51 F 18.0 +input1.bam FBtr0070603 72 56 F 16.0 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 15.0 +input1.bam FBtr0070604 72 18 F 23.0 +input1.bam FBtr0070604 72 22 F 19.0 +input1.bam FBtr0070604 72 30 F 18.0 +input1.bam FBtr0070604 72 31 F 23.0 +input1.bam FBtr0070604 72 32 F 22.0 +input1.bam FBtr0070604 72 57 F 15.0 +input1.bam FBtr0070604 72 72 F 0 +input1.bam FBtr0070911 73 1 F 0 +input1.bam FBtr0070911 73 15 F 21.0 +input1.bam FBtr0070911 73 38 F 15.0 +input1.bam FBtr0070911 73 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 13 F 16.0 +input1.bam FBtr0078490 72 17 F 16.0 +input1.bam FBtr0078490 72 18 F 15.0 +input1.bam FBtr0078490 72 25 F 15.0 +input1.bam FBtr0078490 72 28 F 19.0 +input1.bam FBtr0078490 72 38 F 18.0 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 15.0 +input1.bam FBtr0078580 72 3 F 22.0 +input1.bam FBtr0078580 72 4 F 25.0 +input1.bam FBtr0078580 72 5 F 20.0 +input1.bam FBtr0078580 72 6 F 19.0 +input1.bam FBtr0078580 72 7 F 22.0 +input1.bam FBtr0078580 72 8 F 18.0 +input1.bam FBtr0078580 72 11 F 23.0 +input1.bam FBtr0078580 72 12 F 17.0 +input1.bam FBtr0078580 72 14 F 15.0 +input1.bam FBtr0078580 72 15 F 16.0 +input1.bam FBtr0078580 72 16 F 19.0 +input1.bam FBtr0078580 72 17 F 17.0 +input1.bam FBtr0078580 72 19 F 24.0 +input1.bam FBtr0078580 72 20 F 21.0 +input1.bam FBtr0078580 72 21 F 20.0 +input1.bam FBtr0078580 72 24 F 17.0 +input1.bam FBtr0078580 72 25 F 27.5 +input1.bam FBtr0078580 72 29 F 17.0 +input1.bam FBtr0078580 72 31 F 17.0 +input1.bam FBtr0078580 72 52 F 16.0 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 19.0 +input1.bam FBtr0078790 73 17 F 16.0 +input1.bam FBtr0078790 73 33 F 23.0 +input1.bam FBtr0078790 73 42 F 18.5 +input1.bam FBtr0078790 73 44 F 19.5 +input1.bam FBtr0078790 73 46 F 17.0 +input1.bam FBtr0078790 73 47 F 18.0 +input1.bam FBtr0078790 73 52 F 20.0 +input1.bam FBtr0078790 73 69 R 15.0 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 15.0 +input1.bam FBtr0079064 72 3 F 21.0 +input1.bam FBtr0079064 72 33 F 15.0 +input1.bam FBtr0079064 72 52 F 17.0 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 21.5 +input1.bam FBtr0079090 72 26 F 24.0 +input1.bam FBtr0079090 72 33 F 16.0 +input1.bam FBtr0079090 72 53 F 18.0 +input1.bam FBtr0079090 72 56 R 21.0 +input1.bam FBtr0079090 72 72 F 0 +input1.bam FBtr0079338 73 1 F 0 +input1.bam FBtr0079338 73 12 F 17.0 +input1.bam FBtr0079338 73 13 F 17.5 +input1.bam FBtr0079338 73 14 F 15.0 +input1.bam FBtr0079338 73 17 F 15.0 +input1.bam FBtr0079338 73 25 F 16.0 +input1.bam FBtr0079338 73 42 F 22.0 +input1.bam FBtr0079338 73 43 F 21.0 +input1.bam FBtr0079338 73 46 F 18.0 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 20.0 +input1.bam FBtr0079528 71 3 F 24.0 +input1.bam FBtr0079528 71 4 F 24.0 +input1.bam FBtr0079528 71 8 F 19.5 +input1.bam FBtr0079528 71 10 F 21.0 +input1.bam FBtr0079528 71 11 F 19.0 +input1.bam FBtr0079528 71 13 F 16.0 +input1.bam FBtr0079528 71 14 F 18.5 +input1.bam FBtr0079528 71 16 F 15.0 +input1.bam FBtr0079528 71 17 F 15.0 +input1.bam FBtr0079528 71 18 F 20.0 +input1.bam FBtr0079528 71 28 F 16.0 +input1.bam FBtr0079528 71 35 F 15.0 +input1.bam FBtr0079528 71 36 F 20.0 +input1.bam FBtr0079528 71 37 F 18.0 +input1.bam FBtr0079528 71 51 F 15.0 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 15.0 +input1.bam FBtr0079596 73 3 F 23.0 +input1.bam FBtr0079596 73 4 F 22.0 +input1.bam FBtr0079596 73 5 F 18.5 +input1.bam FBtr0079596 73 6 F 18.0 +input1.bam FBtr0079596 73 8 F 17.0 +input1.bam FBtr0079596 73 9 F 16.0 +input1.bam FBtr0079596 73 10 F 15.0 +input1.bam FBtr0079596 73 11 F 15.0 +input1.bam FBtr0079596 73 12 F 17.0 +input1.bam FBtr0079596 73 13 F 16.0 +input1.bam FBtr0079596 73 14 F 15.0 +input1.bam FBtr0079596 73 15 F 18.0 +input1.bam FBtr0079596 73 16 F 17.0 +input1.bam FBtr0079596 73 17 F 16.0 +input1.bam FBtr0079596 73 18 F 15.0 +input1.bam FBtr0079596 73 19 F 15.0 +input1.bam FBtr0079596 73 53 F 18.5 +input1.bam FBtr0079596 73 54 F 19.5 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 23.0 +input1.bam FBtr0079677 72 5 F 19.0 +input1.bam FBtr0079677 72 52 F 19.0 +input1.bam FBtr0079677 72 53 F 18.0 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 15.0 +input1.bam FBtr0079690 72 22 F 15.0 +input1.bam FBtr0079690 72 27 F 25.0 +input1.bam FBtr0079690 72 33 F 16.0 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 19.0 +input1.bam FBtr0079692 73 18 F 18.0 +input1.bam FBtr0079692 73 25 F 17.0 +input1.bam FBtr0079692 73 32 F 20.0 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 15.0 +input1.bam FBtr0079693 72 25 F 23.0 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 23.0 +input1.bam FBtr0079694 72 18 F 19.0 +input1.bam FBtr0079694 72 52 F 17.0 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 15.0 +input1.bam FBtr0079702 72 19 F 18.0 +input1.bam FBtr0079702 72 56 F 15.0 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 16.0 +input1.bam FBtr0079728 72 8 F 20.0 +input1.bam FBtr0079728 72 19 F 24.0 +input1.bam FBtr0079728 72 33 F 15.0 +input1.bam FBtr0079728 72 56 F 15.0 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 15.0 +input1.bam FBtr0079729 72 13 F 22.0 +input1.bam FBtr0079729 72 52 F 18.0 +input1.bam FBtr0079729 72 57 F 16.0 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 19.5 +input1.bam FBtr0079752 72 7 F 20.0 +input1.bam FBtr0079752 72 12 F 16.0 +input1.bam FBtr0079752 72 33 F 16.0 +input1.bam FBtr0079752 72 52 F 19.5 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 20.0 +input1.bam FBtr0079820 74 46 F 17.0 +input1.bam FBtr0079820 74 48 F 18.0 +input1.bam FBtr0079820 74 49 F 24.0 +input1.bam FBtr0079820 74 51 F 20.0 +input1.bam FBtr0079820 74 54 F 17.0 +input1.bam FBtr0079820 74 55 F 18.0 +input1.bam FBtr0079820 74 56 F 18.5 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 18.0 +input1.bam FBtr0080609 72 3 F 21.0 +input1.bam FBtr0080609 72 4 F 20.0 +input1.bam FBtr0080609 72 5 F 19.0 +input1.bam FBtr0080609 72 7 F 17.0 +input1.bam FBtr0080609 72 8 F 16.0 +input1.bam FBtr0080609 72 9 F 15.0 +input1.bam FBtr0080609 72 12 F 23.0 +input1.bam FBtr0080609 72 15 F 19.0 +input1.bam FBtr0080609 72 16 F 23.0 +input1.bam FBtr0080609 72 17 F 20.5 +input1.bam FBtr0080609 72 19 F 26.0 +input1.bam FBtr0080609 72 20 F 25.0 +input1.bam FBtr0080609 72 42 F 21.0 +input1.bam FBtr0080609 72 51 F 18.0 +input1.bam FBtr0080609 72 52 F 15.0 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 27.0 +input1.bam FBtr0080644 72 4 F 20.5 +input1.bam FBtr0080644 72 7 F 16.0 +input1.bam FBtr0080644 72 12 F 16.0 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 16.0 +input1.bam FBtr0080646 72 6 F 22.0 +input1.bam FBtr0080646 72 7 F 21.0 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 16.0 +input1.bam FBtr0080647 72 3 F 16.0 +input1.bam FBtr0080647 72 6 F 19.0 +input1.bam FBtr0080647 72 8 F 20.0 +input1.bam FBtr0080647 72 11 F 17.0 +input1.bam FBtr0080647 72 12 F 16.0 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 24.0 +input1.bam FBtr0080660 72 7 F 21.0 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 16.0 +input1.bam FBtr0080663 71 3 F 24.0 +input1.bam FBtr0080663 71 4 F 23.5 +input1.bam FBtr0080663 71 7 F 16.0 +input1.bam FBtr0080663 71 8 F 19.5 +input1.bam FBtr0080663 71 12 F 16.0 +input1.bam FBtr0080663 71 14 F 19.0 +input1.bam FBtr0080663 71 15 F 17.0 +input1.bam FBtr0080663 71 16 F 16.0 +input1.bam FBtr0080663 71 17 F 15.0 +input1.bam FBtr0080663 71 26 F 18.0 +input1.bam FBtr0080663 71 32 F 15.5 +input1.bam FBtr0080663 71 50 F 17.0 +input1.bam FBtr0080663 71 51 F 15.0 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 17.0 +input1.bam FBtr0080664 71 3 F 24.0 +input1.bam FBtr0080664 71 4 F 23.5 +input1.bam FBtr0080664 71 6 F 23.0 +input1.bam FBtr0080664 71 7 F 21.0 +input1.bam FBtr0080664 71 8 F 20.0 +input1.bam FBtr0080664 71 9 F 20.0 +input1.bam FBtr0080664 71 11 F 17.0 +input1.bam FBtr0080664 71 12 F 17.0 +input1.bam FBtr0080664 71 13 F 20.0 +input1.bam FBtr0080664 71 14 F 18.0 +input1.bam FBtr0080664 71 16 F 15.0 +input1.bam FBtr0080664 71 17 F 15.5 +input1.bam FBtr0080664 71 18 F 15.0 +input1.bam FBtr0080664 71 21 F 15.0 +input1.bam FBtr0080664 71 28 F 16.0 +input1.bam FBtr0080664 71 32 F 15.0 +input1.bam FBtr0080664 71 33 F 20.0 +input1.bam FBtr0080664 71 34 F 16.0 +input1.bam FBtr0080664 71 35 F 15.0 +input1.bam FBtr0080664 71 36 F 21.0 +input1.bam FBtr0080664 71 37 F 18.0 +input1.bam FBtr0080664 71 38 F 15.0 +input1.bam FBtr0080664 71 50 F 16.0 +input1.bam FBtr0080664 71 51 F 15.0 +input1.bam FBtr0080664 71 52 F 15.0 +input1.bam FBtr0080664 71 56 F 16.0 +input1.bam FBtr0080664 71 71 F 0
Binary file test-data/input1_min0_max10000_cluster0_ylimneg5_pos5_single_plot_counts.pdf has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_min20_max30_counts.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,171 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Counts +input1.bam FBtr0070001 72 1 F 0 +input1.bam FBtr0070001 72 7 F 5 +input1.bam FBtr0070001 72 8 F 3 +input1.bam FBtr0070001 72 11 F 2 +input1.bam FBtr0070001 72 17 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 0 +input1.bam FBtr0070533 72 19 F 5 +input1.bam FBtr0070533 72 20 F 1 +input1.bam FBtr0070533 72 22 F 1 +input1.bam FBtr0070533 72 28 F 1 +input1.bam FBtr0070533 72 32 F 3 +input1.bam FBtr0070533 72 72 F 0 +input1.bam FBtr0070603 72 1 F 0 +input1.bam FBtr0070603 72 3 F 1 +input1.bam FBtr0070603 72 4 F 1 +input1.bam FBtr0070603 72 12 F 1 +input1.bam FBtr0070603 72 13 F 1 +input1.bam FBtr0070603 72 15 F 1 +input1.bam FBtr0070603 72 16 F 1 +input1.bam FBtr0070603 72 17 F 3 +input1.bam FBtr0070603 72 19 F 8 +input1.bam FBtr0070603 72 20 F 2 +input1.bam FBtr0070603 72 21 F 1 +input1.bam FBtr0070603 72 22 F 2 +input1.bam FBtr0070603 72 24 F 1 +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 2 +input1.bam FBtr0070603 72 42 F 1 +input1.bam FBtr0070603 72 72 F 0 +input1.bam FBtr0070604 72 1 F 0 +input1.bam FBtr0070604 72 18 F 1 +input1.bam FBtr0070604 72 31 F 9 +input1.bam FBtr0070604 72 32 F 24 +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 73 F 0 +input1.bam FBtr0078490 72 1 F 0 +input1.bam FBtr0078490 72 28 F 1 +input1.bam FBtr0078490 72 72 F 0 +input1.bam FBtr0078580 72 1 F 417 +input1.bam FBtr0078580 72 3 F 3 +input1.bam FBtr0078580 72 4 F 4 +input1.bam FBtr0078580 72 5 F 4 +input1.bam FBtr0078580 72 6 F 2 +input1.bam FBtr0078580 72 7 F 1 +input1.bam FBtr0078580 72 11 F 1 +input1.bam FBtr0078580 72 12 F 2 +input1.bam FBtr0078580 72 16 F 1 +input1.bam FBtr0078580 72 19 F 1 +input1.bam FBtr0078580 72 20 F 2 +input1.bam FBtr0078580 72 21 F 4 +input1.bam FBtr0078580 72 25 F 2 +input1.bam FBtr0078580 72 72 F 0 +input1.bam FBtr0078790 73 1 F 0 +input1.bam FBtr0078790 73 33 F 1 +input1.bam FBtr0078790 73 42 F 2 +input1.bam FBtr0078790 73 44 F 1 +input1.bam FBtr0078790 73 52 F 1 +input1.bam FBtr0078790 73 73 F 0 +input1.bam FBtr0079064 72 1 F 0 +input1.bam FBtr0079064 72 3 F 1 +input1.bam FBtr0079064 72 72 F 0 +input1.bam FBtr0079090 72 1 F 1 +input1.bam FBtr0079090 72 26 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 42 F 8 +input1.bam FBtr0079338 73 43 F 1 +input1.bam FBtr0079338 73 73 F 0 +input1.bam FBtr0079528 71 1 F 10 +input1.bam FBtr0079528 71 3 F 54 +input1.bam FBtr0079528 71 4 F 2 +input1.bam FBtr0079528 71 8 F 2 +input1.bam FBtr0079528 71 10 F 1 +input1.bam FBtr0079528 71 11 F 1 +input1.bam FBtr0079528 71 18 F 3 +input1.bam FBtr0079528 71 36 F 1 +input1.bam FBtr0079528 71 71 F 0 +input1.bam FBtr0079596 73 1 F 0 +input1.bam FBtr0079596 73 3 F 11 +input1.bam FBtr0079596 73 4 F 30 +input1.bam FBtr0079596 73 13 F 1 +input1.bam FBtr0079596 73 53 F 1 +input1.bam FBtr0079596 73 54 F 1 +input1.bam FBtr0079596 73 73 F 0 +input1.bam FBtr0079677 72 1 F 1 +input1.bam FBtr0079677 72 72 F 0 +input1.bam FBtr0079690 72 1 F 0 +input1.bam FBtr0079690 72 27 F 1 +input1.bam FBtr0079690 72 72 F 0 +input1.bam FBtr0079692 73 1 F 1 +input1.bam FBtr0079692 73 32 F 1 +input1.bam FBtr0079692 73 73 F 0 +input1.bam FBtr0079693 72 1 F 1 +input1.bam FBtr0079693 72 25 F 1 +input1.bam FBtr0079693 72 72 F 0 +input1.bam FBtr0079694 72 1 F 3 +input1.bam FBtr0079694 72 72 F 0 +input1.bam FBtr0079702 72 1 F 0 +input1.bam FBtr0079702 72 72 F 0 +input1.bam FBtr0079728 72 1 F 0 +input1.bam FBtr0079728 72 8 F 1 +input1.bam FBtr0079728 72 19 F 1 +input1.bam FBtr0079728 72 72 F 0 +input1.bam FBtr0079729 72 1 F 0 +input1.bam FBtr0079729 72 13 F 1 +input1.bam FBtr0079729 72 72 F 0 +input1.bam FBtr0079752 72 1 F 1 +input1.bam FBtr0079752 72 7 F 1 +input1.bam FBtr0079752 72 52 F 1 +input1.bam FBtr0079752 72 72 F 0 +input1.bam FBtr0079820 74 1 F 0 +input1.bam FBtr0079820 74 45 F 1 +input1.bam FBtr0079820 74 49 F 1 +input1.bam FBtr0079820 74 51 F 1 +input1.bam FBtr0079820 74 74 F 0 +input1.bam FBtr0080609 72 1 F 3 +input1.bam FBtr0080609 72 3 F 2 +input1.bam FBtr0080609 72 4 F 10 +input1.bam FBtr0080609 72 12 F 1 +input1.bam FBtr0080609 72 16 F 1 +input1.bam FBtr0080609 72 17 F 1 +input1.bam FBtr0080609 72 19 F 1 +input1.bam FBtr0080609 72 20 F 1 +input1.bam FBtr0080609 72 42 F 1 +input1.bam FBtr0080609 72 72 F 0 +input1.bam FBtr0080644 72 1 F 1 +input1.bam FBtr0080644 72 4 F 1 +input1.bam FBtr0080644 72 72 F 0 +input1.bam FBtr0080646 72 1 F 0 +input1.bam FBtr0080646 72 6 F 1 +input1.bam FBtr0080646 72 7 F 1 +input1.bam FBtr0080646 72 72 F 0 +input1.bam FBtr0080647 72 1 F 0 +input1.bam FBtr0080647 72 6 F 1 +input1.bam FBtr0080647 72 8 F 1 +input1.bam FBtr0080647 72 72 F 0 +input1.bam FBtr0080660 72 1 F 0 +input1.bam FBtr0080660 72 4 F 4 +input1.bam FBtr0080660 72 7 F 2 +input1.bam FBtr0080660 72 72 F 0 +input1.bam FBtr0080663 71 1 F 6 +input1.bam FBtr0080663 71 3 F 56 +input1.bam FBtr0080663 71 4 F 4 +input1.bam FBtr0080663 71 8 F 2 +input1.bam FBtr0080663 71 51 F 1 +input1.bam FBtr0080663 71 71 F 0 +input1.bam FBtr0080664 71 1 F 6 +input1.bam FBtr0080664 71 3 F 56 +input1.bam FBtr0080664 71 4 F 4 +input1.bam FBtr0080664 71 6 F 1 +input1.bam FBtr0080664 71 7 F 1 +input1.bam FBtr0080664 71 8 F 3 +input1.bam FBtr0080664 71 9 F 1 +input1.bam FBtr0080664 71 12 F 1 +input1.bam FBtr0080664 71 13 F 2 +input1.bam FBtr0080664 71 33 F 1 +input1.bam FBtr0080664 71 36 F 1 +input1.bam FBtr0080664 71 71 F 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_min20_max30_size.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,263 @@ +Dataset Chromosome Polarity Size Counts +input1.bam FBtr0070001 F 20 4 +input1.bam FBtr0070001 F 21 4 +input1.bam FBtr0070001 F 22 29 +input1.bam FBtr0070001 F 23 15 +input1.bam FBtr0070001 F 24 1 +input1.bam FBtr0070001 R 20 0 +input1.bam FBtr0070001 R 21 0 +input1.bam FBtr0070001 R 22 0 +input1.bam FBtr0070001 R 23 0 +input1.bam FBtr0070001 R 24 0 +input1.bam FBtr0070533 F 20 2 +input1.bam FBtr0070533 F 21 2 +input1.bam FBtr0070533 F 22 4 +input1.bam FBtr0070533 F 23 2 +input1.bam FBtr0070533 F 24 0 +input1.bam FBtr0070533 F 25 1 +input1.bam FBtr0070533 R 20 0 +input1.bam FBtr0070533 R 21 0 +input1.bam FBtr0070533 R 22 0 +input1.bam FBtr0070533 R 23 0 +input1.bam FBtr0070533 R 24 0 +input1.bam FBtr0070533 R 25 0 +input1.bam FBtr0070603 F 20 6 +input1.bam FBtr0070603 F 21 3 +input1.bam FBtr0070603 F 22 3 +input1.bam FBtr0070603 F 23 10 +input1.bam FBtr0070603 F 24 2 +input1.bam FBtr0070603 F 25 5 +input1.bam FBtr0070603 F 26 5 +input1.bam FBtr0070603 F 27 3 +input1.bam FBtr0070603 R 20 0 +input1.bam FBtr0070603 R 21 0 +input1.bam FBtr0070603 R 22 0 +input1.bam FBtr0070603 R 23 0 +input1.bam FBtr0070603 R 24 0 +input1.bam FBtr0070603 R 25 0 +input1.bam FBtr0070603 R 26 0 +input1.bam FBtr0070603 R 27 0 +input1.bam FBtr0070604 F 21 1 +input1.bam FBtr0070604 F 22 23 +input1.bam FBtr0070604 F 23 10 +input1.bam FBtr0070604 R 21 0 +input1.bam FBtr0070604 R 22 0 +input1.bam FBtr0070604 R 23 0 +input1.bam FBtr0070911 F 21 1 +input1.bam FBtr0070911 R 21 0 +input1.bam FBtr0078490 F 23 1 +input1.bam FBtr0078490 R 23 0 +input1.bam FBtr0078580 F 20 9 +input1.bam FBtr0078580 F 21 5 +input1.bam FBtr0078580 F 22 13 +input1.bam FBtr0078580 F 23 5 +input1.bam FBtr0078580 F 24 180 +input1.bam FBtr0078580 F 25 212 +input1.bam FBtr0078580 F 26 1 +input1.bam FBtr0078580 F 27 2 +input1.bam FBtr0078580 F 28 17 +input1.bam FBtr0078580 R 20 0 +input1.bam FBtr0078580 R 21 0 +input1.bam FBtr0078580 R 22 0 +input1.bam FBtr0078580 R 23 0 +input1.bam FBtr0078580 R 24 0 +input1.bam FBtr0078580 R 25 0 +input1.bam FBtr0078580 R 26 0 +input1.bam FBtr0078580 R 27 0 +input1.bam FBtr0078580 R 28 0 +input1.bam FBtr0078790 F 20 2 +input1.bam FBtr0078790 F 21 0 +input1.bam FBtr0078790 F 22 2 +input1.bam FBtr0078790 F 23 1 +input1.bam FBtr0078790 R 20 0 +input1.bam FBtr0078790 R 21 0 +input1.bam FBtr0078790 R 22 0 +input1.bam FBtr0078790 R 23 0 +input1.bam FBtr0079064 F 21 1 +input1.bam FBtr0079064 R 21 0 +input1.bam FBtr0079090 F 21 0 +input1.bam FBtr0079090 F 22 0 +input1.bam FBtr0079090 F 23 0 +input1.bam FBtr0079090 F 24 1 +input1.bam FBtr0079090 F 25 0 +input1.bam FBtr0079090 F 26 0 +input1.bam FBtr0079090 F 27 0 +input1.bam FBtr0079090 F 28 1 +input1.bam FBtr0079090 R 21 1 +input1.bam FBtr0079090 R 22 0 +input1.bam FBtr0079090 R 23 0 +input1.bam FBtr0079090 R 24 0 +input1.bam FBtr0079090 R 25 0 +input1.bam FBtr0079090 R 26 0 +input1.bam FBtr0079090 R 27 0 +input1.bam FBtr0079090 R 28 0 +input1.bam FBtr0079338 F 21 3 +input1.bam FBtr0079338 F 22 6 +input1.bam FBtr0079338 R 21 0 +input1.bam FBtr0079338 R 22 0 +input1.bam FBtr0079528 F 20 12 +input1.bam FBtr0079528 F 21 3 +input1.bam FBtr0079528 F 22 2 +input1.bam FBtr0079528 F 23 3 +input1.bam FBtr0079528 F 24 36 +input1.bam FBtr0079528 F 25 8 +input1.bam FBtr0079528 F 26 5 +input1.bam FBtr0079528 F 27 2 +input1.bam FBtr0079528 F 28 2 +input1.bam FBtr0079528 F 29 1 +input1.bam FBtr0079528 R 20 0 +input1.bam FBtr0079528 R 21 0 +input1.bam FBtr0079528 R 22 0 +input1.bam FBtr0079528 R 23 0 +input1.bam FBtr0079528 R 24 0 +input1.bam FBtr0079528 R 25 0 +input1.bam FBtr0079528 R 26 0 +input1.bam FBtr0079528 R 27 0 +input1.bam FBtr0079528 R 28 0 +input1.bam FBtr0079528 R 29 0 +input1.bam FBtr0079596 F 20 13 +input1.bam FBtr0079596 F 21 3 +input1.bam FBtr0079596 F 22 16 +input1.bam FBtr0079596 F 23 8 +input1.bam FBtr0079596 F 24 0 +input1.bam FBtr0079596 F 25 0 +input1.bam FBtr0079596 F 26 3 +input1.bam FBtr0079596 F 27 1 +input1.bam FBtr0079596 R 20 0 +input1.bam FBtr0079596 R 21 0 +input1.bam FBtr0079596 R 22 0 +input1.bam FBtr0079596 R 23 0 +input1.bam FBtr0079596 R 24 0 +input1.bam FBtr0079596 R 25 0 +input1.bam FBtr0079596 R 26 0 +input1.bam FBtr0079596 R 27 0 +input1.bam FBtr0079677 F 23 1 +input1.bam FBtr0079677 R 23 0 +input1.bam FBtr0079690 F 25 1 +input1.bam FBtr0079690 R 25 0 +input1.bam FBtr0079692 F 20 1 +input1.bam FBtr0079692 F 21 0 +input1.bam FBtr0079692 F 22 0 +input1.bam FBtr0079692 F 23 1 +input1.bam FBtr0079692 R 20 0 +input1.bam FBtr0079692 R 21 0 +input1.bam FBtr0079692 R 22 0 +input1.bam FBtr0079692 R 23 0 +input1.bam FBtr0079693 F 23 1 +input1.bam FBtr0079693 F 24 1 +input1.bam FBtr0079693 R 23 0 +input1.bam FBtr0079693 R 24 0 +input1.bam FBtr0079694 F 23 1 +input1.bam FBtr0079694 F 24 1 +input1.bam FBtr0079694 F 25 1 +input1.bam FBtr0079694 R 23 0 +input1.bam FBtr0079694 R 24 0 +input1.bam FBtr0079694 R 25 0 +input1.bam FBtr0079728 F 20 1 +input1.bam FBtr0079728 F 21 0 +input1.bam FBtr0079728 F 22 0 +input1.bam FBtr0079728 F 23 0 +input1.bam FBtr0079728 F 24 1 +input1.bam FBtr0079728 R 20 0 +input1.bam FBtr0079728 R 21 0 +input1.bam FBtr0079728 R 22 0 +input1.bam FBtr0079728 R 23 0 +input1.bam FBtr0079728 R 24 0 +input1.bam FBtr0079729 F 22 1 +input1.bam FBtr0079729 R 22 0 +input1.bam FBtr0079752 F 20 2 +input1.bam FBtr0079752 F 21 0 +input1.bam FBtr0079752 F 22 0 +input1.bam FBtr0079752 F 23 0 +input1.bam FBtr0079752 F 24 1 +input1.bam FBtr0079752 R 20 0 +input1.bam FBtr0079752 R 21 0 +input1.bam FBtr0079752 R 22 0 +input1.bam FBtr0079752 R 23 0 +input1.bam FBtr0079752 R 24 0 +input1.bam FBtr0079820 F 20 2 +input1.bam FBtr0079820 F 21 0 +input1.bam FBtr0079820 F 22 0 +input1.bam FBtr0079820 F 23 0 +input1.bam FBtr0079820 F 24 1 +input1.bam FBtr0079820 R 20 0 +input1.bam FBtr0079820 R 21 0 +input1.bam FBtr0079820 R 22 0 +input1.bam FBtr0079820 R 23 0 +input1.bam FBtr0079820 R 24 0 +input1.bam FBtr0080609 F 20 10 +input1.bam FBtr0080609 F 21 4 +input1.bam FBtr0080609 F 22 0 +input1.bam FBtr0080609 F 23 4 +input1.bam FBtr0080609 F 24 1 +input1.bam FBtr0080609 F 25 1 +input1.bam FBtr0080609 F 26 1 +input1.bam FBtr0080609 R 20 0 +input1.bam FBtr0080609 R 21 0 +input1.bam FBtr0080609 R 22 0 +input1.bam FBtr0080609 R 23 0 +input1.bam FBtr0080609 R 24 0 +input1.bam FBtr0080609 R 25 0 +input1.bam FBtr0080609 R 26 0 +input1.bam FBtr0080644 F 24 1 +input1.bam FBtr0080644 F 25 0 +input1.bam FBtr0080644 F 26 0 +input1.bam FBtr0080644 F 27 1 +input1.bam FBtr0080644 R 24 0 +input1.bam FBtr0080644 R 25 0 +input1.bam FBtr0080644 R 26 0 +input1.bam FBtr0080644 R 27 0 +input1.bam FBtr0080646 F 21 1 +input1.bam FBtr0080646 F 22 1 +input1.bam FBtr0080646 R 21 0 +input1.bam FBtr0080646 R 22 0 +input1.bam FBtr0080647 F 20 1 +input1.bam FBtr0080647 F 21 0 +input1.bam FBtr0080647 F 22 1 +input1.bam FBtr0080647 R 20 0 +input1.bam FBtr0080647 R 21 0 +input1.bam FBtr0080647 R 22 0 +input1.bam FBtr0080660 F 21 2 +input1.bam FBtr0080660 F 22 0 +input1.bam FBtr0080660 F 23 0 +input1.bam FBtr0080660 F 24 4 +input1.bam FBtr0080660 R 21 0 +input1.bam FBtr0080660 R 22 0 +input1.bam FBtr0080660 R 23 0 +input1.bam FBtr0080660 R 24 0 +input1.bam FBtr0080663 F 20 10 +input1.bam FBtr0080663 F 21 0 +input1.bam FBtr0080663 F 22 1 +input1.bam FBtr0080663 F 23 7 +input1.bam FBtr0080663 F 24 33 +input1.bam FBtr0080663 F 25 10 +input1.bam FBtr0080663 F 26 6 +input1.bam FBtr0080663 F 27 0 +input1.bam FBtr0080663 F 28 2 +input1.bam FBtr0080663 R 20 0 +input1.bam FBtr0080663 R 21 0 +input1.bam FBtr0080663 R 22 0 +input1.bam FBtr0080663 R 23 0 +input1.bam FBtr0080663 R 24 0 +input1.bam FBtr0080663 R 25 0 +input1.bam FBtr0080663 R 26 0 +input1.bam FBtr0080663 R 27 0 +input1.bam FBtr0080663 R 28 0 +input1.bam FBtr0080664 F 20 12 +input1.bam FBtr0080664 F 21 5 +input1.bam FBtr0080664 F 22 0 +input1.bam FBtr0080664 F 23 11 +input1.bam FBtr0080664 F 24 33 +input1.bam FBtr0080664 F 25 10 +input1.bam FBtr0080664 F 26 4 +input1.bam FBtr0080664 F 27 0 +input1.bam FBtr0080664 F 28 2 +input1.bam FBtr0080664 R 20 0 +input1.bam FBtr0080664 R 21 0 +input1.bam FBtr0080664 R 22 0 +input1.bam FBtr0080664 R 23 0 +input1.bam FBtr0080664 R 24 0 +input1.bam FBtr0080664 R 25 0 +input1.bam FBtr0080664 R 26 0 +input1.bam FBtr0080664 R 27 0 +input1.bam FBtr0080664 R 28 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1_size.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,605 @@ +Dataset Chromosome Polarity Size Counts +input1.bam FBtr0070001 F 16 2 +input1.bam FBtr0070001 F 17 1 +input1.bam FBtr0070001 F 18 0 +input1.bam FBtr0070001 F 19 1 +input1.bam FBtr0070001 F 20 4 +input1.bam FBtr0070001 F 21 4 +input1.bam FBtr0070001 F 22 29 +input1.bam FBtr0070001 F 23 15 +input1.bam FBtr0070001 F 24 1 +input1.bam FBtr0070001 R 16 0 +input1.bam FBtr0070001 R 17 0 +input1.bam FBtr0070001 R 18 0 +input1.bam FBtr0070001 R 19 0 +input1.bam FBtr0070001 R 20 0 +input1.bam FBtr0070001 R 21 0 +input1.bam FBtr0070001 R 22 0 +input1.bam FBtr0070001 R 23 0 +input1.bam FBtr0070001 R 24 0 +input1.bam FBtr0070533 F 15 2 +input1.bam FBtr0070533 F 16 1 +input1.bam FBtr0070533 F 17 1 +input1.bam FBtr0070533 F 18 6 +input1.bam FBtr0070533 F 19 3 +input1.bam FBtr0070533 F 20 2 +input1.bam FBtr0070533 F 21 2 +input1.bam FBtr0070533 F 22 4 +input1.bam FBtr0070533 F 23 2 +input1.bam FBtr0070533 F 24 0 +input1.bam FBtr0070533 F 25 1 +input1.bam FBtr0070533 R 15 0 +input1.bam FBtr0070533 R 16 0 +input1.bam FBtr0070533 R 17 0 +input1.bam FBtr0070533 R 18 0 +input1.bam FBtr0070533 R 19 0 +input1.bam FBtr0070533 R 20 0 +input1.bam FBtr0070533 R 21 0 +input1.bam FBtr0070533 R 22 0 +input1.bam FBtr0070533 R 23 0 +input1.bam FBtr0070533 R 24 0 +input1.bam FBtr0070533 R 25 0 +input1.bam FBtr0070603 F 15 9 +input1.bam FBtr0070603 F 16 6 +input1.bam FBtr0070603 F 17 10 +input1.bam FBtr0070603 F 18 7 +input1.bam FBtr0070603 F 19 1 +input1.bam FBtr0070603 F 20 6 +input1.bam FBtr0070603 F 21 3 +input1.bam FBtr0070603 F 22 3 +input1.bam FBtr0070603 F 23 10 +input1.bam FBtr0070603 F 24 2 +input1.bam FBtr0070603 F 25 5 +input1.bam FBtr0070603 F 26 5 +input1.bam FBtr0070603 F 27 3 +input1.bam FBtr0070603 R 15 0 +input1.bam FBtr0070603 R 16 0 +input1.bam FBtr0070603 R 17 0 +input1.bam FBtr0070603 R 18 0 +input1.bam FBtr0070603 R 19 0 +input1.bam FBtr0070603 R 20 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_single_chr_x_6_single_plot_coverage.tab Sat Apr 07 06:14:50 2018 -0400 @@ -0,0 +1,481 @@ +Dataset Chromosome Chrom_length Coordinate Polarity Coverage +input_single_chr.bam_0 1 80 1 F 1 +input_single_chr.bam_0 1 80 2 F 1 +input_single_chr.bam_0 1 80 3 F 1 +input_single_chr.bam_0 1 80 4 F 1 +input_single_chr.bam_0 1 80 5 F 1 +input_single_chr.bam_0 1 80 6 F 1 +input_single_chr.bam_0 1 80 7 F 1 +input_single_chr.bam_0 1 80 8 F 1 +input_single_chr.bam_0 1 80 9 F 1 +input_single_chr.bam_0 1 80 10 F 1 +input_single_chr.bam_0 1 80 11 F 1 +input_single_chr.bam_0 1 80 12 F 1 +input_single_chr.bam_0 1 80 13 F 1 +input_single_chr.bam_0 1 80 14 F 1 +input_single_chr.bam_0 1 80 15 F 1 +input_single_chr.bam_0 1 80 16 F 1 +input_single_chr.bam_0 1 80 17 F 1 +input_single_chr.bam_0 1 80 18 F 1 +input_single_chr.bam_0 1 80 19 F 1 +input_single_chr.bam_0 1 80 20 F 1 +input_single_chr.bam_0 1 80 21 F 1 +input_single_chr.bam_0 1 80 22 F 1 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+input_single_chr.bam_2 1 80 1 F 1 +input_single_chr.bam_2 1 80 2 F 1 +input_single_chr.bam_2 1 80 3 F 1 +input_single_chr.bam_2 1 80 4 F 1 +input_single_chr.bam_2 1 80 5 F 1 +input_single_chr.bam_2 1 80 6 F 1 +input_single_chr.bam_2 1 80 7 F 1 +input_single_chr.bam_2 1 80 8 F 1 +input_single_chr.bam_2 1 80 9 F 1 +input_single_chr.bam_2 1 80 10 F 1 +input_single_chr.bam_2 1 80 11 F 1 +input_single_chr.bam_2 1 80 12 F 1 +input_single_chr.bam_2 1 80 13 F 1 +input_single_chr.bam_2 1 80 14 F 1 +input_single_chr.bam_2 1 80 15 F 1 +input_single_chr.bam_2 1 80 16 F 1 +input_single_chr.bam_2 1 80 17 F 1 +input_single_chr.bam_2 1 80 18 F 1 +input_single_chr.bam_2 1 80 19 F 1 +input_single_chr.bam_2 1 80 20 F 1 +input_single_chr.bam_2 1 80 21 F 1 +input_single_chr.bam_2 1 80 22 F 1 +input_single_chr.bam_2 1 80 23 F 1 +input_single_chr.bam_2 1 80 24 F 1 +input_single_chr.bam_2 1 80 25 F 1 +input_single_chr.bam_2 1 80 26 F 1 +input_single_chr.bam_2 1 80 27 F 1 +input_single_chr.bam_2 1 80 28 F 1 +input_single_chr.bam_2 1 80 29 F 1 +input_single_chr.bam_2 1 80 30 F 1 +input_single_chr.bam_2 1 80 31 F 1 +input_single_chr.bam_2 1 80 32 F 1 +input_single_chr.bam_2 1 80 33 F 1 +input_single_chr.bam_2 1 80 34 F 1 +input_single_chr.bam_2 1 80 35 F 1 +input_single_chr.bam_2 1 80 36 F 1 +input_single_chr.bam_2 1 80 37 F 1 +input_single_chr.bam_2 1 80 38 F 1 +input_single_chr.bam_2 1 80 39 F 1 +input_single_chr.bam_2 1 80 40 F 1 +input_single_chr.bam_2 1 80 41 F 1 +input_single_chr.bam_2 1 80 42 F 1 +input_single_chr.bam_2 1 80 43 F 1 +input_single_chr.bam_2 1 80 44 F 1 +input_single_chr.bam_2 1 80 45 F 1 +input_single_chr.bam_2 1 80 46 F 1 +input_single_chr.bam_2 1 80 47 F 1 +input_single_chr.bam_2 1 80 48 F 1 +input_single_chr.bam_2 1 80 49 F 1 +input_single_chr.bam_2 1 80 50 F 1 +input_single_chr.bam_2 1 80 51 F 1 +input_single_chr.bam_2 1 80 52 F 1 +input_single_chr.bam_2 1 80 53 F 1 +input_single_chr.bam_2 1 80 54 F 1 +input_single_chr.bam_2 1 80 55 F 1 +input_single_chr.bam_2 1 80 56 F 1 +input_single_chr.bam_2 1 80 57 F 1 +input_single_chr.bam_2 1 80 58 F 1 +input_single_chr.bam_2 1 80 59 F 1 +input_single_chr.bam_2 1 80 60 F 1 +input_single_chr.bam_2 1 80 61 F 1 +input_single_chr.bam_2 1 80 62 F 1 +input_single_chr.bam_2 1 80 63 F 1 +input_single_chr.bam_2 1 80 64 F 1 +input_single_chr.bam_2 1 80 65 F 1 +input_single_chr.bam_2 1 80 66 F 1 +input_single_chr.bam_2 1 80 67 F 1 +input_single_chr.bam_2 1 80 68 F 1 +input_single_chr.bam_2 1 80 69 F 1 +input_single_chr.bam_2 1 80 70 F 1 +input_single_chr.bam_2 1 80 71 F 1 +input_single_chr.bam_2 1 80 72 F 1 +input_single_chr.bam_2 1 80 73 F 1 +input_single_chr.bam_2 1 80 74 F 1 +input_single_chr.bam_2 1 80 75 F 1 +input_single_chr.bam_2 1 80 76 F 1 +input_single_chr.bam_2 1 80 77 F 1 +input_single_chr.bam_2 1 80 78 F 1 +input_single_chr.bam_2 1 80 79 F 1 +input_single_chr.bam_2 1 80 80 F 1 +input_single_chr.bam_3 1 80 1 F 1 +input_single_chr.bam_3 1 80 2 F 1 +input_single_chr.bam_3 1 80 3 F 1 +input_single_chr.bam_3 1 80 4 F 1 +input_single_chr.bam_3 1 80 5 F 1 +input_single_chr.bam_3 1 80 6 F 1 +input_single_chr.bam_3 1 80 7 F 1 +input_single_chr.bam_3 1 80 8 F 1 +input_single_chr.bam_3 1 80 9 F 1 +input_single_chr.bam_3 1 80 10 F 1 +input_single_chr.bam_3 1 80 11 F 1 +input_single_chr.bam_3 1 80 12 F 1 +input_single_chr.bam_3 1 80 13 F 1 +input_single_chr.bam_3 1 80 14 F 1 +input_single_chr.bam_3 1 80 15 F 1 +input_single_chr.bam_3 1 80 16 F 1 +input_single_chr.bam_3 1 80 17 F 1 +input_single_chr.bam_3 1 80 18 F 1 +input_single_chr.bam_3 1 80 19 F 1 +input_single_chr.bam_3 1 80 20 F 1 +input_single_chr.bam_3 1 80 21 F 1 +input_single_chr.bam_3 1 80 22 F 1 +input_single_chr.bam_3 1 80 23 F 1 +input_single_chr.bam_3 1 80 24 F 1 +input_single_chr.bam_3 1 80 25 F 1 +input_single_chr.bam_3 1 80 26 F 1 +input_single_chr.bam_3 1 80 27 F 1 +input_single_chr.bam_3 1 80 28 F 1 +input_single_chr.bam_3 1 80 29 F 1 +input_single_chr.bam_3 1 80 30 F 1 +input_single_chr.bam_3 1 80 31 F 1 +input_single_chr.bam_3 1 80 32 F 1 +input_single_chr.bam_3 1 80 33 F 1 +input_single_chr.bam_3 1 80 34 F 1 +input_single_chr.bam_3 1 80 35 F 1 +input_single_chr.bam_3 1 80 36 F 1 +input_single_chr.bam_3 1 80 37 F 1 +input_single_chr.bam_3 1 80 38 F 1 +input_single_chr.bam_3 1 80 39 F 1 +input_single_chr.bam_3 1 80 40 F 1 +input_single_chr.bam_3 1 80 41 F 1 +input_single_chr.bam_3 1 80 42 F 1 +input_single_chr.bam_3 1 80 43 F 1 +input_single_chr.bam_3 1 80 44 F 1 +input_single_chr.bam_3 1 80 45 F 1 +input_single_chr.bam_3 1 80 46 F 1 +input_single_chr.bam_3 1 80 47 F 1 +input_single_chr.bam_3 1 80 48 F 1 +input_single_chr.bam_3 1 80 49 F 1 +input_single_chr.bam_3 1 80 50 F 1 +input_single_chr.bam_3 1 80 51 F 1 +input_single_chr.bam_3 1 80 52 F 1 +input_single_chr.bam_3 1 80 53 F 1 +input_single_chr.bam_3 1 80 54 F 1 +input_single_chr.bam_3 1 80 55 F 1 +input_single_chr.bam_3 1 80 56 F 1 +input_single_chr.bam_3 1 80 57 F 1 +input_single_chr.bam_3 1 80 58 F 1 +input_single_chr.bam_3 1 80 59 F 1 +input_single_chr.bam_3 1 80 60 F 1 +input_single_chr.bam_3 1 80 61 F 1 +input_single_chr.bam_3 1 80 62 F 1 +input_single_chr.bam_3 1 80 63 F 1 +input_single_chr.bam_3 1 80 64 F 1 +input_single_chr.bam_3 1 80 65 F 1 +input_single_chr.bam_3 1 80 66 F 1 +input_single_chr.bam_3 1 80 67 F 1 +input_single_chr.bam_3 1 80 68 F 1 +input_single_chr.bam_3 1 80 69 F 1 +input_single_chr.bam_3 1 80 70 F 1 +input_single_chr.bam_3 1 80 71 F 1 +input_single_chr.bam_3 1 80 72 F 1 +input_single_chr.bam_3 1 80 73 F 1 +input_single_chr.bam_3 1 80 74 F 1 +input_single_chr.bam_3 1 80 75 F 1 +input_single_chr.bam_3 1 80 76 F 1 +input_single_chr.bam_3 1 80 77 F 1 +input_single_chr.bam_3 1 80 78 F 1 +input_single_chr.bam_3 1 80 79 F 1 +input_single_chr.bam_3 1 80 80 F 1 +input_single_chr.bam_4 1 80 1 F 1 +input_single_chr.bam_4 1 80 2 F 1 +input_single_chr.bam_4 1 80 3 F 1 +input_single_chr.bam_4 1 80 4 F 1 +input_single_chr.bam_4 1 80 5 F 1 +input_single_chr.bam_4 1 80 6 F 1 +input_single_chr.bam_4 1 80 7 F 1 +input_single_chr.bam_4 1 80 8 F 1 +input_single_chr.bam_4 1 80 9 F 1 +input_single_chr.bam_4 1 80 10 F 1 +input_single_chr.bam_4 1 80 11 F 1 +input_single_chr.bam_4 1 80 12 F 1 +input_single_chr.bam_4 1 80 13 F 1 +input_single_chr.bam_4 1 80 14 F 1 +input_single_chr.bam_4 1 80 15 F 1 +input_single_chr.bam_4 1 80 16 F 1 +input_single_chr.bam_4 1 80 17 F 1 +input_single_chr.bam_4 1 80 18 F 1 +input_single_chr.bam_4 1 80 19 F 1 +input_single_chr.bam_4 1 80 20 F 1 +input_single_chr.bam_4 1 80 21 F 1 +input_single_chr.bam_4 1 80 22 F 1 +input_single_chr.bam_4 1 80 23 F 1 +input_single_chr.bam_4 1 80 24 F 1 +input_single_chr.bam_4 1 80 25 F 1 +input_single_chr.bam_4 1 80 26 F 1 +input_single_chr.bam_4 1 80 27 F 1 +input_single_chr.bam_4 1 80 28 F 1 +input_single_chr.bam_4 1 80 29 F 1 +input_single_chr.bam_4 1 80 30 F 1 +input_single_chr.bam_4 1 80 31 F 1 +input_single_chr.bam_4 1 80 32 F 1 +input_single_chr.bam_4 1 80 33 F 1 +input_single_chr.bam_4 1 80 34 F 1 +input_single_chr.bam_4 1 80 35 F 1 +input_single_chr.bam_4 1 80 36 F 1 +input_single_chr.bam_4 1 80 37 F 1 +input_single_chr.bam_4 1 80 38 F 1 +input_single_chr.bam_4 1 80 39 F 1 +input_single_chr.bam_4 1 80 40 F 1 +input_single_chr.bam_4 1 80 41 F 1 +input_single_chr.bam_4 1 80 42 F 1 +input_single_chr.bam_4 1 80 43 F 1 +input_single_chr.bam_4 1 80 44 F 1 +input_single_chr.bam_4 1 80 45 F 1 +input_single_chr.bam_4 1 80 46 F 1 +input_single_chr.bam_4 1 80 47 F 1 +input_single_chr.bam_4 1 80 48 F 1 +input_single_chr.bam_4 1 80 49 F 1 +input_single_chr.bam_4 1 80 50 F 1 +input_single_chr.bam_4 1 80 51 F 1 +input_single_chr.bam_4 1 80 52 F 1 +input_single_chr.bam_4 1 80 53 F 1 +input_single_chr.bam_4 1 80 54 F 1 +input_single_chr.bam_4 1 80 55 F 1 +input_single_chr.bam_4 1 80 56 F 1 +input_single_chr.bam_4 1 80 57 F 1 +input_single_chr.bam_4 1 80 58 F 1 +input_single_chr.bam_4 1 80 59 F 1 +input_single_chr.bam_4 1 80 60 F 1 +input_single_chr.bam_4 1 80 61 F 1 +input_single_chr.bam_4 1 80 62 F 1 +input_single_chr.bam_4 1 80 63 F 1 +input_single_chr.bam_4 1 80 64 F 1 +input_single_chr.bam_4 1 80 65 F 1 +input_single_chr.bam_4 1 80 66 F 1 +input_single_chr.bam_4 1 80 67 F 1 +input_single_chr.bam_4 1 80 68 F 1 +input_single_chr.bam_4 1 80 69 F 1 +input_single_chr.bam_4 1 80 70 F 1 +input_single_chr.bam_4 1 80 71 F 1 +input_single_chr.bam_4 1 80 72 F 1 +input_single_chr.bam_4 1 80 73 F 1 +input_single_chr.bam_4 1 80 74 F 1 +input_single_chr.bam_4 1 80 75 F 1 +input_single_chr.bam_4 1 80 76 F 1 +input_single_chr.bam_4 1 80 77 F 1 +input_single_chr.bam_4 1 80 78 F 1 +input_single_chr.bam_4 1 80 79 F 1 +input_single_chr.bam_4 1 80 80 F 1 +input_single_chr.bam_5 1 80 1 F 1 +input_single_chr.bam_5 1 80 2 F 1 +input_single_chr.bam_5 1 80 3 F 1 +input_single_chr.bam_5 1 80 4 F 1 +input_single_chr.bam_5 1 80 5 F 1 +input_single_chr.bam_5 1 80 6 F 1 +input_single_chr.bam_5 1 80 7 F 1 +input_single_chr.bam_5 1 80 8 F 1 +input_single_chr.bam_5 1 80 9 F 1 +input_single_chr.bam_5 1 80 10 F 1 +input_single_chr.bam_5 1 80 11 F 1 +input_single_chr.bam_5 1 80 12 F 1 +input_single_chr.bam_5 1 80 13 F 1 +input_single_chr.bam_5 1 80 14 F 1 +input_single_chr.bam_5 1 80 15 F 1 +input_single_chr.bam_5 1 80 16 F 1 +input_single_chr.bam_5 1 80 17 F 1 +input_single_chr.bam_5 1 80 18 F 1 +input_single_chr.bam_5 1 80 19 F 1 +input_single_chr.bam_5 1 80 20 F 1 +input_single_chr.bam_5 1 80 21 F 1 +input_single_chr.bam_5 1 80 22 F 1 +input_single_chr.bam_5 1 80 23 F 1 +input_single_chr.bam_5 1 80 24 F 1 +input_single_chr.bam_5 1 80 25 F 1 +input_single_chr.bam_5 1 80 26 F 1 +input_single_chr.bam_5 1 80 27 F 1 +input_single_chr.bam_5 1 80 28 F 1 +input_single_chr.bam_5 1 80 29 F 1 +input_single_chr.bam_5 1 80 30 F 1 +input_single_chr.bam_5 1 80 31 F 1 +input_single_chr.bam_5 1 80 32 F 1 +input_single_chr.bam_5 1 80 33 F 1 +input_single_chr.bam_5 1 80 34 F 1 +input_single_chr.bam_5 1 80 35 F 1 +input_single_chr.bam_5 1 80 36 F 1 +input_single_chr.bam_5 1 80 37 F 1 +input_single_chr.bam_5 1 80 38 F 1 +input_single_chr.bam_5 1 80 39 F 1 +input_single_chr.bam_5 1 80 40 F 1 +input_single_chr.bam_5 1 80 41 F 1 +input_single_chr.bam_5 1 80 42 F 1 +input_single_chr.bam_5 1 80 43 F 1 +input_single_chr.bam_5 1 80 44 F 1 +input_single_chr.bam_5 1 80 45 F 1 +input_single_chr.bam_5 1 80 46 F 1 +input_single_chr.bam_5 1 80 47 F 1 +input_single_chr.bam_5 1 80 48 F 1 +input_single_chr.bam_5 1 80 49 F 1 +input_single_chr.bam_5 1 80 50 F 1 +input_single_chr.bam_5 1 80 51 F 1 +input_single_chr.bam_5 1 80 52 F 1 +input_single_chr.bam_5 1 80 53 F 1 +input_single_chr.bam_5 1 80 54 F 1 +input_single_chr.bam_5 1 80 55 F 1 +input_single_chr.bam_5 1 80 56 F 1 +input_single_chr.bam_5 1 80 57 F 1 +input_single_chr.bam_5 1 80 58 F 1 +input_single_chr.bam_5 1 80 59 F 1 +input_single_chr.bam_5 1 80 60 F 1 +input_single_chr.bam_5 1 80 61 F 1 +input_single_chr.bam_5 1 80 62 F 1 +input_single_chr.bam_5 1 80 63 F 1 +input_single_chr.bam_5 1 80 64 F 1 +input_single_chr.bam_5 1 80 65 F 1 +input_single_chr.bam_5 1 80 66 F 1 +input_single_chr.bam_5 1 80 67 F 1 +input_single_chr.bam_5 1 80 68 F 1 +input_single_chr.bam_5 1 80 69 F 1 +input_single_chr.bam_5 1 80 70 F 1 +input_single_chr.bam_5 1 80 71 F 1 +input_single_chr.bam_5 1 80 72 F 1 +input_single_chr.bam_5 1 80 73 F 1 +input_single_chr.bam_5 1 80 74 F 1 +input_single_chr.bam_5 1 80 75 F 1 +input_single_chr.bam_5 1 80 76 F 1 +input_single_chr.bam_5 1 80 77 F 1 +input_single_chr.bam_5 1 80 78 F 1 +input_single_chr.bam_5 1 80 79 F 1 +input_single_chr.bam_5 1 80 80 F 1
--- a/test-data/mean.tab Tue Mar 06 06:11:55 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,617 +0,0 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Mean -input1.bam FBtr0070001 72 1 F 17.0 -input1.bam FBtr0070001 72 7 F 20.3 -input1.bam FBtr0070001 72 8 F 21.3 -input1.bam FBtr0070001 72 11 F 20.5 -input1.bam FBtr0070001 72 16 F 19.0 -input1.bam FBtr0070001 72 17 F 23.0 -input1.bam FBtr0070001 72 18 F 16.0 -input1.bam FBtr0070001 72 27 F 23.5 -input1.bam FBtr0070001 72 30 F 23.0 -input1.bam FBtr0070001 72 31 F 23.0 -input1.bam FBtr0070001 72 32 F 22.0 -input1.bam FBtr0070001 72 34 F 20.0 -input1.bam FBtr0070001 72 72 F 0 -input1.bam FBtr0070533 72 1 F 15.0 -input1.bam FBtr0070533 72 12 F 18.0 -input1.bam FBtr0070533 72 15 F 15.0 -input1.bam FBtr0070533 72 19 F 21.8 -input1.bam FBtr0070533 72 20 F 23.0 -input1.bam FBtr0070533 72 21 F 18.0 -input1.bam FBtr0070533 72 22 F 20.0 -input1.bam FBtr0070533 72 25 F 17.0 -input1.bam FBtr0070533 72 26 F 16.0 -input1.bam FBtr0070533 72 28 F 25.0 -input1.bam FBtr0070533 72 32 F 20.5 -input1.bam FBtr0070533 72 35 F 19.0 -input1.bam FBtr0070533 72 37 F 19.0 -input1.bam FBtr0070533 72 38 F 18.0 -input1.bam FBtr0070533 72 72 F 0 -input1.bam FBtr0070603 72 1 F 16.5 -input1.bam FBtr0070603 72 3 F 21.0 -input1.bam FBtr0070603 72 4 F 20.0 -input1.bam FBtr0070603 72 6 F 18.0 -input1.bam FBtr0070603 72 7 F 17.1 -input1.bam FBtr0070603 72 8 F 16.0 -input1.bam FBtr0070603 72 9 F 15.0 -input1.bam FBtr0070603 72 12 F 20.0 -input1.bam FBtr0070603 72 13 F 22.0 -input1.bam FBtr0070603 72 15 F 18.5 -input1.bam FBtr0070603 72 16 F 20.5 -input1.bam FBtr0070603 72 17 F 24.0 -input1.bam FBtr0070603 72 18 F 16.0 -input1.bam FBtr0070603 72 19 F 22.6 -input1.bam FBtr0070603 72 20 F 21.0 -input1.bam FBtr0070603 72 21 F 25.0 -input1.bam FBtr0070603 72 22 F 20.7 -input1.bam FBtr0070603 72 24 F 19.5 -input1.bam FBtr0070603 72 25 F 23.0 -input1.bam FBtr0070603 72 26 F 25.8 -input1.bam FBtr0070603 72 27 F 26.3 -input1.bam FBtr0070603 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