Mercurial > repos > artbio > small_rna_maps
changeset 32:f2e7ad3058e8 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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--- a/small_rna_maps.py Sun Oct 06 21:11:19 2019 -0400 +++ b/small_rna_maps.py Sun May 09 17:11:00 2021 +0000 @@ -319,8 +319,8 @@ Strandbias = round(strandness['F'] / float(Strandbias), 2) else: Strandbias = 2 - Mean = numpy.mean(sizeness.values()) - StDev = numpy.std(sizeness.values()) + Mean = numpy.mean(list(sizeness.values())) + StDev = numpy.std(list(sizeness.values())) for size in sizeness: if StDev: sizeness[size] = (sizeness[size] - Mean) / StDev
--- a/small_rna_maps.r Sun Oct 06 21:11:19 2019 -0400 +++ b/small_rna_maps.r Sun May 09 17:11:00 2021 +0000 @@ -1,6 +1,9 @@ ## Setup R error handling to go to stderr -options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = F, + error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) + } +) options(warn = -1) library(RColorBrewer) library(lattice) @@ -11,165 +14,164 @@ option_list <- list( - 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") + 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) +args <- parse_args(parser) # data frames implementation ## first table -Table = read.delim(args$first_dataframe, header=T, row.names=NULL) -colnames(Table)[1] <- "Dataset" +table <- read.delim(args$first_dataframe, header = T, row.names = NULL) +colnames(table)[1] <- "Dataset" dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility -Table <- Table[,!(names(Table) %in% dropcol)] +table <- table[, !(names(table) %in% dropcol)] 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) +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 + i <- 1 for (sample in samples) { - # Warning - # Here the column is hard coded as the last column (dangerous) + # Warning Here the column is hard coded as the last column (dangerous) # because its name changes with the method - Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i] - i = i + 1 + table[, length(table)][table$Dataset == sample] <- table[, length(table)][table$Dataset == sample] * norm_factors[i] + i <- i + 1 } } -genes=unique(Table$Chromosome) -per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x)) -per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) ) -n_genes=length(per_gene_readmap) +genes <- unique(table$Chromosome) +per_gene_readmap <- lapply(genes, function(x) subset(table, Chromosome == x)) +per_gene_limit <- lapply(genes, function(x) c(1, unique(subset(table, Chromosome == x)$Chrom_length))) +n_genes <- length(per_gene_readmap) # second table -if (args$extra_plot_method != '') { - ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL) - colnames(ExtraTable)[1] <- "Dataset" - dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility - Table <- Table[,!(names(Table) %in% dropcol)] - if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') { - ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) +if (args$extra_plot_method != "") { + extra_table <- read.delim(args$extra_dataframe, header = T, row.names = NULL) + colnames(extra_table)[1] <- "Dataset" + dropcol <- c("Strandness", "z.score") + table <- table[, !(names(table) %in% dropcol)] + if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size") { + extra_table <- within(extra_table, Counts[Polarity == "R"] <- (Counts[Polarity == "R"] * -1)) } if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") { - i = 1 + i <- 1 for (sample in samples) { - ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i] - i = i + 1 + extra_table[, length(extra_table)][extra_table$Dataset == sample] <- extra_table[, length(extra_table)][extra_table$Dataset == sample] * norm_factors[i] + i <- i + 1 } } - per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x)) + per_gene_size <- lapply(genes, function(x) subset(extra_table, Chromosome == x)) } ## functions -globalbc = function(df, global="", ...) { +globalbc <- function(df, global = "", ...) { if (global == "yes") { - bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), + bc <- barchart(Counts ~ as.factor(Size) | factor(Dataset, levels = unique(Dataset)), data = df, origin = 0, - horizontal=FALSE, - col=c("darkblue"), - scales=list(y=list(tick.number=4, rot=90, relation="same", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), - xlab=list(label=bottom_first_method[[args$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"), + horizontal = FALSE, + col = c("darkblue"), + scales = list(y = list(tick.number = 4, rot = 90, relation = "same", 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$first_plot_method]], + layout = c(2, 6), newpage = T, + as.table = TRUE, + aspect = 0.5, + strip = strip.custom(par.strip.text = list(cex = 1), which.given = 1, bg = "lightblue"), ... ) } else { - bc <- barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset)), + bc <- barchart(Counts ~ as.factor(Size) | factor(Dataset, levels = unique(Dataset)), data = df, origin = 0, - horizontal=FALSE, - group=Polarity, - stack=TRUE, - col=c('red', 'blue'), - scales=list(y=list(tick.number=4, rot=90, relation="same", cex=0.5, alternating=T), x=list(rot=0, cex=0.6, tck=0.5, alternating=c(3,3))), - xlab=list(label=bottom_first_method[[args$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"), + horizontal = FALSE, + group = Polarity, + stack = TRUE, + col = c("red", "blue"), + scales = list(y = list(tick.number = 4, rot = 90, relation = "same", 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 (exists('ymin', where=args)){ - min=args$ymin - }else{ - min='' +plot_unit <- function(df, method = args$first_plot_method, ...) { + if (exists("ymin", where = args)) { + min <- args$ymin + } else { + min <- "" } - if ((exists('ymax', where=args))){ - max=args$ymax - }else{ - max='' + 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, + 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), + horizontal = FALSE, + group = Polarity, + col = c("red", "blue"), + par.strip.text = list(cex = 0.7), ...) - p=combineLimits(p) + 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= ifelse(method=='Coverage', 'l', '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, ylim=ylimits, - as.table=T, + p <- xyplot(eval(as.name(method)) ~ Coordinate | factor(Dataset, levels = unique(Dataset)) + factor(Chromosome, levels = unique(Chromosome)), + data = df, + type = ifelse(method == "Coverage", "l", "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, ylim = ylimits, + as.table = T, origin = 0, - horizontal=FALSE, - group=Polarity, - col=c("red","blue"), - par.strip.text = list(cex=0.7), + horizontal = FALSE, + group = Polarity, + col = c("red", "blue"), + par.strip.text = list(cex = 0.7), ...) - p=combineLimits(p) + p <- combineLimits(p) } else { - p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0, - horizontal=FALSE, - group=Polarity, - stack=TRUE, - col=c('red', 'blue'), - scales=list(y=list(rot=90, relation="free", cex=0.7), x=list(rot=0, cex=0.7, axs="i", tck=c(1,0))), + 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), + as.table = TRUE, + par.strip.text = list(cex = 0.6), ...) - p=combineLimits(p) + p <- combineLimits(p) } return(p) } @@ -177,88 +179,95 @@ ## 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),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="Coverage depth", Median="Median size", Mean="Mean size", Size="Read count") -bottom_first_method =list(Counts="Coordinates (nucleotides)",Coverage="Coordinates (nucleotides)", Median="Coordinates (nucleotides)", Mean="Coordinates (nucleotides)", Size="Sizes of reads") -bottom_extra_method =list(Counts="Coordinates (nucleotides)",Coverage="Coordinates (nucleotides)", Median="Coordinates (nucleotides)", Mean="Coordinates (nucleotides)", Size="Sizes of reads") +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 = "Coverage depth", Median = "Median size", Mean = "Mean size", Size = "Read count") +bottom_first_method <- list(Counts = "Coordinates (nucleotides)", Coverage = "Coordinates (nucleotides)", Median = "Coordinates (nucleotides)", Mean = "Coordinates (nucleotides)", Size = "Sizes of reads") +bottom_extra_method <- list(Counts = "Coordinates (nucleotides)", Coverage = "Coordinates (nucleotides)", Median = "Coordinates (nucleotides)", Mean = "Coordinates (nucleotides)", 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) - 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$extra_plot_method]]), gp=gpar(cex=1), just="bottom", vjust=2) + page_height <- 15 + rows_per_page <- 10 + graph_heights <- c(40, 30, 40, 30, 40, 30, 40, 30, 40, 30, 10) + page_width <- 8.2677 * n_samples / 2 + pdf(file = args$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$extra_plot_method]]), gp = gpar(cex = 1), just = "bottom", vjust = 2) ) ) do.call(grid.arrange, args_list) } - devname=dev.off() + devname <- dev.off() } single_plot <- function(...) { - width = 8.2677 * n_samples / 2 - rows_per_page=8 - graph_heights=c(rep(40,8),10) - pdf(file=args$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) 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$first_plot_method]], gp=gpar(cex=1), just="bottom", vjust=2) + width <- 8.2677 * n_samples / 2 + rows_per_page <- 8 + graph_heights <- c(rep(40, 8), 10) + pdf(file = args$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$first_plot_method]], gp = gpar(cex = 1), just = "bottom", vjust = 2) ) ) do.call(grid.arrange, args_list) } - devname=dev.off() + devname <- dev.off() } # main -if (args$extra_plot_method != '') { double_plot() } -if (args$extra_plot_method == '' & !exists('global', where=args)) { +if (args$extra_plot_method != "") { + double_plot() +} +if (args$extra_plot_method == "" & !exists("global", where = args)) { single_plot() } -if (exists('global', where=args)) { - pdf(file=args$output, paper="special", height=11.69) - Table <- within(Table, Counts[Polarity=="R"] <- abs(Counts[Polarity=="R"])) # retropedalage +if (exists("global", where = args)) { + pdf(file = args$output, paper = "special", height = 11.69) + table <- within(table, Counts[Polarity == "R"] <- abs(Counts[Polarity == "R"])) library(reshape2) - ml = melt(Table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size")) + ml <- melt(table, id.vars = c("Dataset", "Chromosome", "Polarity", "Size")) if (args$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") + 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") + castml <- dcast(ml, Dataset + Size ~ variable, function(x) sum(x)) + bc <- globalbc(castml, global = "yes") } plot(bc) - devname=dev.off() + devname <- dev.off() } -
--- a/small_rna_maps.xml Sun Oct 06 21:11:19 2019 -0400 +++ b/small_rna_maps.xml Sun May 09 17:11:00 2021 +0000 @@ -1,15 +1,15 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="2.16.1"> +<tool id="small_rna_maps" name="small_rna_maps" version="3.0.0"> <description></description> <requirements> - <requirement type="package" version="1.11.2=py27_0">numpy</requirement> - <requirement type="package" version="0.15.3=py27hda2845c_1">pysam</requirement> - <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement> - <requirement type="package" version="0.6_28=r36h6115d3f_1002">r-latticeextra</requirement> - <requirement type="package" version="2.3=r36h6115d3f_1002">r-gridextra</requirement> - <requirement type="package" version="1.4.3=r36h29659fb_0">r-reshape2</requirement> - <requirement type="package" version="0.6.6">sambamba</requirement> - <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement> - <requirement type="package" version="64.2=he1b5a44_1">icu</requirement> + <requirement type="package" version="1.20.2=py38h9894fe3_0">numpy</requirement> + <requirement type="package" version="0.16.0.1=py38hbdc2ae9_1">pysam</requirement> + <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> + <requirement type="package" version="0.6_29=r40h6115d3f_1">r-latticeextra</requirement> + <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement> + <requirement type="package" version="1.4.4=r40h0357c0b_1">r-reshape2</requirement> + <requirement type="package" version="0.8.0=h984e79f_0">sambamba</requirement> + <requirement type="package" version="1.10=h2e538c0_3">samtools</requirement> + <requirement type="package" version="68.1=h58526e2_0">icu</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" />
--- a/test-data/bed1.bed Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/bed1.bed Sun May 09 17:11:00 2021 +0000 @@ -1,55 +1,55 @@ -FBtr0070001 6 39 cluster_1 12 + 0.363636363636 -FBtr0070001 26 53 cluster_2 42 + 1.55555555556 -FBtr0070533 18 41 cluster_3 7 + 0.304347826087 +FBtr0070001 6 39 cluster_1 12 + 0.36363636363636365 +FBtr0070001 26 53 cluster_2 42 + 1.5555555555555556 +FBtr0070533 18 41 cluster_3 7 + 0.30434782608695654 FBtr0070533 27 55 cluster_4 7 + 0.25 -FBtr0070603 0 23 cluster_5 2 + 0.0869565217391 -FBtr0070603 11 53 cluster_6 35 + 0.833333333333 -FBtr0070603 41 62 cluster_7 1 + 0.047619047619 -FBtr0070604 17 40 cluster_8 2 + 0.0869565217391 -FBtr0070604 30 53 cluster_9 34 + 1.47826086957 -FBtr0070911 14 35 cluster_10 1 + 0.047619047619 -FBtr0078490 27 50 cluster_11 1 + 0.0434782608696 -FBtr0078580 0 52 cluster_12 452 + 8.69230769231 -FBtr0078790 0 19 cluster_13 1 + 0.0526315789474 -FBtr0078790 32 55 cluster_14 1 + 0.0434782608696 -FBtr0078790 41 63 cluster_15 4 + 0.181818181818 +FBtr0070603 0 23 cluster_5 2 + 0.08695652173913043 +FBtr0070603 11 53 cluster_6 35 + 0.8333333333333334 +FBtr0070603 41 62 cluster_7 1 + 0.047619047619047616 +FBtr0070604 17 40 cluster_8 2 + 0.08695652173913043 +FBtr0070604 30 53 cluster_9 34 + 1.4782608695652173 +FBtr0070911 14 35 cluster_10 1 + 0.047619047619047616 +FBtr0078490 27 50 cluster_11 1 + 0.043478260869565216 +FBtr0078580 0 52 cluster_12 452 + 8.692307692307692 +FBtr0078790 0 19 cluster_13 1 + 0.05263157894736842 +FBtr0078790 32 55 cluster_14 1 + 0.043478260869565216 +FBtr0078790 41 63 cluster_15 4 + 0.18181818181818182 FBtr0078790 51 71 cluster_16 1 + 0.05 -FBtr0079064 0 23 cluster_17 1 + 0.0434782608696 -FBtr0079090 0 28 cluster_18 1 + 0.0357142857143 -FBtr0079090 25 49 cluster_19 1 + 0.0416666666667 -FBtr0079090 35 56 cluster_20 1 - 0.047619047619 -FBtr0079338 12 31 cluster_21 1 + 0.0526315789474 -FBtr0079338 41 63 cluster_22 9 + 0.409090909091 -FBtr0079528 0 38 cluster_23 77 + 2.02631578947 +FBtr0079064 0 23 cluster_17 1 + 0.043478260869565216 +FBtr0079090 0 28 cluster_18 1 + 0.03571428571428571 +FBtr0079090 25 49 cluster_19 1 + 0.041666666666666664 +FBtr0079090 35 56 cluster_20 1 - 0.047619047619047616 +FBtr0079338 12 31 cluster_21 1 + 0.05263157894736842 +FBtr0079338 41 63 cluster_22 9 + 0.4090909090909091 +FBtr0079528 0 38 cluster_23 77 + 2.026315789473684 FBtr0079528 35 55 cluster_24 1 + 0.05 -FBtr0079596 0 24 cluster_25 50 + 2.08333333333 -FBtr0079596 12 33 cluster_26 1 + 0.047619047619 -FBtr0079596 52 73 cluster_27 3 + 0.142857142857 -FBtr0079677 0 23 cluster_28 2 + 0.0869565217391 -FBtr0079677 51 70 cluster_29 1 + 0.0526315789474 +FBtr0079596 0 24 cluster_25 50 + 2.0833333333333335 +FBtr0079596 12 33 cluster_26 1 + 0.047619047619047616 +FBtr0079596 52 73 cluster_27 3 + 0.14285714285714285 +FBtr0079677 0 23 cluster_28 2 + 0.08695652173913043 +FBtr0079677 51 70 cluster_29 1 + 0.05263157894736842 FBtr0079690 26 51 cluster_30 1 + 0.04 -FBtr0079692 0 23 cluster_31 2 + 0.0869565217391 +FBtr0079692 0 23 cluster_31 2 + 0.08695652173913043 FBtr0079692 31 51 cluster_32 1 + 0.05 -FBtr0079693 0 24 cluster_33 1 + 0.0416666666667 -FBtr0079693 24 47 cluster_34 1 + 0.0434782608696 +FBtr0079693 0 24 cluster_33 1 + 0.041666666666666664 +FBtr0079693 24 47 cluster_34 1 + 0.043478260869565216 FBtr0079694 0 25 cluster_35 3 + 0.12 -FBtr0079694 17 36 cluster_36 1 + 0.0526315789474 +FBtr0079694 17 36 cluster_36 1 + 0.05263157894736842 FBtr0079728 7 27 cluster_37 1 + 0.05 -FBtr0079728 18 42 cluster_38 1 + 0.0416666666667 -FBtr0079729 12 34 cluster_39 1 + 0.0454545454545 -FBtr0079752 0 24 cluster_40 1 + 0.0416666666667 +FBtr0079728 18 42 cluster_38 1 + 0.041666666666666664 +FBtr0079729 12 34 cluster_39 1 + 0.045454545454545456 +FBtr0079752 0 24 cluster_40 1 + 0.041666666666666664 FBtr0079752 6 26 cluster_41 1 + 0.05 FBtr0079752 51 71 cluster_42 2 + 0.1 FBtr0079820 44 74 cluster_43 6 + 0.2 -FBtr0080609 0 23 cluster_44 17 + 0.739130434783 -FBtr0080609 11 44 cluster_45 6 + 0.181818181818 -FBtr0080609 41 62 cluster_46 1 + 0.047619047619 -FBtr0080644 0 27 cluster_47 2 + 0.0740740740741 -FBtr0080646 0 27 cluster_48 2 + 0.0740740740741 -FBtr0080647 0 27 cluster_49 2 + 0.0740740740741 -FBtr0080660 0 27 cluster_50 6 + 0.222222222222 -FBtr0080663 0 27 cluster_51 69 + 2.55555555556 -FBtr0080663 13 32 cluster_52 2 + 0.105263157895 +FBtr0080609 0 23 cluster_44 17 + 0.7391304347826086 +FBtr0080609 11 44 cluster_45 6 + 0.18181818181818182 +FBtr0080609 41 62 cluster_46 1 + 0.047619047619047616 +FBtr0080644 0 27 cluster_47 2 + 0.07407407407407407 +FBtr0080646 0 27 cluster_48 2 + 0.07407407407407407 +FBtr0080647 0 27 cluster_49 2 + 0.07407407407407407 +FBtr0080660 0 27 cluster_50 6 + 0.2222222222222222 +FBtr0080663 0 27 cluster_51 69 + 2.5555555555555554 +FBtr0080663 13 32 cluster_52 2 + 0.10526315789473684 FBtr0080663 50 70 cluster_53 1 + 0.05 -FBtr0080664 0 35 cluster_54 78 + 2.22857142857 -FBtr0080664 32 56 cluster_55 2 + 0.0833333333333 +FBtr0080664 0 35 cluster_54 78 + 2.2285714285714286 +FBtr0080664 32 56 cluster_55 2 + 0.08333333333333333
--- a/test-data/bed2.bed Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/bed2.bed Sun May 09 17:11:00 2021 +0000 @@ -1,55 +1,55 @@ -FBtr0070001 6 39 cluster_1 12 . 0.363636363636 -FBtr0070001 26 53 cluster_2 42 . 1.55555555556 -FBtr0070533 18 41 cluster_3 7 . 0.304347826087 +FBtr0070001 6 39 cluster_1 12 . 0.36363636363636365 +FBtr0070001 26 53 cluster_2 42 . 1.5555555555555556 +FBtr0070533 18 41 cluster_3 7 . 0.30434782608695654 FBtr0070533 27 55 cluster_4 7 . 0.25 -FBtr0070603 0 23 cluster_5 2 . 0.0869565217391 -FBtr0070603 11 53 cluster_6 35 . 0.833333333333 -FBtr0070603 41 62 cluster_7 1 . 0.047619047619 -FBtr0070604 17 40 cluster_8 2 . 0.0869565217391 -FBtr0070604 30 53 cluster_9 34 . 1.47826086957 -FBtr0070911 14 35 cluster_10 1 . 0.047619047619 -FBtr0078490 27 50 cluster_11 1 . 0.0434782608696 -FBtr0078580 0 52 cluster_12 452 . 8.69230769231 -FBtr0078790 0 19 cluster_13 1 . 0.0526315789474 -FBtr0078790 32 55 cluster_14 1 . 0.0434782608696 -FBtr0078790 41 63 cluster_15 4 . 0.181818181818 +FBtr0070603 0 23 cluster_5 2 . 0.08695652173913043 +FBtr0070603 11 53 cluster_6 35 . 0.8333333333333334 +FBtr0070603 41 62 cluster_7 1 . 0.047619047619047616 +FBtr0070604 17 40 cluster_8 2 . 0.08695652173913043 +FBtr0070604 30 53 cluster_9 34 . 1.4782608695652173 +FBtr0070911 14 35 cluster_10 1 . 0.047619047619047616 +FBtr0078490 27 50 cluster_11 1 . 0.043478260869565216 +FBtr0078580 0 52 cluster_12 452 . 8.692307692307692 +FBtr0078790 0 19 cluster_13 1 . 0.05263157894736842 +FBtr0078790 32 55 cluster_14 1 . 0.043478260869565216 +FBtr0078790 41 63 cluster_15 4 . 0.18181818181818182 FBtr0078790 51 71 cluster_16 1 . 0.05 -FBtr0079064 0 23 cluster_17 1 . 0.0434782608696 -FBtr0079090 0 28 cluster_18 1 . 0.0357142857143 -FBtr0079090 25 49 cluster_19 1 . 0.0416666666667 -FBtr0079090 35 56 cluster_20 1 . 0.047619047619 -FBtr0079338 12 31 cluster_21 1 . 0.0526315789474 -FBtr0079338 41 63 cluster_22 9 . 0.409090909091 -FBtr0079528 0 38 cluster_23 77 . 2.02631578947 +FBtr0079064 0 23 cluster_17 1 . 0.043478260869565216 +FBtr0079090 0 28 cluster_18 1 . 0.03571428571428571 +FBtr0079090 25 49 cluster_19 1 . 0.041666666666666664 +FBtr0079090 35 56 cluster_20 1 . 0.047619047619047616 +FBtr0079338 12 31 cluster_21 1 . 0.05263157894736842 +FBtr0079338 41 63 cluster_22 9 . 0.4090909090909091 +FBtr0079528 0 38 cluster_23 77 . 2.026315789473684 FBtr0079528 35 55 cluster_24 1 . 0.05 -FBtr0079596 0 24 cluster_25 50 . 2.08333333333 -FBtr0079596 12 33 cluster_26 1 . 0.047619047619 -FBtr0079596 52 73 cluster_27 3 . 0.142857142857 -FBtr0079677 0 23 cluster_28 2 . 0.0869565217391 -FBtr0079677 51 70 cluster_29 1 . 0.0526315789474 +FBtr0079596 0 24 cluster_25 50 . 2.0833333333333335 +FBtr0079596 12 33 cluster_26 1 . 0.047619047619047616 +FBtr0079596 52 73 cluster_27 3 . 0.14285714285714285 +FBtr0079677 0 23 cluster_28 2 . 0.08695652173913043 +FBtr0079677 51 70 cluster_29 1 . 0.05263157894736842 FBtr0079690 26 51 cluster_30 1 . 0.04 -FBtr0079692 0 23 cluster_31 2 . 0.0869565217391 +FBtr0079692 0 23 cluster_31 2 . 0.08695652173913043 FBtr0079692 31 51 cluster_32 1 . 0.05 -FBtr0079693 0 24 cluster_33 1 . 0.0416666666667 -FBtr0079693 24 47 cluster_34 1 . 0.0434782608696 +FBtr0079693 0 24 cluster_33 1 . 0.041666666666666664 +FBtr0079693 24 47 cluster_34 1 . 0.043478260869565216 FBtr0079694 0 25 cluster_35 3 . 0.12 -FBtr0079694 17 36 cluster_36 1 . 0.0526315789474 +FBtr0079694 17 36 cluster_36 1 . 0.05263157894736842 FBtr0079728 7 27 cluster_37 1 . 0.05 -FBtr0079728 18 42 cluster_38 1 . 0.0416666666667 -FBtr0079729 12 34 cluster_39 1 . 0.0454545454545 -FBtr0079752 0 24 cluster_40 1 . 0.0416666666667 +FBtr0079728 18 42 cluster_38 1 . 0.041666666666666664 +FBtr0079729 12 34 cluster_39 1 . 0.045454545454545456 +FBtr0079752 0 24 cluster_40 1 . 0.041666666666666664 FBtr0079752 6 26 cluster_41 1 . 0.05 FBtr0079752 51 71 cluster_42 2 . 0.1 FBtr0079820 44 74 cluster_43 6 . 0.2 -FBtr0080609 0 23 cluster_44 17 . 0.739130434783 -FBtr0080609 11 44 cluster_45 6 . 0.181818181818 -FBtr0080609 41 62 cluster_46 1 . 0.047619047619 -FBtr0080644 0 27 cluster_47 2 . 0.0740740740741 -FBtr0080646 0 27 cluster_48 2 . 0.0740740740741 -FBtr0080647 0 27 cluster_49 2 . 0.0740740740741 -FBtr0080660 0 27 cluster_50 6 . 0.222222222222 -FBtr0080663 0 27 cluster_51 69 . 2.55555555556 -FBtr0080663 13 32 cluster_52 2 . 0.105263157895 +FBtr0080609 0 23 cluster_44 17 . 0.7391304347826086 +FBtr0080609 11 44 cluster_45 6 . 0.18181818181818182 +FBtr0080609 41 62 cluster_46 1 . 0.047619047619047616 +FBtr0080644 0 27 cluster_47 2 . 0.07407407407407407 +FBtr0080646 0 27 cluster_48 2 . 0.07407407407407407 +FBtr0080647 0 27 cluster_49 2 . 0.07407407407407407 +FBtr0080660 0 27 cluster_50 6 . 0.2222222222222222 +FBtr0080663 0 27 cluster_51 69 . 2.5555555555555554 +FBtr0080663 13 32 cluster_52 2 . 0.10526315789473684 FBtr0080663 50 70 cluster_53 1 . 0.05 -FBtr0080664 0 35 cluster_54 78 . 2.22857142857 -FBtr0080664 32 56 cluster_55 2 . 0.0833333333333 +FBtr0080664 0 35 cluster_54 78 . 2.2285714285714286 +FBtr0080664 32 56 cluster_55 2 . 0.08333333333333333
--- a/test-data/bed3.bed Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/bed3.bed Sun May 09 17:11:00 2021 +0000 @@ -1,55 +1,55 @@ -FBtr0070001 6 39 cluster_1 12 + 0.363636363636 -FBtr0070001 26 53 cluster_2 42 + 1.55555555556 -FBtr0070533 18 41 cluster_3 7 + 0.304347826087 +FBtr0070001 6 39 cluster_1 12 + 0.36363636363636365 +FBtr0070001 26 53 cluster_2 42 + 1.5555555555555556 +FBtr0070533 18 41 cluster_3 7 + 0.30434782608695654 FBtr0070533 27 55 cluster_4 7 + 0.25 -FBtr0070603 0 23 cluster_5 2 + 0.0869565217391 -FBtr0070603 11 53 cluster_6 35 + 0.833333333333 -FBtr0070603 41 62 cluster_7 1 + 0.047619047619 -FBtr0070604 17 40 cluster_8 2 + 0.0869565217391 -FBtr0070604 30 53 cluster_9 34 + 1.47826086957 -FBtr0070911 14 35 cluster_10 1 + 0.047619047619 -FBtr0078490 27 50 cluster_11 1 + 0.0434782608696 -FBtr0078580 0 52 cluster_12 452 + 8.69230769231 -FBtr0078790 0 19 cluster_13 1 + 0.0526315789474 -FBtr0078790 32 55 cluster_14 1 + 0.0434782608696 -FBtr0078790 41 63 cluster_15 4 + 0.181818181818 +FBtr0070603 0 23 cluster_5 2 + 0.08695652173913043 +FBtr0070603 11 53 cluster_6 35 + 0.8333333333333334 +FBtr0070603 41 62 cluster_7 1 + 0.047619047619047616 +FBtr0070604 17 40 cluster_8 2 + 0.08695652173913043 +FBtr0070604 30 53 cluster_9 34 + 1.4782608695652173 +FBtr0070911 14 35 cluster_10 1 + 0.047619047619047616 +FBtr0078490 27 50 cluster_11 1 + 0.043478260869565216 +FBtr0078580 0 52 cluster_12 452 + 8.692307692307692 +FBtr0078790 0 19 cluster_13 1 + 0.05263157894736842 +FBtr0078790 32 55 cluster_14 1 + 0.043478260869565216 +FBtr0078790 41 63 cluster_15 4 + 0.18181818181818182 FBtr0078790 51 71 cluster_16 1 + 0.05 -FBtr0079064 0 23 cluster_17 1 + 0.0434782608696 -FBtr0079090 0 28 cluster_18 1 + 0.0357142857143 -FBtr0079090 25 49 cluster_19 1 + 0.0416666666667 -FBtr0079090 35 56 cluster_20 1 - 0.047619047619 -FBtr0079338 12 31 cluster_21 1 + 0.0526315789474 -FBtr0079338 41 63 cluster_22 9 + 0.409090909091 -FBtr0079528 0 38 cluster_23 77 + 2.02631578947 +FBtr0079064 0 23 cluster_17 1 + 0.043478260869565216 +FBtr0079090 0 28 cluster_18 1 + 0.03571428571428571 +FBtr0079090 25 49 cluster_19 1 + 0.041666666666666664 +FBtr0079090 35 56 cluster_20 1 - 0.047619047619047616 +FBtr0079338 12 31 cluster_21 1 + 0.05263157894736842 +FBtr0079338 41 63 cluster_22 9 + 0.4090909090909091 +FBtr0079528 0 38 cluster_23 77 + 2.026315789473684 FBtr0079528 35 55 cluster_24 1 + 0.05 -FBtr0079596 0 24 cluster_25 50 + 2.08333333333 -FBtr0079596 12 33 cluster_26 1 + 0.047619047619 -FBtr0079596 52 73 cluster_27 3 + 0.142857142857 -FBtr0079677 0 23 cluster_28 2 + 0.0869565217391 -FBtr0079677 51 70 cluster_29 1 + 0.0526315789474 +FBtr0079596 0 24 cluster_25 50 + 2.0833333333333335 +FBtr0079596 12 33 cluster_26 1 + 0.047619047619047616 +FBtr0079596 52 73 cluster_27 3 + 0.14285714285714285 +FBtr0079677 0 23 cluster_28 2 + 0.08695652173913043 +FBtr0079677 51 70 cluster_29 1 + 0.05263157894736842 FBtr0079690 26 51 cluster_30 1 + 0.04 -FBtr0079692 0 23 cluster_31 2 + 0.0869565217391 +FBtr0079692 0 23 cluster_31 2 + 0.08695652173913043 FBtr0079692 31 51 cluster_32 1 + 0.05 -FBtr0079693 0 24 cluster_33 1 + 0.0416666666667 -FBtr0079693 24 47 cluster_34 1 + 0.0434782608696 +FBtr0079693 0 24 cluster_33 1 + 0.041666666666666664 +FBtr0079693 24 47 cluster_34 1 + 0.043478260869565216 FBtr0079694 0 25 cluster_35 3 + 0.12 -FBtr0079694 17 36 cluster_36 1 + 0.0526315789474 +FBtr0079694 17 36 cluster_36 1 + 0.05263157894736842 FBtr0079728 7 27 cluster_37 1 + 0.05 -FBtr0079728 18 42 cluster_38 1 + 0.0416666666667 -FBtr0079729 12 34 cluster_39 1 + 0.0454545454545 -FBtr0079752 0 24 cluster_40 1 + 0.0416666666667 +FBtr0079728 18 42 cluster_38 1 + 0.041666666666666664 +FBtr0079729 12 34 cluster_39 1 + 0.045454545454545456 +FBtr0079752 0 24 cluster_40 1 + 0.041666666666666664 FBtr0079752 6 26 cluster_41 1 + 0.05 FBtr0079752 51 71 cluster_42 2 + 0.1 FBtr0079820 44 74 cluster_43 6 + 0.2 -FBtr0080609 0 23 cluster_44 17 + 0.739130434783 -FBtr0080609 11 44 cluster_45 6 + 0.181818181818 -FBtr0080609 41 62 cluster_46 1 + 0.047619047619 -FBtr0080644 0 27 cluster_47 2 + 0.0740740740741 -FBtr0080646 0 27 cluster_48 2 + 0.0740740740741 -FBtr0080647 0 27 cluster_49 2 + 0.0740740740741 -FBtr0080660 0 27 cluster_50 6 + 0.222222222222 -FBtr0080663 0 27 cluster_51 69 + 2.55555555556 -FBtr0080663 13 32 cluster_52 2 + 0.105263157895 +FBtr0080609 0 23 cluster_44 17 + 0.7391304347826086 +FBtr0080609 11 44 cluster_45 6 + 0.18181818181818182 +FBtr0080609 41 62 cluster_46 1 + 0.047619047619047616 +FBtr0080644 0 27 cluster_47 2 + 0.07407407407407407 +FBtr0080646 0 27 cluster_48 2 + 0.07407407407407407 +FBtr0080647 0 27 cluster_49 2 + 0.07407407407407407 +FBtr0080660 0 27 cluster_50 6 + 0.2222222222222222 +FBtr0080663 0 27 cluster_51 69 + 2.5555555555555554 +FBtr0080663 13 32 cluster_52 2 + 0.10526315789473684 FBtr0080663 50 70 cluster_53 1 + 0.05 -FBtr0080664 0 35 cluster_54 78 + 2.22857142857 -FBtr0080664 32 56 cluster_55 2 + 0.0833333333333 +FBtr0080664 0 35 cluster_54 78 + 2.2285714285714286 +FBtr0080664 32 56 cluster_55 2 + 0.08333333333333333
--- a/test-data/bed4.bed Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/bed4.bed Sun May 09 17:11:00 2021 +0000 @@ -1,7 +1,7 @@ -FBtr0070001 26 53 cluster_1 42 + 1.55555555556 -FBtr0070604 30 53 cluster_2 34 + 1.47826086957 -FBtr0078580 0 52 cluster_3 452 + 8.69230769231 -FBtr0079528 0 38 cluster_4 77 + 2.02631578947 -FBtr0079596 0 24 cluster_5 50 + 2.08333333333 -FBtr0080663 0 27 cluster_6 69 + 2.55555555556 -FBtr0080664 0 35 cluster_7 78 + 2.22857142857 +FBtr0070001 26 53 cluster_1 42 + 1.5555555555555556 +FBtr0070604 30 53 cluster_2 34 + 1.4782608695652173 +FBtr0078580 0 52 cluster_3 452 + 8.692307692307692 +FBtr0079528 0 38 cluster_4 77 + 2.026315789473684 +FBtr0079596 0 24 cluster_5 50 + 2.0833333333333335 +FBtr0080663 0 27 cluster_6 69 + 2.5555555555555554 +FBtr0080664 0 35 cluster_7 78 + 2.2285714285714286
--- a/test-data/bed5.bed Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/bed5.bed Sun May 09 17:11:00 2021 +0000 @@ -1,10 +1,10 @@ -FBtr0070001 26 53 cluster_1 42 . 1.55555555556 -FBtr0070603 11 53 cluster_2 35 . 0.833333333333 -FBtr0070604 30 53 cluster_3 34 . 1.47826086957 -FBtr0078580 0 52 cluster_4 452 . 8.69230769231 -FBtr0079338 41 63 cluster_5 9 . 0.409090909091 -FBtr0079528 0 38 cluster_6 77 . 2.02631578947 -FBtr0079596 0 24 cluster_7 50 . 2.08333333333 -FBtr0080609 0 23 cluster_8 17 . 0.739130434783 -FBtr0080663 0 27 cluster_9 69 . 2.55555555556 -FBtr0080664 0 35 cluster_10 78 . 2.22857142857 +FBtr0070001 26 53 cluster_1 42 . 1.5555555555555556 +FBtr0070603 11 53 cluster_2 35 . 0.8333333333333334 +FBtr0070604 30 53 cluster_3 34 . 1.4782608695652173 +FBtr0078580 0 52 cluster_4 452 . 8.692307692307692 +FBtr0079338 41 63 cluster_5 9 . 0.4090909090909091 +FBtr0079528 0 38 cluster_6 77 . 2.026315789473684 +FBtr0079596 0 24 cluster_7 50 . 2.0833333333333335 +FBtr0080609 0 23 cluster_8 17 . 0.7391304347826086 +FBtr0080663 0 27 cluster_9 69 . 2.5555555555555554 +FBtr0080664 0 35 cluster_10 78 . 2.2285714285714286
--- a/test-data/clustering.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/clustering.tab Sun May 09 17:11:00 2021 +0000 @@ -1,97 +1,97 @@ # Dataset Chromosome Chrom_length Coordinate Polarity Counts Start-End Cluster Size density -input1.bam FBtr0070001 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070001 72 12 F 12 7-39 33 0.363636363636 -input1.bam FBtr0070001 72 30 F 42 27-53 27 1.55555555556 -input1.bam FBtr0070001 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070533 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070533 72 20 F 7 19-41 23 0.304347826087 -input1.bam FBtr0070533 72 32 F 7 28-55 28 0.25 -input1.bam FBtr0070533 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070603 72 2 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0070603 72 23 F 35 12-53 42 0.833333333333 -input1.bam FBtr0070603 72 42 F 1 42-62 21 0.047619047619 -input1.bam FBtr0070603 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070604 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070604 72 20 F 2 18-40 23 0.0869565217391 -input1.bam FBtr0070604 72 31 F 34 31-53 23 1.47826086957 -input1.bam FBtr0070604 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070911 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0070911 73 15 F 1 15-35 21 0.047619047619 -input1.bam FBtr0070911 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0078490 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0078490 72 28 F 1 28-50 23 0.0434782608696 -input1.bam FBtr0078490 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078580 72 13 F 452 1-52 52 8.69230769231 -input1.bam FBtr0078580 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078790 73 1 F 1 1-19 19 0.0526315789474 -input1.bam FBtr0078790 73 33 F 1 33-55 23 0.0434782608696 -input1.bam FBtr0078790 73 43 F 4 42-63 22 0.181818181818 -input1.bam FBtr0078790 73 52 F 1 52-71 20 0.05 -input1.bam FBtr0078790 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079064 72 2 F 1 1-23 23 0.0434782608696 -input1.bam FBtr0079064 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079090 72 1 F 1 1-28 28 0.0357142857143 -input1.bam FBtr0079090 72 26 F 1 26-49 24 0.0416666666667 -input1.bam FBtr0079090 72 56 R 1 36-56 21 0.047619047619 -input1.bam FBtr0079090 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079338 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0079338 73 13 F 1 13-31 19 0.0526315789474 -input1.bam FBtr0079338 73 42 F 9 42-63 22 0.409090909091 -input1.bam FBtr0079338 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079528 71 9 F 77 1-38 38 2.02631578947 -input1.bam FBtr0079528 71 36 F 1 36-55 20 0.05 -input1.bam FBtr0079528 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0079596 73 3 F 50 1-24 24 2.08333333333 -input1.bam FBtr0079596 73 13 F 1 13-33 21 0.047619047619 -input1.bam FBtr0079596 73 53 F 3 53-73 21 0.142857142857 -input1.bam FBtr0079596 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079677 72 3 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0079677 72 52 F 1 52-70 19 0.0526315789474 -input1.bam FBtr0079677 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079690 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079690 72 27 F 1 27-51 25 0.04 -input1.bam FBtr0079690 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079692 73 1 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0079692 73 32 F 1 32-51 20 0.05 -input1.bam FBtr0079692 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079693 72 1 F 1 1-24 24 0.0416666666667 -input1.bam FBtr0079693 72 25 F 1 25-47 23 0.0434782608696 -input1.bam FBtr0079693 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079694 72 1 F 3 1-25 25 0.12 -input1.bam FBtr0079694 72 18 F 1 18-36 19 0.0526315789474 -input1.bam FBtr0079694 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079702 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079702 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079728 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079728 72 8 F 1 8-27 20 0.05 -input1.bam FBtr0079728 72 19 F 1 19-42 24 0.0416666666667 -input1.bam FBtr0079728 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079729 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079729 72 13 F 1 13-34 22 0.0454545454545 -input1.bam FBtr0079729 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079752 72 1 F 1 1-24 24 0.0416666666667 -input1.bam FBtr0079752 72 7 F 1 7-26 20 0.05 -input1.bam FBtr0079752 72 52 F 2 52-71 20 0.1 -input1.bam FBtr0079752 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079820 74 1 F 0 1-1 1 0.0 -input1.bam FBtr0079820 74 50 F 6 45-74 30 0.2 -input1.bam FBtr0079820 74 74 F 0 74-74 1 0.0 -input1.bam FBtr0080609 72 3 F 17 1-23 23 0.739130434783 -input1.bam FBtr0080609 72 16 F 6 12-44 33 0.181818181818 -input1.bam FBtr0080609 72 42 F 1 42-62 21 0.047619047619 -input1.bam FBtr0080609 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080644 72 2 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080644 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080646 72 4 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080646 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080647 72 4 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080647 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080660 72 4 F 6 1-27 27 0.222222222222 -input1.bam FBtr0080660 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080663 71 4 F 69 1-27 27 2.55555555556 -input1.bam FBtr0080663 71 14 F 2 14-32 19 0.105263157895 -input1.bam FBtr0080663 71 51 F 1 51-70 20 0.05 -input1.bam FBtr0080663 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0080664 71 9 F 78 1-35 35 2.22857142857 -input1.bam FBtr0080664 71 34 F 2 33-56 24 0.0833333333333 -input1.bam FBtr0080664 71 71 F 0 71-71 1 0.0 +input1.bam FBtr0070001 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070001 72 12.0 F 12 7-39 33 0.36363636363636365 +input1.bam FBtr0070001 72 30.5 F 42 27-53 27 1.5555555555555556 +input1.bam FBtr0070001 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070533 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070533 72 20.5 F 7 19-41 23 0.30434782608695654 +input1.bam FBtr0070533 72 32.5 F 7 28-55 28 0.25 +input1.bam FBtr0070533 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070603 72 2.5 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0070603 72 23.0 F 35 12-53 42 0.8333333333333334 +input1.bam FBtr0070603 72 42.0 F 1 42-62 21 0.047619047619047616 +input1.bam FBtr0070603 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070604 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070604 72 20.0 F 2 18-40 23 0.08695652173913043 +input1.bam FBtr0070604 72 31.5 F 34 31-53 23 1.4782608695652173 +input1.bam FBtr0070604 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070911 73 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070911 73 15.0 F 1 15-35 21 0.047619047619047616 +input1.bam FBtr0070911 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0078490 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0078490 72 28.0 F 1 28-50 23 0.043478260869565216 +input1.bam FBtr0078490 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0078580 72 13.0 F 452 1-52 52 8.692307692307692 +input1.bam FBtr0078580 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0078790 73 1.0 F 1 1-19 19 0.05263157894736842 +input1.bam FBtr0078790 73 33.0 F 1 33-55 23 0.043478260869565216 +input1.bam FBtr0078790 73 43.0 F 4 42-63 22 0.18181818181818182 +input1.bam FBtr0078790 73 52.0 F 1 52-71 20 0.05 +input1.bam FBtr0078790 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079064 72 2.0 F 1 1-23 23 0.043478260869565216 +input1.bam FBtr0079064 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079090 72 1.0 F 1 1-28 28 0.03571428571428571 +input1.bam FBtr0079090 72 26.0 F 1 26-49 24 0.041666666666666664 +input1.bam FBtr0079090 72 56.0 R 1 36-56 21 0.047619047619047616 +input1.bam FBtr0079090 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079338 73 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079338 73 13.0 F 1 13-31 19 0.05263157894736842 +input1.bam FBtr0079338 73 42.5 F 9 42-63 22 0.4090909090909091 +input1.bam FBtr0079338 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079528 71 9.5 F 77 1-38 38 2.026315789473684 +input1.bam FBtr0079528 71 36.0 F 1 36-55 20 0.05 +input1.bam FBtr0079528 71 71.0 F 0 71-71 1 0.0 +input1.bam FBtr0079596 73 3.5 F 50 1-24 24 2.0833333333333335 +input1.bam FBtr0079596 73 13.0 F 1 13-33 21 0.047619047619047616 +input1.bam FBtr0079596 73 53.5 F 3 53-73 21 0.14285714285714285 +input1.bam FBtr0079596 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079677 72 3.0 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0079677 72 52.0 F 1 52-70 19 0.05263157894736842 +input1.bam FBtr0079677 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079690 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079690 72 27.0 F 1 27-51 25 0.04 +input1.bam FBtr0079690 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079692 73 1.0 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0079692 73 32.0 F 1 32-51 20 0.05 +input1.bam FBtr0079692 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079693 72 1.0 F 1 1-24 24 0.041666666666666664 +input1.bam FBtr0079693 72 25.0 F 1 25-47 23 0.043478260869565216 +input1.bam FBtr0079693 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079694 72 1.0 F 3 1-25 25 0.12 +input1.bam FBtr0079694 72 18.0 F 1 18-36 19 0.05263157894736842 +input1.bam FBtr0079694 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079702 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079702 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079728 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079728 72 8.0 F 1 8-27 20 0.05 +input1.bam FBtr0079728 72 19.0 F 1 19-42 24 0.041666666666666664 +input1.bam FBtr0079728 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079729 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079729 72 13.0 F 1 13-34 22 0.045454545454545456 +input1.bam FBtr0079729 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079752 72 1.0 F 1 1-24 24 0.041666666666666664 +input1.bam FBtr0079752 72 7.0 F 1 7-26 20 0.05 +input1.bam FBtr0079752 72 52.0 F 2 52-71 20 0.1 +input1.bam FBtr0079752 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079820 74 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079820 74 50.5 F 6 45-74 30 0.2 +input1.bam FBtr0079820 74 74.0 F 0 74-74 1 0.0 +input1.bam FBtr0080609 72 3.0 F 17 1-23 23 0.7391304347826086 +input1.bam FBtr0080609 72 16.0 F 6 12-44 33 0.18181818181818182 +input1.bam FBtr0080609 72 42.0 F 1 42-62 21 0.047619047619047616 +input1.bam FBtr0080609 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080644 72 2.5 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080644 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080646 72 4.0 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080646 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080647 72 4.5 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080647 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080660 72 4.0 F 6 1-27 27 0.2222222222222222 +input1.bam FBtr0080660 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080663 71 4.5 F 69 1-27 27 2.5555555555555554 +input1.bam FBtr0080663 71 14.0 F 2 14-32 19 0.10526315789473684 +input1.bam FBtr0080663 71 51.0 F 1 51-70 20 0.05 +input1.bam FBtr0080663 71 71.0 F 0 71-71 1 0.0 +input1.bam FBtr0080664 71 9.0 F 78 1-35 35 2.2285714285714286 +input1.bam FBtr0080664 71 34.5 F 2 33-56 24 0.08333333333333333 +input1.bam FBtr0080664 71 71.0 F 0 71-71 1 0.0
--- a/test-data/clustering_unstranded.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/clustering_unstranded.tab Sun May 09 17:11:00 2021 +0000 @@ -1,97 +1,97 @@ # Dataset Chromosome Chrom_length Coordinate Polarity Counts Start-End Cluster Size density -input1.bam FBtr0070001 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070001 72 12 F 12 7-39 33 0.363636363636 -input1.bam FBtr0070001 72 30 F 42 27-53 27 1.55555555556 -input1.bam FBtr0070001 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070533 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070533 72 20 F 7 19-41 23 0.304347826087 -input1.bam FBtr0070533 72 32 F 7 28-55 28 0.25 -input1.bam FBtr0070533 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070603 72 2 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0070603 72 23 F 35 12-53 42 0.833333333333 -input1.bam FBtr0070603 72 42 F 1 42-62 21 0.047619047619 -input1.bam FBtr0070603 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070604 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0070604 72 20 F 2 18-40 23 0.0869565217391 -input1.bam FBtr0070604 72 31 F 34 31-53 23 1.47826086957 -input1.bam FBtr0070604 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0070911 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0070911 73 15 F 1 15-35 21 0.047619047619 -input1.bam FBtr0070911 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0078490 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0078490 72 28 F 1 28-50 23 0.0434782608696 -input1.bam FBtr0078490 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078580 72 13 F 452 1-52 52 8.69230769231 -input1.bam FBtr0078580 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0078790 73 1 F 1 1-19 19 0.0526315789474 -input1.bam FBtr0078790 73 33 F 1 33-55 23 0.0434782608696 -input1.bam FBtr0078790 73 43 F 4 42-63 22 0.181818181818 -input1.bam FBtr0078790 73 52 F 1 52-71 20 0.05 -input1.bam FBtr0078790 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079064 72 2 F 1 1-23 23 0.0434782608696 -input1.bam FBtr0079064 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079090 72 1 F 1 1-28 28 0.0357142857143 -input1.bam FBtr0079090 72 26 F 1 26-49 24 0.0416666666667 -input1.bam FBtr0079090 72 36 F 1 36-56 21 0.047619047619 -input1.bam FBtr0079090 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079338 73 1 F 0 1-1 1 0.0 -input1.bam FBtr0079338 73 13 F 1 13-31 19 0.0526315789474 -input1.bam FBtr0079338 73 42 F 9 42-63 22 0.409090909091 -input1.bam FBtr0079338 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079528 71 9 F 77 1-38 38 2.02631578947 -input1.bam FBtr0079528 71 36 F 1 36-55 20 0.05 -input1.bam FBtr0079528 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0079596 73 3 F 50 1-24 24 2.08333333333 -input1.bam FBtr0079596 73 13 F 1 13-33 21 0.047619047619 -input1.bam FBtr0079596 73 53 F 3 53-73 21 0.142857142857 -input1.bam FBtr0079596 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079677 72 3 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0079677 72 52 F 1 52-70 19 0.0526315789474 -input1.bam FBtr0079677 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079690 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079690 72 27 F 1 27-51 25 0.04 -input1.bam FBtr0079690 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079692 73 1 F 2 1-23 23 0.0869565217391 -input1.bam FBtr0079692 73 32 F 1 32-51 20 0.05 -input1.bam FBtr0079692 73 73 F 0 73-73 1 0.0 -input1.bam FBtr0079693 72 1 F 1 1-24 24 0.0416666666667 -input1.bam FBtr0079693 72 25 F 1 25-47 23 0.0434782608696 -input1.bam FBtr0079693 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079694 72 1 F 3 1-25 25 0.12 -input1.bam FBtr0079694 72 18 F 1 18-36 19 0.0526315789474 -input1.bam FBtr0079694 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079702 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079702 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079728 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079728 72 8 F 1 8-27 20 0.05 -input1.bam FBtr0079728 72 19 F 1 19-42 24 0.0416666666667 -input1.bam FBtr0079728 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079729 72 1 F 0 1-1 1 0.0 -input1.bam FBtr0079729 72 13 F 1 13-34 22 0.0454545454545 -input1.bam FBtr0079729 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079752 72 1 F 1 1-24 24 0.0416666666667 -input1.bam FBtr0079752 72 7 F 1 7-26 20 0.05 -input1.bam FBtr0079752 72 52 F 2 52-71 20 0.1 -input1.bam FBtr0079752 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0079820 74 1 F 0 1-1 1 0.0 -input1.bam FBtr0079820 74 50 F 6 45-74 30 0.2 -input1.bam FBtr0079820 74 74 F 0 74-74 1 0.0 -input1.bam FBtr0080609 72 3 F 17 1-23 23 0.739130434783 -input1.bam FBtr0080609 72 16 F 6 12-44 33 0.181818181818 -input1.bam FBtr0080609 72 42 F 1 42-62 21 0.047619047619 -input1.bam FBtr0080609 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080644 72 2 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080644 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080646 72 4 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080646 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080647 72 4 F 2 1-27 27 0.0740740740741 -input1.bam FBtr0080647 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080660 72 4 F 6 1-27 27 0.222222222222 -input1.bam FBtr0080660 72 72 F 0 72-72 1 0.0 -input1.bam FBtr0080663 71 4 F 69 1-27 27 2.55555555556 -input1.bam FBtr0080663 71 14 F 2 14-32 19 0.105263157895 -input1.bam FBtr0080663 71 51 F 1 51-70 20 0.05 -input1.bam FBtr0080663 71 71 F 0 71-71 1 0.0 -input1.bam FBtr0080664 71 9 F 78 1-35 35 2.22857142857 -input1.bam FBtr0080664 71 34 F 2 33-56 24 0.0833333333333 -input1.bam FBtr0080664 71 71 F 0 71-71 1 0.0 +input1.bam FBtr0070001 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070001 72 12.0 F 12 7-39 33 0.36363636363636365 +input1.bam FBtr0070001 72 30.5 F 42 27-53 27 1.5555555555555556 +input1.bam FBtr0070001 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070533 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070533 72 20.5 F 7 19-41 23 0.30434782608695654 +input1.bam FBtr0070533 72 32.5 F 7 28-55 28 0.25 +input1.bam FBtr0070533 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070603 72 2.5 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0070603 72 23.0 F 35 12-53 42 0.8333333333333334 +input1.bam FBtr0070603 72 42.0 F 1 42-62 21 0.047619047619047616 +input1.bam FBtr0070603 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070604 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070604 72 20.0 F 2 18-40 23 0.08695652173913043 +input1.bam FBtr0070604 72 31.5 F 34 31-53 23 1.4782608695652173 +input1.bam FBtr0070604 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0070911 73 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0070911 73 15.0 F 1 15-35 21 0.047619047619047616 +input1.bam FBtr0070911 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0078490 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0078490 72 28.0 F 1 28-50 23 0.043478260869565216 +input1.bam FBtr0078490 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0078580 72 13.0 F 452 1-52 52 8.692307692307692 +input1.bam FBtr0078580 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0078790 73 1.0 F 1 1-19 19 0.05263157894736842 +input1.bam FBtr0078790 73 33.0 F 1 33-55 23 0.043478260869565216 +input1.bam FBtr0078790 73 43.0 F 4 42-63 22 0.18181818181818182 +input1.bam FBtr0078790 73 52.0 F 1 52-71 20 0.05 +input1.bam FBtr0078790 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079064 72 2.0 F 1 1-23 23 0.043478260869565216 +input1.bam FBtr0079064 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079090 72 1.0 F 1 1-28 28 0.03571428571428571 +input1.bam FBtr0079090 72 26.0 F 1 26-49 24 0.041666666666666664 +input1.bam FBtr0079090 72 36.0 F 1 36-56 21 0.047619047619047616 +input1.bam FBtr0079090 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079338 73 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079338 73 13.0 F 1 13-31 19 0.05263157894736842 +input1.bam FBtr0079338 73 42.5 F 9 42-63 22 0.4090909090909091 +input1.bam FBtr0079338 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079528 71 9.5 F 77 1-38 38 2.026315789473684 +input1.bam FBtr0079528 71 36.0 F 1 36-55 20 0.05 +input1.bam FBtr0079528 71 71.0 F 0 71-71 1 0.0 +input1.bam FBtr0079596 73 3.5 F 50 1-24 24 2.0833333333333335 +input1.bam FBtr0079596 73 13.0 F 1 13-33 21 0.047619047619047616 +input1.bam FBtr0079596 73 53.5 F 3 53-73 21 0.14285714285714285 +input1.bam FBtr0079596 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079677 72 3.0 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0079677 72 52.0 F 1 52-70 19 0.05263157894736842 +input1.bam FBtr0079677 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079690 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079690 72 27.0 F 1 27-51 25 0.04 +input1.bam FBtr0079690 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079692 73 1.0 F 2 1-23 23 0.08695652173913043 +input1.bam FBtr0079692 73 32.0 F 1 32-51 20 0.05 +input1.bam FBtr0079692 73 73.0 F 0 73-73 1 0.0 +input1.bam FBtr0079693 72 1.0 F 1 1-24 24 0.041666666666666664 +input1.bam FBtr0079693 72 25.0 F 1 25-47 23 0.043478260869565216 +input1.bam FBtr0079693 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079694 72 1.0 F 3 1-25 25 0.12 +input1.bam FBtr0079694 72 18.0 F 1 18-36 19 0.05263157894736842 +input1.bam FBtr0079694 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079702 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079702 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079728 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079728 72 8.0 F 1 8-27 20 0.05 +input1.bam FBtr0079728 72 19.0 F 1 19-42 24 0.041666666666666664 +input1.bam FBtr0079728 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079729 72 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079729 72 13.0 F 1 13-34 22 0.045454545454545456 +input1.bam FBtr0079729 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079752 72 1.0 F 1 1-24 24 0.041666666666666664 +input1.bam FBtr0079752 72 7.0 F 1 7-26 20 0.05 +input1.bam FBtr0079752 72 52.0 F 2 52-71 20 0.1 +input1.bam FBtr0079752 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0079820 74 1.0 F 0 1-1 1 0.0 +input1.bam FBtr0079820 74 50.5 F 6 45-74 30 0.2 +input1.bam FBtr0079820 74 74.0 F 0 74-74 1 0.0 +input1.bam FBtr0080609 72 3.0 F 17 1-23 23 0.7391304347826086 +input1.bam FBtr0080609 72 16.0 F 6 12-44 33 0.18181818181818182 +input1.bam FBtr0080609 72 42.0 F 1 42-62 21 0.047619047619047616 +input1.bam FBtr0080609 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080644 72 2.5 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080644 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080646 72 4.0 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080646 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080647 72 4.5 F 2 1-27 27 0.07407407407407407 +input1.bam FBtr0080647 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080660 72 4.0 F 6 1-27 27 0.2222222222222222 +input1.bam FBtr0080660 72 72.0 F 0 72-72 1 0.0 +input1.bam FBtr0080663 71 4.5 F 69 1-27 27 2.5555555555555554 +input1.bam FBtr0080663 71 14.0 F 2 14-32 19 0.10526315789473684 +input1.bam FBtr0080663 71 51.0 F 1 51-70 20 0.05 +input1.bam FBtr0080663 71 71.0 F 0 71-71 1 0.0 +input1.bam FBtr0080664 71 9.0 F 78 1-35 35 2.2285714285714286 +input1.bam FBtr0080664 71 34.5 F 2 33-56 24 0.08333333333333333 +input1.bam FBtr0080664 71 71.0 F 0 71-71 1 0.0
--- a/test-data/input1_input2_size.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/input1_input2_size.tab Sun May 09 17:11:00 2021 +0000 @@ -208,17 +208,17 @@ input1.bam FBtr0079694 F 27 0 1.0 -0.756 input1.bam FBtr0079694 F 28 0 1.0 -0.756 input1.bam FBtr0079694 F 29 0 1.0 -0.756 -input1.bam FBtr0079702 F 19 0 2 0.0 -input1.bam FBtr0079702 F 20 0 2 0.0 -input1.bam FBtr0079702 F 21 0 2 0.0 -input1.bam FBtr0079702 F 22 0 2 0.0 -input1.bam FBtr0079702 F 23 0 2 0.0 -input1.bam FBtr0079702 F 24 0 2 0.0 -input1.bam FBtr0079702 F 25 0 2 0.0 -input1.bam FBtr0079702 F 26 0 2 0.0 -input1.bam FBtr0079702 F 27 0 2 0.0 -input1.bam FBtr0079702 F 28 0 2 0.0 -input1.bam FBtr0079702 F 29 0 2 0.0 +input1.bam FBtr0079702 F 19 0 2 0 +input1.bam FBtr0079702 F 20 0 2 0 +input1.bam FBtr0079702 F 21 0 2 0 +input1.bam FBtr0079702 F 22 0 2 0 +input1.bam FBtr0079702 F 23 0 2 0 +input1.bam FBtr0079702 F 24 0 2 0 +input1.bam FBtr0079702 F 25 0 2 0 +input1.bam FBtr0079702 F 26 0 2 0 +input1.bam FBtr0079702 F 27 0 2 0 +input1.bam FBtr0079702 F 28 0 2 0 +input1.bam FBtr0079702 F 29 0 2 0 input1.bam FBtr0079728 F 19 0 1.0 -0.471 input1.bam FBtr0079728 F 20 1 1.0 2.121 input1.bam FBtr0079728 F 21 0 1.0 -0.471 @@ -428,17 +428,17 @@ input2.bam FBtr0078790 F 27 0 1.0 -0.566 input2.bam FBtr0078790 F 28 0 1.0 -0.566 input2.bam FBtr0078790 F 29 0 1.0 -0.566 -input2.bam FBtr0079064 F 19 0 2 0.0 -input2.bam FBtr0079064 F 20 0 2 0.0 -input2.bam FBtr0079064 F 21 0 2 0.0 -input2.bam FBtr0079064 F 22 0 2 0.0 -input2.bam FBtr0079064 F 23 0 2 0.0 -input2.bam FBtr0079064 F 24 0 2 0.0 -input2.bam FBtr0079064 F 25 0 2 0.0 -input2.bam FBtr0079064 F 26 0 2 0.0 -input2.bam FBtr0079064 F 27 0 2 0.0 -input2.bam FBtr0079064 F 28 0 2 0.0 -input2.bam FBtr0079064 F 29 0 2 0.0 +input2.bam FBtr0079064 F 19 0 2 0 +input2.bam FBtr0079064 F 20 0 2 0 +input2.bam FBtr0079064 F 21 0 2 0 +input2.bam FBtr0079064 F 22 0 2 0 +input2.bam FBtr0079064 F 23 0 2 0 +input2.bam FBtr0079064 F 24 0 2 0 +input2.bam FBtr0079064 F 25 0 2 0 +input2.bam FBtr0079064 F 26 0 2 0 +input2.bam FBtr0079064 F 27 0 2 0 +input2.bam FBtr0079064 F 28 0 2 0 +input2.bam FBtr0079064 F 29 0 2 0 input2.bam FBtr0079090 F 19 0 1.0 -0.316 input2.bam FBtr0079090 F 20 0 1.0 -0.316 input2.bam FBtr0079090 F 21 1 1.0 3.162 @@ -549,39 +549,39 @@ input2.bam FBtr0079694 F 27 0 1.0 -0.316 input2.bam FBtr0079694 F 28 0 1.0 -0.316 input2.bam FBtr0079694 F 29 0 1.0 -0.316 -input2.bam FBtr0079702 F 19 0 2 0.0 -input2.bam FBtr0079702 F 20 0 2 0.0 -input2.bam FBtr0079702 F 21 0 2 0.0 -input2.bam FBtr0079702 F 22 0 2 0.0 -input2.bam FBtr0079702 F 23 0 2 0.0 -input2.bam FBtr0079702 F 24 0 2 0.0 -input2.bam FBtr0079702 F 25 0 2 0.0 -input2.bam FBtr0079702 F 26 0 2 0.0 -input2.bam FBtr0079702 F 27 0 2 0.0 -input2.bam FBtr0079702 F 28 0 2 0.0 -input2.bam FBtr0079702 F 29 0 2 0.0 -input2.bam FBtr0079728 F 19 0 2 0.0 -input2.bam FBtr0079728 F 20 0 2 0.0 -input2.bam FBtr0079728 F 21 0 2 0.0 -input2.bam FBtr0079728 F 22 0 2 0.0 -input2.bam FBtr0079728 F 23 0 2 0.0 -input2.bam FBtr0079728 F 24 0 2 0.0 -input2.bam FBtr0079728 F 25 0 2 0.0 -input2.bam FBtr0079728 F 26 0 2 0.0 -input2.bam FBtr0079728 F 27 0 2 0.0 -input2.bam FBtr0079728 F 28 0 2 0.0 -input2.bam FBtr0079728 F 29 0 2 0.0 -input2.bam FBtr0079729 F 19 0 2 0.0 -input2.bam FBtr0079729 F 20 0 2 0.0 -input2.bam FBtr0079729 F 21 0 2 0.0 -input2.bam FBtr0079729 F 22 0 2 0.0 -input2.bam FBtr0079729 F 23 0 2 0.0 -input2.bam FBtr0079729 F 24 0 2 0.0 -input2.bam FBtr0079729 F 25 0 2 0.0 -input2.bam FBtr0079729 F 26 0 2 0.0 -input2.bam FBtr0079729 F 27 0 2 0.0 -input2.bam FBtr0079729 F 28 0 2 0.0 -input2.bam FBtr0079729 F 29 0 2 0.0 +input2.bam FBtr0079702 F 19 0 2 0 +input2.bam FBtr0079702 F 20 0 2 0 +input2.bam FBtr0079702 F 21 0 2 0 +input2.bam FBtr0079702 F 22 0 2 0 +input2.bam FBtr0079702 F 23 0 2 0 +input2.bam FBtr0079702 F 24 0 2 0 +input2.bam FBtr0079702 F 25 0 2 0 +input2.bam FBtr0079702 F 26 0 2 0 +input2.bam FBtr0079702 F 27 0 2 0 +input2.bam FBtr0079702 F 28 0 2 0 +input2.bam FBtr0079702 F 29 0 2 0 +input2.bam FBtr0079728 F 19 0 2 0 +input2.bam FBtr0079728 F 20 0 2 0 +input2.bam FBtr0079728 F 21 0 2 0 +input2.bam FBtr0079728 F 22 0 2 0 +input2.bam FBtr0079728 F 23 0 2 0 +input2.bam FBtr0079728 F 24 0 2 0 +input2.bam FBtr0079728 F 25 0 2 0 +input2.bam FBtr0079728 F 26 0 2 0 +input2.bam FBtr0079728 F 27 0 2 0 +input2.bam FBtr0079728 F 28 0 2 0 +input2.bam FBtr0079728 F 29 0 2 0 +input2.bam FBtr0079729 F 19 0 2 0 +input2.bam FBtr0079729 F 20 0 2 0 +input2.bam FBtr0079729 F 21 0 2 0 +input2.bam FBtr0079729 F 22 0 2 0 +input2.bam FBtr0079729 F 23 0 2 0 +input2.bam FBtr0079729 F 24 0 2 0 +input2.bam FBtr0079729 F 25 0 2 0 +input2.bam FBtr0079729 F 26 0 2 0 +input2.bam FBtr0079729 F 27 0 2 0 +input2.bam FBtr0079729 F 28 0 2 0 +input2.bam FBtr0079729 F 29 0 2 0 input2.bam FBtr0079752 F 19 0 1.0 -0.316 input2.bam FBtr0079752 F 20 0 1.0 -0.316 input2.bam FBtr0079752 F 21 0 1.0 -0.316 @@ -615,17 +615,17 @@ input2.bam FBtr0080609 F 27 0 1.0 -0.693 input2.bam FBtr0080609 F 28 0 1.0 -0.693 input2.bam FBtr0080609 F 29 0 1.0 -0.693 -input2.bam FBtr0080644 F 19 0 2 0.0 -input2.bam FBtr0080644 F 20 0 2 0.0 -input2.bam FBtr0080644 F 21 0 2 0.0 -input2.bam FBtr0080644 F 22 0 2 0.0 -input2.bam FBtr0080644 F 23 0 2 0.0 -input2.bam FBtr0080644 F 24 0 2 0.0 -input2.bam FBtr0080644 F 25 0 2 0.0 -input2.bam FBtr0080644 F 26 0 2 0.0 -input2.bam FBtr0080644 F 27 0 2 0.0 -input2.bam FBtr0080644 F 28 0 2 0.0 -input2.bam FBtr0080644 F 29 0 2 0.0 +input2.bam FBtr0080644 F 19 0 2 0 +input2.bam FBtr0080644 F 20 0 2 0 +input2.bam FBtr0080644 F 21 0 2 0 +input2.bam FBtr0080644 F 22 0 2 0 +input2.bam FBtr0080644 F 23 0 2 0 +input2.bam FBtr0080644 F 24 0 2 0 +input2.bam FBtr0080644 F 25 0 2 0 +input2.bam FBtr0080644 F 26 0 2 0 +input2.bam FBtr0080644 F 27 0 2 0 +input2.bam FBtr0080644 F 28 0 2 0 +input2.bam FBtr0080644 F 29 0 2 0 input2.bam FBtr0080646 F 19 0 1.0 -0.316 input2.bam FBtr0080646 F 20 0 1.0 -0.316 input2.bam FBtr0080646 F 21 1 1.0 3.162 @@ -637,28 +637,28 @@ input2.bam FBtr0080646 F 27 0 1.0 -0.316 input2.bam FBtr0080646 F 28 0 1.0 -0.316 input2.bam FBtr0080646 F 29 0 1.0 -0.316 -input2.bam FBtr0080647 F 19 0 2 0.0 -input2.bam FBtr0080647 F 20 0 2 0.0 -input2.bam FBtr0080647 F 21 0 2 0.0 -input2.bam FBtr0080647 F 22 0 2 0.0 -input2.bam FBtr0080647 F 23 0 2 0.0 -input2.bam FBtr0080647 F 24 0 2 0.0 -input2.bam FBtr0080647 F 25 0 2 0.0 -input2.bam FBtr0080647 F 26 0 2 0.0 -input2.bam FBtr0080647 F 27 0 2 0.0 -input2.bam FBtr0080647 F 28 0 2 0.0 -input2.bam FBtr0080647 F 29 0 2 0.0 -input2.bam FBtr0080660 F 19 0 2 0.0 -input2.bam FBtr0080660 F 20 0 2 0.0 -input2.bam FBtr0080660 F 21 0 2 0.0 -input2.bam FBtr0080660 F 22 0 2 0.0 -input2.bam FBtr0080660 F 23 0 2 0.0 -input2.bam FBtr0080660 F 24 0 2 0.0 -input2.bam FBtr0080660 F 25 0 2 0.0 -input2.bam FBtr0080660 F 26 0 2 0.0 -input2.bam FBtr0080660 F 27 0 2 0.0 -input2.bam FBtr0080660 F 28 0 2 0.0 -input2.bam FBtr0080660 F 29 0 2 0.0 +input2.bam FBtr0080647 F 19 0 2 0 +input2.bam FBtr0080647 F 20 0 2 0 +input2.bam FBtr0080647 F 21 0 2 0 +input2.bam FBtr0080647 F 22 0 2 0 +input2.bam FBtr0080647 F 23 0 2 0 +input2.bam FBtr0080647 F 24 0 2 0 +input2.bam FBtr0080647 F 25 0 2 0 +input2.bam FBtr0080647 F 26 0 2 0 +input2.bam FBtr0080647 F 27 0 2 0 +input2.bam FBtr0080647 F 28 0 2 0 +input2.bam FBtr0080647 F 29 0 2 0 +input2.bam FBtr0080660 F 19 0 2 0 +input2.bam FBtr0080660 F 20 0 2 0 +input2.bam FBtr0080660 F 21 0 2 0 +input2.bam FBtr0080660 F 22 0 2 0 +input2.bam FBtr0080660 F 23 0 2 0 +input2.bam FBtr0080660 F 24 0 2 0 +input2.bam FBtr0080660 F 25 0 2 0 +input2.bam FBtr0080660 F 26 0 2 0 +input2.bam FBtr0080660 F 27 0 2 0 +input2.bam FBtr0080660 F 28 0 2 0 +input2.bam FBtr0080660 F 29 0 2 0 input2.bam FBtr0080663 F 19 9 1.0 2.093 input2.bam FBtr0080663 F 20 7 1.0 1.463 input2.bam FBtr0080663 F 21 4 1.0 0.516
--- a/test-data/input1_mean.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/input1_mean.tab Sun May 09 17:11:00 2021 +0000 @@ -28,7 +28,7 @@ input1.bam FBtr0070603 72 15 F 20.0 input1.bam FBtr0070603 72 16 F 24.0 input1.bam FBtr0070603 72 17 F 24.0 -input1.bam FBtr0070603 72 19 F 23.3 +input1.bam FBtr0070603 72 19 F 23.2 input1.bam FBtr0070603 72 20 F 24.0 input1.bam FBtr0070603 72 21 F 25.0 input1.bam FBtr0070603 72 22 F 20.7 @@ -54,7 +54,7 @@ input1.bam FBtr0078490 72 72 F 0 input1.bam FBtr0078580 72 1 F 24.5 input1.bam FBtr0078580 72 3 F 22.0 -input1.bam FBtr0078580 72 4 F 25.3 +input1.bam FBtr0078580 72 4 F 25.2 input1.bam FBtr0078580 72 5 F 21.0 input1.bam FBtr0078580 72 6 F 21.0 input1.bam FBtr0078580 72 7 F 22.0 @@ -64,7 +64,7 @@ input1.bam FBtr0078580 72 16 F 20.3 input1.bam FBtr0078580 72 19 F 24.0 input1.bam FBtr0078580 72 20 F 21.0 -input1.bam FBtr0078580 72 21 F 20.3 +input1.bam FBtr0078580 72 21 F 20.2 input1.bam FBtr0078580 72 25 F 27.5 input1.bam FBtr0078580 72 72 F 0 input1.bam FBtr0078790 73 1 F 19.0 @@ -169,7 +169,7 @@ input1.bam FBtr0080660 72 72 F 0 input1.bam FBtr0080663 71 1 F 26.0 input1.bam FBtr0080663 71 3 F 23.7 -input1.bam FBtr0080663 71 4 F 23.3 +input1.bam FBtr0080663 71 4 F 23.2 input1.bam FBtr0080663 71 8 F 19.7 input1.bam FBtr0080663 71 14 F 19.0 input1.bam FBtr0080663 71 51 F 20.0
--- a/test-data/input1_min20_max30_size.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/input1_min20_max30_size.tab Sun May 09 17:11:00 2021 +0000 @@ -208,17 +208,17 @@ input1.bam FBtr0079694 F 27 0 1.0 -0.756 input1.bam FBtr0079694 F 28 0 1.0 -0.756 input1.bam FBtr0079694 F 29 0 1.0 -0.756 -input1.bam FBtr0079702 F 19 0 2 0.0 -input1.bam FBtr0079702 F 20 0 2 0.0 -input1.bam FBtr0079702 F 21 0 2 0.0 -input1.bam FBtr0079702 F 22 0 2 0.0 -input1.bam FBtr0079702 F 23 0 2 0.0 -input1.bam FBtr0079702 F 24 0 2 0.0 -input1.bam FBtr0079702 F 25 0 2 0.0 -input1.bam FBtr0079702 F 26 0 2 0.0 -input1.bam FBtr0079702 F 27 0 2 0.0 -input1.bam FBtr0079702 F 28 0 2 0.0 -input1.bam FBtr0079702 F 29 0 2 0.0 +input1.bam FBtr0079702 F 19 0 2 0 +input1.bam FBtr0079702 F 20 0 2 0 +input1.bam FBtr0079702 F 21 0 2 0 +input1.bam FBtr0079702 F 22 0 2 0 +input1.bam FBtr0079702 F 23 0 2 0 +input1.bam FBtr0079702 F 24 0 2 0 +input1.bam FBtr0079702 F 25 0 2 0 +input1.bam FBtr0079702 F 26 0 2 0 +input1.bam FBtr0079702 F 27 0 2 0 +input1.bam FBtr0079702 F 28 0 2 0 +input1.bam FBtr0079702 F 29 0 2 0 input1.bam FBtr0079728 F 19 0 1.0 -0.471 input1.bam FBtr0079728 F 20 1 1.0 2.121 input1.bam FBtr0079728 F 21 0 1.0 -0.471
--- a/test-data/size12.tab Sun Oct 06 21:11:19 2019 -0400 +++ b/test-data/size12.tab Sun May 09 17:11:00 2021 +0000 @@ -1,59 +1,59 @@ # Dataset Chromosome Polarity Size Counts Strandness z-score -size1.bam PbANKA_00_v3_archived_contig_1 F 19 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 20 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 21 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 22 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 23 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 24 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 25 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 26 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 27 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 28 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_1 F 29 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 19 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 20 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 21 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 22 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 23 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 24 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 25 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 26 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 27 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 28 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_2 F 29 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 19 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 20 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 21 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 22 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 23 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 24 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 25 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 26 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 27 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 28 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_3 F 29 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 19 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 20 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 21 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 22 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 23 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 24 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 25 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 26 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 27 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 28 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_4 F 29 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 19 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 20 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 21 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 22 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 23 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 24 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 25 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 26 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 27 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 28 0 2 0.0 -size1.bam PbANKA_00_v3_archived_contig_5 F 29 0 2 0.0 +size1.bam PbANKA_00_v3_archived_contig_1 F 19 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 20 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 21 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 22 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 23 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 24 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 25 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 26 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 27 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 28 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_1 F 29 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 19 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 20 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 21 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 22 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 23 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 24 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 25 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 26 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 27 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 28 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_2 F 29 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 19 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 20 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 21 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 22 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 23 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 24 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 25 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 26 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 27 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 28 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_3 F 29 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 19 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 20 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 21 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 22 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 23 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 24 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 25 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 26 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 27 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 28 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_4 F 29 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 19 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 20 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 21 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 22 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 23 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 24 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 25 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 26 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 27 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 28 0 2 0 +size1.bam PbANKA_00_v3_archived_contig_5 F 29 0 2 0 size1.bam PbANKA_01_v3 F 19 3 0.46 1.768 size1.bam PbANKA_01_v3 F 20 4 0.46 0.795 size1.bam PbANKA_01_v3 F 21 2 0.46 -0.177 @@ -417,50 +417,50 @@ size2.bam PbANKA_00_v3_archived_contig_1 F 27 0 1.0 -0.471 size2.bam PbANKA_00_v3_archived_contig_1 F 28 0 1.0 -0.471 size2.bam PbANKA_00_v3_archived_contig_1 F 29 0 1.0 -0.471 -size2.bam PbANKA_00_v3_archived_contig_2 F 19 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 20 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 21 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 22 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 23 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 24 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 25 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 26 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 27 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 28 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_2 F 29 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 19 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 20 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 21 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 22 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 23 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 24 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 25 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 26 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 27 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 28 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_3 F 29 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 19 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 20 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 21 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 22 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 23 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 24 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 25 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 26 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 27 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 28 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_4 F 29 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 19 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 20 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 21 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 22 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 23 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 24 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 25 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 26 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 27 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 28 0 2 0.0 -size2.bam PbANKA_00_v3_archived_contig_5 F 29 0 2 0.0 +size2.bam PbANKA_00_v3_archived_contig_2 F 19 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 20 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 21 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 22 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 23 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 24 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 25 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 26 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 27 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 28 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_2 F 29 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 19 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 20 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 21 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 22 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 23 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 24 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 25 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 26 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 27 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 28 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_3 F 29 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 19 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 20 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 21 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 22 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 23 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 24 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 25 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 26 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 27 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 28 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_4 F 29 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 19 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 20 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 21 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 22 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 23 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 24 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 25 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 26 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 27 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 28 0 2 0 +size2.bam PbANKA_00_v3_archived_contig_5 F 29 0 2 0 size2.bam PbANKA_01_v3 F 19 9 0.41 2.224 size2.bam PbANKA_01_v3 F 20 3 0.41 0.839 size2.bam PbANKA_01_v3 F 21 6 0.41 0.608