| Next changeset 1:c24765926774 (2019-03-26) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8 |
|
added:
get_deseq_dataset.R ruvseq.R ruvseq.xml test-data/GSM461176_untreat_single.counts test-data/GSM461176_untreat_single.counts.noheader test-data/GSM461177_untreat_paired.counts test-data/GSM461177_untreat_paired.counts.noheader test-data/GSM461178_untreat_paired.counts test-data/GSM461178_untreat_paired.counts.noheader test-data/GSM461179_treat_single.counts test-data/GSM461179_treat_single.counts.noheader test-data/GSM461180_treat_paired.counts test-data/GSM461180_treat_paired.counts.noheader test-data/GSM461181_treat_paired.counts test-data/GSM461181_treat_paired.counts.noheader test-data/GSM461182_untreat_single.counts test-data/GSM461182_untreat_single.counts.noheader test-data/ruvseq_diag.pdf test-data/ruvseq_diag_sailfish.pdf test-data/sailfish/sailfish_quant.sf1.tab test-data/sailfish/sailfish_quant.sf2.tab test-data/sailfish/sailfish_quant.sf3.tab test-data/sailfish/sailfish_quant.sf4.tab test-data/sailfish/sailfish_quant.sf5.tab test-data/sailfish/sailfish_quant.sf6.tab test-data/tx2gene.tab |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 get_deseq_dataset.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_deseq_dataset.R Wed Sep 05 15:54:16 2018 -0400 |
| [ |
| @@ -0,0 +1,69 @@ +get_deseq_dataset <- function(sampleTable, header, designFormula, tximport, txtype, tx2gene) { + + dir <- "" + + if (!is.null(header)) { + hasHeader <- TRUE + } else { + hasHeader <- FALSE + } + + if (!is.null(tximport)) { + if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport") + if (tolower(file_ext(opt$tx2gene)) == "gtf") { + gtfFile <-tx2gene + } else { + gtfFile <- NULL + tx2gene <- read.table(tx2gene, header=FALSE) + } + useTXI <- TRUE + } else { + useTXI <- FALSE + } + + if (!useTXI & hasHeader) { + countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)}) + tbl <- do.call("cbind", countfiles) + colnames(tbl) <- rownames(sampleTable) # take sample ids from header + + # check for htseq report lines (from DESeqDataSetFromHTSeqCount function) + oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual", + "not_aligned", "alignment_not_unique") + specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames + tbl <- tbl[!specialRows, , drop = FALSE] + + dds <- DESeqDataSetFromMatrix(countData = tbl, + colData = subset(sampleTable, select=-(filename)), + design = designFormula) + } else if (!useTXI & !hasHeader) { + + # construct the object from HTSeq files + dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, + directory = dir, + design = designFormula) + colnames(dds) <- row.names(sampleTable) + + } else { + # construct the object using tximport + # first need to make the tx2gene table + # this takes ~2-3 minutes using Bioconductor functions + if (!is.null(gtfFile)) { + suppressPackageStartupMessages({ + library("GenomicFeatures") + }) + txdb <- makeTxDbFromGFF(gtfFile, format="gtf") + k <- keys(txdb, keytype = "GENEID") + df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME") + tx2gene <- df[, 2:1] # tx ID, then gene ID + } + library("tximport") + txiFiles <- as.character(sampleTable$filename) + labs <- row.names(sampleTable) + names(txiFiles) <- labs + txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene) + dds <- DESeqDataSetFromTximport(txi, + subset(sampleTable, select=-c(filename)), + designFormula) + } + return(dds) +} |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 ruvseq.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ruvseq.R Wed Sep 05 15:54:16 2018 -0400 |
| [ |
| @@ -0,0 +1,198 @@ +# setup R error handling to go to stderr +library("getopt") +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(stringAsFactors = FALSE, useFancyQuotes = FALSE) + +setup_cmdline_options <- function() { + args <- commandArgs(trailingOnly = TRUE) + spec <- matrix(c( + "help", "h", 0, "logical", + "alpha", "a", 1, "double", + "min_mean_count", "min_c", 1, "double", + "min_k", "min_k", 1, "double", + "max_k", "max_k", 1, "double", + "sample_json", "s", 1, "character", + "plots" , "p", 1, "character", + "header", "H", 0, "logical", + "txtype", "y", 1, "character", + "tx2gene", "x", 1, "character"), # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF) + byrow=TRUE, ncol=4) + + opt <- getopt(spec) + # if help was asked for print a friendly message + # and exit with a non-zero error code + if (!is.null(opt$help)) { + cat(getopt(spec, usage=TRUE)) + q(status=1) + } else { + load_libraries() + } + return(opt) +} + +load_libraries <- function() { + # Allows displaying help without waiting for libraries to load + library("tools") + library("jsonlite") + library("reshape2") + library("RUVSeq") + library("RColorBrewer") + library("tximport") + library("DESeq2") + library("ggrepel") +} + +source_local <- function(fname){ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Source get_deseq_dataset.R for getting deseq dataset from htseq/featurecounts/tximport +source_local('get_deseq_dataset.R') + +# RUVseq function definitions + +plot_pca_rle <- function (set, title) { + x <- pData(set)[,1] + colors <- brewer.pal(3, "Set2") + label <- paste0(' for ', title) + plotRLE(set, outline=FALSE, ylim=c(-4, 4), col=colors[x]) + title(main=paste0("RLE", label)) + plotPCA(set, col=colors[x], cex=1.2) + title(main=paste0("PCA", label)) +} + +plot_factors_of_unwanted_variation <- function(set, method, k){ + pd <- pData(set) + pd['sample'] <- row.names(pd) + colnames(pd)[1] <- 'condition' + d = melt(pd, id.vars = c('sample', 'condition')) + d['x'] <- 1 # There is no information on the X, so we just fake it to be able to do a scatterplot + print(ggplot(d, aes(x=x, y=value, color=condition, label=sample)) + + geom_point() + + ggtitle(paste0('Factors of unwanted variation for method: ', method, ", k=", k)) + + facet_wrap( ~ variable, scales = "free_x") + + geom_text_repel() + + theme(axis.title.x=element_blank(), + axis.text.x=element_blank(), + axis.ticks.x=element_blank(), + plot.title = element_text(hjust = 0.5)) + ) +} + +create_seq_expression_set <- function (dds, min_mean_count) { + count_values <- counts(dds) + filter <- apply(count_values, 1, function(x) mean(x) > min_mean_count) + filtered <- count_values[filter,] + set = newSeqExpressionSet(as.matrix(count_values), + phenoData = data.frame(colData(dds)$condition, row.names=colnames(filtered))) + plot_pca_rle(set = set, title = 'raw data') + set <- betweenLaneNormalization(set, which="upper") + plot_pca_rle(set = set, title = 'upper quartile normalized') + return(set) +} + +get_empirical_control_genes <- function(set, cutoff_p) { + x <- pData(set)[,1] + design <- model.matrix(~x, data=pData(set)) + y <- DGEList(counts=counts(set), group=x) + y <- calcNormFactors(y, method="upperquartile") + y <- estimateGLMCommonDisp(y, design) + y <- estimateGLMTagwiseDisp(y, design) + fit <- glmFit(y, design) + lrt <- glmLRT(fit, coef=2) + top <- topTags(lrt, n=nrow(set))$table + top_rows <- rownames(top)[which(top$PValue > cutoff_p)] + empirical <- rownames(set)[which(!(rownames(set) %in% top_rows))] + return(empirical) +} + +ruv_control_gene_method <- function(set, k, control_genes='empirical', cutoff_p=0.2) { + if (control_genes == 'empirical') { + control_genes = get_empirical_control_genes(set, cutoff_p=cutoff_p) + } + set <- RUVg(set, control_genes, k=k) + plot_pca_rle(set, paste0("RUVg with empirical control genes, k=", k)) + plot_factors_of_unwanted_variation(set, method="RUVg with empirical control genes", k=k) + return(set) +} + +ruv_residual_method <- function(set, k) { + genes <- rownames(counts(set)) + x <- pData(set)[,1] + # Initial edger residuals + design <- model.matrix(~x, data=pData(set)) + y <- DGEList(counts=counts(set), group=x) + y <- calcNormFactors(y, method="upperquartile") + y <- estimateGLMCommonDisp(y, design) + y <- estimateGLMTagwiseDisp(y, design) + fit <- glmFit(y, design) + res <- residuals(fit, type="deviance") + set <- RUVr(set, genes, k=k, res) + plot_pca_rle(set = set, title = paste0('RUVr using residuals, k=', k)) + plot_factors_of_unwanted_variation(set, method="RUVr using residuals", k=k) + return(set) +} + +ruv_replicate_method <- function (set, k) { + genes <- rownames(counts(set)) + x <- pData(set)[,1] + differences <- makeGroups(x) + set <- RUVs(set, genes, k=k, differences) + plot_pca_rle(set, paste0('RUVs with replicate samples, k=', k)) + plot_factors_of_unwanted_variation(set, method="RUVs using replicates", k=k) + return(set) +} + +get_differentially_expressed_genes <- function(dds, contrast, alpha=0.01) { + r <- results(dds, contrast=contrast, alpha=alpha) + return(rownames(r[which(r$padj < alpha),])) +} + +opt <- setup_cmdline_options() +alpha <- opt$alpha +min_k <- opt$min_k +max_k <- opt$max_k +sample_json <- fromJSON(opt$sample_json) +sample_paths <- sample_json$path +sample_names <- sample_json$label +condition <- as.factor(sample_json$condition) +sampleTable <- data.frame(samplename=sample_names, + filename = sample_paths, + condition=condition) +rownames(sampleTable) <- sample_names + +dds <- get_deseq_dataset(sampleTable, header=opt$header, designFormula= ~ condition, tximport=opt$txtype, txtype=opt$txtype, tx2gene=opt$tx2gene) +if (!is.null(opt$plots)) { + pdf(opt$plots) +} + +# Run through the ruvseq variants +set <- create_seq_expression_set(dds, min_mean_count = opt$min_mean_count) +result <- list(no_correction = set) +for (k in seq(min_k, max_k)) { + result[[paste0('residual_method_k', k)]] <- ruv_residual_method(set, k=k) + result[[paste0('replicate_method_k', k)]] <- ruv_replicate_method(set, k=k) + result[[paste0('control_method_k', k)]] <- ruv_control_gene_method(set, k=k, cutoff_p=0.5) +} + +for (name in names(result)) { + if (!startsWith(name, "no_correction")) { + set <- result[[name]] + unwanted_variation <- pData(set) + df <- data.frame(identifier = rownames(unwanted_variation)) + df <- cbind(df, unwanted_variation) + colnames(df)[2] <- 'condition' + write.table(df, file=paste0("batch_effects_", name, ".tabular"), sep="\t", quote=F, row.names=F) + } +} + +# close the plot device +if (!is.null(opt$plots)) { + cat("closing plot device\n") + dev.off() +} + +cat("Session information:\n\n") +sessionInfo() |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 ruvseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ruvseq.xml Wed Sep 05 15:54:16 2018 -0400 |
| [ |
| b'@@ -0,0 +1,307 @@\n+<tool id="ruvseq" name="Remove Unwanted Variation" version="1.12.0">\n+ <description>from RNA-seq data</description>\n+ <requirements>\n+ <requirement type="package" version="1.12.0">bioconductor-ruvseq</requirement>\n+ <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>\n+ <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>\n+ <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>\n+ <requirement type="package" version="0.6.5">r-ggrepel</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="Execution halted"\n+ source="both"\n+ level="fatal"\n+ description="Execution halted." />\n+ <regex match="Error in"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ <regex match="Fatal error"\n+ source="both"\n+ level="fatal"\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ </stdio>\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\\$otherPkgs\\$RUVSeq\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n+ <command><![CDATA[\n+#if $tximport.tximport_selector == \'tximport\':\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ ln -s \'$tximport.mapping_format.gtf_file\' mapping.gtf &&\n+ #else:\n+ ln -s \'$tximport.mapping_format.tabular_file\' mapping.txt &&\n+ #end if\n+#end if\n+\n+Rscript \'${__tool_directory__}/ruvseq.R\'\n+#if $pdf:\n+ -p \'$plots\'\n+#end if\n+\n+--sample_json \'$sampleTable\'\n+\n+$header\n+\n+--min_k $min_k\n+--max_k $max_k\n+\n+#if $tximport.tximport_selector == \'tximport\':\n+ --txtype $tximport.txtype\n+ #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n+ --tx2gene mapping.gtf\n+ #else:\n+ --tx2gene mapping.txt\n+ #end if\n+#end if\n+]]></command>\n+ <configfiles>\n+ <configfile name="sampleTable">\n+#import json\n+#set sample_table = []\n+#for $level in $rep_factorLevel:\n+ #for $file in $level.countsFile:\n+ #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)})\n+ #end for\n+#end for\n+#echo json.dumps($sample_table)\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">\n+ <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be \'tumor\', \'normal\', \'treated\' or \'control\'"\n+ help="Only letters, numbers and underscores will be retained in this field">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ </param>\n+ <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>\n+ </repeat>\n+ <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" />\n+ <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" />\n+ <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" />\n+ <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />\n+\n+ <conditional name="tximport">\n+ <param name="tximport_selector"'..b't_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+RUVSeq normalizes RNA-seq data using factor analysis of control genes or samples. RUVSeq has been designed for detecting unwanted variation using replicate sample information. The current RUVSeq Galaxy tool only implements estimating unwanted variation for primary factors.\n+RUVSeq implements 3 different methods for the estimation of unwanted variation:\n+\n+RUVg estimates the factors of unwanted variation using control genes\n+\n+RUVs estimates the factors of unwanted variation using replicate samples\n+\n+RUVr estimating the factors of unwanted variation using residuals.\n+\n+This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that\n+may be used for differential expression analsys.\n+\n+-----\n+\n+**Inputs**\n+\n+**Count Files**\n+\n+RUVSeq_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No.\n+\n+RUVSeq_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.\n+\n+**Salmon or Sailfish Files**\n+\n+Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.\n+\n+Example:\n+\n+============ ========== =============== =========== ===========\n+Name Length EffectiveLength TPM NumReads\n+------------ ---------- --------------- ----------- -----------\n+NR_001526 164 20.4518 0 0\n+NR_001526_1 164 20.4518 0 0\n+NR_001526_2 164 20.4518 0 0\n+NM_130786 1764 1956.04 2.47415 109.165\n+NR_015380 2129 2139.53 1.77331 85.5821\n+NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05\n+NM_001198819 9527 7964.62 0 0\n+NM_001198820 9410 7855.78 0 0\n+NM_014576 9267 7714.88 0.0481114 8.37255\n+============ ========== =============== =========== ===========\n+\n+**kallisto Files**\n+\n+kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.\n+\n+Example:\n+\n+============ ========== =============== =========== ===========\n+target_id length eff_length est_counts tpm\n+------------ ---------- --------------- ----------- -----------\n+NR_001526 164 20.4518 0 0\n+NR_001526_1 164 20.4518 0 0\n+NR_001526_2 164 20.4518 0 0\n+NM_130786 1764 1956.04 109.165 2.47415\n+NR_015380 2129 2139.53 85.5821 1.77331\n+NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07\n+NM_001198819 9527 7964.62 0 0\n+NM_001198820 9410 7855.78 0 0\n+NM_014576 9267 7714.88 8.37255 0.0481114\n+============ ========== =============== =========== ===========\n+\n+-----\n+\n+**Output**\n+\n+RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF.\n+\n+.. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html\n+.. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.2931</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461176_untreat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461176_untreat_single.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\tuntreat1\n+FBgn0000003\t0\n+FBgn0000008\t15\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t1227\n+FBgn0000018\t92\n+FBgn0000022\t1\n+FBgn0000024\t0\n+FBgn0000028\t0\n+FBgn0000032\t233\n+FBgn0000036\t0\n+FBgn0000037\t2\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t16319\n+FBgn0000043\t5625\n+FBgn0000044\t13\n+FBgn0000045\t1\n+FBgn0000046\t4\n+FBgn0000047\t2\n+FBgn0000052\t488\n+FBgn0000053\t376\n+FBgn0000054\t142\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t159\n+FBgn0000061\t0\n+FBgn0000063\t100\n+FBgn0000064\t1808\n+FBgn0000071\t29\n+FBgn0000075\t1\n+FBgn0000077\t40\n+FBgn0000078\t5\n+FBgn0000079\t28\n+FBgn0000083\t1286\n+FBgn0000084\t399\n+FBgn0000092\t3\n+FBgn0000094\t4\n+FBgn0000097\t749\n+FBgn0000099\t0\n+FBgn0000100\t6534\n+FBgn0000108\t12\n+FBgn0000109\t20\n+FBgn0000114\t1\n+FBgn0000115\t148\n+FBgn0000116\t95\n+FBgn0000117\t2488\n+FBgn0000119\t133\n+FBgn0000120\t0\n+FBgn0000121\t0\n+FBgn0000137\t0\n+FBgn0000139\t186\n+FBgn0000140\t233\n+FBgn0000142\t463\n+FBgn0000146\t293\n+FBgn0000147\t72\n+FBgn0000150\t1863\n+FBgn0000152\t100\n+FBgn0000153\t4\n+FBgn0000157\t0\n+FBgn0000158\t5\n+FBgn0000163\t193\n+FBgn0000166\t0\n+FBgn0000171\t1422\n+FBgn0000173\t334\n+FBgn0000179\t0\n+FBgn0000180\t7\n+FBgn0000181\t3954\n+FBgn0000182\t1\n+FBgn0000183\t622\n+FBgn0000206\t0\n+FBgn0000210\t360\n+FBgn0000212\t792\n+FBgn0000216\t0\n+FBgn0000221\t52\n+FBgn0000227\t0\n+FBgn0000228\t196\n+FBgn0000229\t209\n+FBgn0000233\t1\n+FBgn0000239\t549\n+FBgn0000241\t2\n+FBgn0000242\t36\n+FBgn0000244\t133\n+FBgn0000246\t52\n+FBgn0000247\t641\n+FBgn0000250\t649\n+FBgn0000251\t0\n+FBgn0000253\t2925\n+FBgn0000256\t661\n+FBgn0000257\t168\n+FBgn0000258\t303\n+FBgn0000259\t675\n+FBgn0000261\t451\n+FBgn0000273\t608\n+FBgn0000274\t0\n+FBgn0000276\t12\n+FBgn0000277\t7\n+FBgn0000278\t8\n+FBgn0000279\t19\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t1022\n+FBgn0000286\t138\n+FBgn0000287\t0\n+FBgn0000289\t806\n+FBgn0000299\t10675\n+FBgn0000303\t2\n+FBgn0000307\t435\n+FBgn0000308\t5033\n+FBgn0000313\t15\n+FBgn0000316\t1\n+FBgn0000317\t341\n+FBgn0000318\t227\n+FBgn0000319\t2803\n+FBgn0000320\t0\n+FBgn0000326\t62\n+FBgn0000330\t34\n+FBgn0000337\t3\n+FBgn0000338\t432\n+FBgn0000339\t146\n+FBgn0000346\t20\n+FBgn0000351\t2\n+FBgn0000352\t188\n+FBgn0000355\t1\n+FBgn0000356\t0\n+FBgn0000357\t0\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t2\n+FBgn0000370\t2764\n+FBgn0000376\t246\n+FBgn0000377\t196\n+FBgn0000382\t206\n+FBgn0000384\t97\n+FBgn0000392\t212\n+FBgn0000394\t138\n+FBgn0000395\t159\n+FBgn0000404\t630\n+FBgn0000405\t460\n+FBgn0000406\t108\n+FBgn0000409\t1159\n+FBgn0000411\t0\n+FBgn0000412\t674\n+FBgn0000413\t553\n+FBgn0000414\t521\n+FBgn0000416\t10382\n+FBgn0000422\t0\n+FBgn0000426\t206\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t134\n+FBgn0000448\t0\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t567\n+FBgn0000455\t110\n+FBgn0000459\t1\n+FBgn0000463\t0\n+FBgn0000464\t376\n+FBgn0000472\t880\n+FBgn0000473\t3\n+FBgn0000477\t0\n+FBgn0000479\t221\n+FBgn0000482\t226\n+FBgn0000489\t18\n+FBgn0000490\t34\n+FBgn0000492\t0\n+FBgn0000497\t1\n+FBgn0000499\t226\n+FBgn0000500\t1\n+FBgn0000504\t2\n+FBgn0000520\t118\n+FBgn0000524\t170\n+FBgn0000527\t24\n+FBgn0000529\t0\n+FBgn0000533\t1\n+FBgn0000535\t62\n+FBgn0000536\t221\n+FBgn0000541\t1488\n+FBgn0000542\t36\n+FBgn0000543\t142\n+FBgn0000546\t224\n+FBgn0000547\t66\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t49589\n+FBgn0000557\t7\n+FBgn0000559\t23660\n+FBgn0000560\t0\n+FBgn0000562\t379\n+FBgn0000564\t0\n+FBgn0000565\t107\n+FBgn0000566\t181\n+FBgn0000567\t61\n+FBgn0000568\t1058\n+FBgn0000575\t323\n+FBgn0000576\t0\n+FBgn0000577\t1\n+FBgn0000578\t1493\n+FBgn0000579\t1621\n+FBgn0000581\t898\n+FBgn0000588\t93\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t5\n+FBgn0000606\t0\n+FBgn0000611\t351\n+FBgn0000615\t72\n+FBgn0000617\t151\n+FBgn0000618\t36\n+FBgn0000625\t0\n+FBgn0000629\t219\n+FBgn0000630\t4\n+FBgn0000633\t8\n+FBgn0000634\t73\n+FBgn0000635\t29\n+FBgn0000636\t10\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t1\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t306\n+FBgn0000667\t342\n+FBgn0000709\t566\n+FBgn0000711\t268\n+FBgn0000715\t1\n+FBgn0000719\t541\n+FBgn0000721\t193\n+FBgn0000723\t482\n+FBgn0000808\t31\n+FBgn0000810\t99\n+FBgn0000826\t23\n+FBgn0000927\t2\n+FBgn0000928\t130\n+FBgn0000964\t0\n+FBgn0000986\t457\n+FBgn0000996\t339\n+FBgn0001075\t9\n+FBgn0001077\t0\n+FBgn0001078\t252\n+FBgn0001079\t79\n+FBgn0001083\t30\n+FB'..b'0030344\t303\n+FBgn0030345\t52\n+FBgn0030346\t42\n+FBgn0030347\t65\n+FBgn0030348\t0\n+FBgn0030349\t425\n+FBgn0030350\t222\n+FBgn0030351\t26\n+FBgn0030352\t48\n+FBgn0030354\t419\n+FBgn0030356\t0\n+FBgn0030357\t25\n+FBgn0030358\t53\n+FBgn0030359\t0\n+FBgn0030360\t4\n+FBgn0030361\t22\n+FBgn0030362\t1711\n+FBgn0030364\t139\n+FBgn0030365\t170\n+FBgn0030366\t995\n+FBgn0030367\t6\n+FBgn0030369\t11\n+FBgn0030370\t0\n+FBgn0030373\t79\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t27\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t54\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t5\n+FBgn0030398\t0\n+FBgn0030399\t0\n+FBgn0030400\t327\n+FBgn0030403\t211\n+FBgn0030406\t39\n+FBgn0030407\t8\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t21\n+FBgn0030411\t22\n+FBgn0030412\t389\n+FBgn0030417\t28\n+FBgn0030418\t61\n+FBgn0030420\t325\n+FBgn0030421\t33\n+FBgn0030425\t2\n+FBgn0030429\t0\n+FBgn0030431\t116\n+FBgn0030432\t3\n+FBgn0030433\t81\n+FBgn0030434\t177\n+FBgn0030435\t171\n+FBgn0030437\t0\n+FBgn0030438\t2\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t101\n+FBgn0030448\t117\n+FBgn0030449\t2\n+FBgn0030451\t241\n+FBgn0030452\t243\n+FBgn0030455\t0\n+FBgn0030456\t116\n+FBgn0030457\t126\n+FBgn0030459\t2\n+FBgn0030460\t64\n+FBgn0030462\t0\n+FBgn0030465\t145\n+FBgn0030466\t484\n+FBgn0030467\t172\n+FBgn0030468\t409\n+FBgn0030469\t459\n+FBgn0030474\t213\n+FBgn0030477\t0\n+FBgn0030478\t345\n+FBgn0030479\t80\n+FBgn0030480\t36\n+FBgn0030481\t93\n+FBgn0030482\t1080\n+FBgn0030483\t3\n+FBgn0030484\t353\n+FBgn0030485\t79\n+FBgn0030486\t518\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t175\n+FBgn0030500\t159\n+FBgn0030501\t387\n+FBgn0030502\t662\n+FBgn0030503\t34\n+FBgn0030504\t663\n+FBgn0030505\t492\n+FBgn0030506\t98\n+FBgn0030507\t73\n+FBgn0030508\t2\n+FBgn0030509\t0\n+FBgn0030510\t76\n+FBgn0030511\t35\n+FBgn0030512\t236\n+FBgn0030514\t374\n+FBgn0030518\t44\n+FBgn0030519\t231\n+FBgn0030520\t1189\n+FBgn0030521\t988\n+FBgn0030522\t43\n+FBgn0030524\t1\n+FBgn0030525\t2\n+FBgn0030528\t27\n+FBgn0030529\t2794\n+FBgn0030530\t409\n+FBgn0030532\t490\n+FBgn0030536\t3\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t50\n+FBgn0030551\t0\n+FBgn0030552\t93\n+FBgn0030554\t70\n+FBgn0030555\t36\n+FBgn0030556\t306\n+FBgn0030558\t0\n+FBgn0030559\t0\n+FBgn0030562\t5\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t49\n+FBgn0030572\t83\n+FBgn0030573\t14\n+FBgn0030574\t2\n+FBgn0030575\t8\n+FBgn0030576\t74\n+FBgn0030577\t1\n+FBgn0030578\t0\n+FBgn0030581\t105\n+FBgn0030582\t235\n+FBgn0030583\t5\n+FBgn0030584\t90\n+FBgn0030586\t1\n+FBgn0030587\t2\n+FBgn0030588\t43\n+FBgn0030589\t2\n+FBgn0030590\t6\n+FBgn0030591\t3\n+FBgn0030592\t6\n+FBgn0030593\t3\n+FBgn0030594\t3\n+FBgn0030595\t1\n+FBgn0030596\t10\n+FBgn0030597\t4\n+FBgn0030598\t4\n+FBgn0030599\t3\n+FBgn0030600\t485\n+FBgn0030603\t151\n+FBgn0030605\t159\n+FBgn0030606\t113\n+FBgn0030607\t4\n+FBgn0030608\t0\n+FBgn0030610\t83\n+FBgn0030611\t26\n+FBgn0030612\t74\n+FBgn0030613\t2\n+FBgn0030614\t0\n+FBgn0030615\t14\n+FBgn0030616\t6872\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t58\n+FBgn0030626\t135\n+FBgn0030627\t161\n+FBgn0030628\t141\n+FBgn0030629\t31\n+FBgn0030630\t108\n+FBgn0030631\t274\n+FBgn0030634\t4\n+FBgn0030636\t4\n+FBgn0030638\t154\n+FBgn0030640\t0\n+FBgn0030641\t5\n+FBgn0030642\t5\n+FBgn0030643\t1\n+FBgn0030645\t23\n+FBgn0030646\t51\n+FBgn0030647\t3\n+FBgn0030648\t81\n+FBgn0030653\t44\n+FBgn0030654\t27\n+FBgn0030655\t65\n+FBgn0030657\t22\n+FBgn0030658\t245\n+FBgn0030659\t111\n+FBgn0030660\t30\n+FBgn0030661\t4\n+FBgn0030662\t135\n+FBgn0030663\t0\n+FBgn0030664\t5\n+FBgn0030665\t2\n+FBgn0030666\t5\n+FBgn0030667\t33\n+FBgn0030668\t65\n+FBgn0030669\t54\n+FBgn0030670\t151\n+FBgn0030671\t66\n+FBgn0030672\t1376\n+FBgn0030673\t22\n+FBgn0030674\t2023\n+FBgn0030675\t14\n+FBgn0030676\t4\n+FBgn0030678\t45\n+FBgn0030679\t119\n+FBgn0030680\t136\n+FBgn0030683\t45\n+FBgn0030684\t0\n+FBgn0030685\t663\n+FBgn0030686\t126\n+FBgn0030687\t146\n+FBgn0030688\t0\n+FBgn0030691\t7\n+FBgn0030692\t186\n+FBgn0030693\t95\n+FBgn0030694\t59\n+no_feature\t172410\n+ambiguous\t33519\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t8666693\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461176_untreat_single.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461176_untreat_single.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t15\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t1227\n+FBgn0000018\t92\n+FBgn0000022\t1\n+FBgn0000024\t0\n+FBgn0000028\t0\n+FBgn0000032\t233\n+FBgn0000036\t0\n+FBgn0000037\t2\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t16319\n+FBgn0000043\t5625\n+FBgn0000044\t13\n+FBgn0000045\t1\n+FBgn0000046\t4\n+FBgn0000047\t2\n+FBgn0000052\t488\n+FBgn0000053\t376\n+FBgn0000054\t142\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t159\n+FBgn0000061\t0\n+FBgn0000063\t100\n+FBgn0000064\t1808\n+FBgn0000071\t29\n+FBgn0000075\t1\n+FBgn0000077\t40\n+FBgn0000078\t5\n+FBgn0000079\t28\n+FBgn0000083\t1286\n+FBgn0000084\t399\n+FBgn0000092\t3\n+FBgn0000094\t4\n+FBgn0000097\t749\n+FBgn0000099\t0\n+FBgn0000100\t6534\n+FBgn0000108\t12\n+FBgn0000109\t20\n+FBgn0000114\t1\n+FBgn0000115\t148\n+FBgn0000116\t95\n+FBgn0000117\t2488\n+FBgn0000119\t133\n+FBgn0000120\t0\n+FBgn0000121\t0\n+FBgn0000137\t0\n+FBgn0000139\t186\n+FBgn0000140\t233\n+FBgn0000142\t463\n+FBgn0000146\t293\n+FBgn0000147\t72\n+FBgn0000150\t1863\n+FBgn0000152\t100\n+FBgn0000153\t4\n+FBgn0000157\t0\n+FBgn0000158\t5\n+FBgn0000163\t193\n+FBgn0000166\t0\n+FBgn0000171\t1422\n+FBgn0000173\t334\n+FBgn0000179\t0\n+FBgn0000180\t7\n+FBgn0000181\t3954\n+FBgn0000182\t1\n+FBgn0000183\t622\n+FBgn0000206\t0\n+FBgn0000210\t360\n+FBgn0000212\t792\n+FBgn0000216\t0\n+FBgn0000221\t52\n+FBgn0000227\t0\n+FBgn0000228\t196\n+FBgn0000229\t209\n+FBgn0000233\t1\n+FBgn0000239\t549\n+FBgn0000241\t2\n+FBgn0000242\t36\n+FBgn0000244\t133\n+FBgn0000246\t52\n+FBgn0000247\t641\n+FBgn0000250\t649\n+FBgn0000251\t0\n+FBgn0000253\t2925\n+FBgn0000256\t661\n+FBgn0000257\t168\n+FBgn0000258\t303\n+FBgn0000259\t675\n+FBgn0000261\t451\n+FBgn0000273\t608\n+FBgn0000274\t0\n+FBgn0000276\t12\n+FBgn0000277\t7\n+FBgn0000278\t8\n+FBgn0000279\t19\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t1022\n+FBgn0000286\t138\n+FBgn0000287\t0\n+FBgn0000289\t806\n+FBgn0000299\t10675\n+FBgn0000303\t2\n+FBgn0000307\t435\n+FBgn0000308\t5033\n+FBgn0000313\t15\n+FBgn0000316\t1\n+FBgn0000317\t341\n+FBgn0000318\t227\n+FBgn0000319\t2803\n+FBgn0000320\t0\n+FBgn0000326\t62\n+FBgn0000330\t34\n+FBgn0000337\t3\n+FBgn0000338\t432\n+FBgn0000339\t146\n+FBgn0000346\t20\n+FBgn0000351\t2\n+FBgn0000352\t188\n+FBgn0000355\t1\n+FBgn0000356\t0\n+FBgn0000357\t0\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t2\n+FBgn0000370\t2764\n+FBgn0000376\t246\n+FBgn0000377\t196\n+FBgn0000382\t206\n+FBgn0000384\t97\n+FBgn0000392\t212\n+FBgn0000394\t138\n+FBgn0000395\t159\n+FBgn0000404\t630\n+FBgn0000405\t460\n+FBgn0000406\t108\n+FBgn0000409\t1159\n+FBgn0000411\t0\n+FBgn0000412\t674\n+FBgn0000413\t553\n+FBgn0000414\t521\n+FBgn0000416\t10382\n+FBgn0000422\t0\n+FBgn0000426\t206\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t134\n+FBgn0000448\t0\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t567\n+FBgn0000455\t110\n+FBgn0000459\t1\n+FBgn0000463\t0\n+FBgn0000464\t376\n+FBgn0000472\t880\n+FBgn0000473\t3\n+FBgn0000477\t0\n+FBgn0000479\t221\n+FBgn0000482\t226\n+FBgn0000489\t18\n+FBgn0000490\t34\n+FBgn0000492\t0\n+FBgn0000497\t1\n+FBgn0000499\t226\n+FBgn0000500\t1\n+FBgn0000504\t2\n+FBgn0000520\t118\n+FBgn0000524\t170\n+FBgn0000527\t24\n+FBgn0000529\t0\n+FBgn0000533\t1\n+FBgn0000535\t62\n+FBgn0000536\t221\n+FBgn0000541\t1488\n+FBgn0000542\t36\n+FBgn0000543\t142\n+FBgn0000546\t224\n+FBgn0000547\t66\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t49589\n+FBgn0000557\t7\n+FBgn0000559\t23660\n+FBgn0000560\t0\n+FBgn0000562\t379\n+FBgn0000564\t0\n+FBgn0000565\t107\n+FBgn0000566\t181\n+FBgn0000567\t61\n+FBgn0000568\t1058\n+FBgn0000575\t323\n+FBgn0000576\t0\n+FBgn0000577\t1\n+FBgn0000578\t1493\n+FBgn0000579\t1621\n+FBgn0000581\t898\n+FBgn0000588\t93\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t5\n+FBgn0000606\t0\n+FBgn0000611\t351\n+FBgn0000615\t72\n+FBgn0000617\t151\n+FBgn0000618\t36\n+FBgn0000625\t0\n+FBgn0000629\t219\n+FBgn0000630\t4\n+FBgn0000633\t8\n+FBgn0000634\t73\n+FBgn0000635\t29\n+FBgn0000636\t10\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t1\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t306\n+FBgn0000667\t342\n+FBgn0000709\t566\n+FBgn0000711\t268\n+FBgn0000715\t1\n+FBgn0000719\t541\n+FBgn0000721\t193\n+FBgn0000723\t482\n+FBgn0000808\t31\n+FBgn0000810\t99\n+FBgn0000826\t23\n+FBgn0000927\t2\n+FBgn0000928\t130\n+FBgn0000964\t0\n+FBgn0000986\t457\n+FBgn0000996\t339\n+FBgn0001075\t9\n+FBgn0001077\t0\n+FBgn0001078\t252\n+FBgn0001079\t79\n+FBgn0001083\t30\n+FBgn0001084\t12\n+FBg'..b'0030344\t303\n+FBgn0030345\t52\n+FBgn0030346\t42\n+FBgn0030347\t65\n+FBgn0030348\t0\n+FBgn0030349\t425\n+FBgn0030350\t222\n+FBgn0030351\t26\n+FBgn0030352\t48\n+FBgn0030354\t419\n+FBgn0030356\t0\n+FBgn0030357\t25\n+FBgn0030358\t53\n+FBgn0030359\t0\n+FBgn0030360\t4\n+FBgn0030361\t22\n+FBgn0030362\t1711\n+FBgn0030364\t139\n+FBgn0030365\t170\n+FBgn0030366\t995\n+FBgn0030367\t6\n+FBgn0030369\t11\n+FBgn0030370\t0\n+FBgn0030373\t79\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t27\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t54\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t5\n+FBgn0030398\t0\n+FBgn0030399\t0\n+FBgn0030400\t327\n+FBgn0030403\t211\n+FBgn0030406\t39\n+FBgn0030407\t8\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t21\n+FBgn0030411\t22\n+FBgn0030412\t389\n+FBgn0030417\t28\n+FBgn0030418\t61\n+FBgn0030420\t325\n+FBgn0030421\t33\n+FBgn0030425\t2\n+FBgn0030429\t0\n+FBgn0030431\t116\n+FBgn0030432\t3\n+FBgn0030433\t81\n+FBgn0030434\t177\n+FBgn0030435\t171\n+FBgn0030437\t0\n+FBgn0030438\t2\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t101\n+FBgn0030448\t117\n+FBgn0030449\t2\n+FBgn0030451\t241\n+FBgn0030452\t243\n+FBgn0030455\t0\n+FBgn0030456\t116\n+FBgn0030457\t126\n+FBgn0030459\t2\n+FBgn0030460\t64\n+FBgn0030462\t0\n+FBgn0030465\t145\n+FBgn0030466\t484\n+FBgn0030467\t172\n+FBgn0030468\t409\n+FBgn0030469\t459\n+FBgn0030474\t213\n+FBgn0030477\t0\n+FBgn0030478\t345\n+FBgn0030479\t80\n+FBgn0030480\t36\n+FBgn0030481\t93\n+FBgn0030482\t1080\n+FBgn0030483\t3\n+FBgn0030484\t353\n+FBgn0030485\t79\n+FBgn0030486\t518\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t175\n+FBgn0030500\t159\n+FBgn0030501\t387\n+FBgn0030502\t662\n+FBgn0030503\t34\n+FBgn0030504\t663\n+FBgn0030505\t492\n+FBgn0030506\t98\n+FBgn0030507\t73\n+FBgn0030508\t2\n+FBgn0030509\t0\n+FBgn0030510\t76\n+FBgn0030511\t35\n+FBgn0030512\t236\n+FBgn0030514\t374\n+FBgn0030518\t44\n+FBgn0030519\t231\n+FBgn0030520\t1189\n+FBgn0030521\t988\n+FBgn0030522\t43\n+FBgn0030524\t1\n+FBgn0030525\t2\n+FBgn0030528\t27\n+FBgn0030529\t2794\n+FBgn0030530\t409\n+FBgn0030532\t490\n+FBgn0030536\t3\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t50\n+FBgn0030551\t0\n+FBgn0030552\t93\n+FBgn0030554\t70\n+FBgn0030555\t36\n+FBgn0030556\t306\n+FBgn0030558\t0\n+FBgn0030559\t0\n+FBgn0030562\t5\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t49\n+FBgn0030572\t83\n+FBgn0030573\t14\n+FBgn0030574\t2\n+FBgn0030575\t8\n+FBgn0030576\t74\n+FBgn0030577\t1\n+FBgn0030578\t0\n+FBgn0030581\t105\n+FBgn0030582\t235\n+FBgn0030583\t5\n+FBgn0030584\t90\n+FBgn0030586\t1\n+FBgn0030587\t2\n+FBgn0030588\t43\n+FBgn0030589\t2\n+FBgn0030590\t6\n+FBgn0030591\t3\n+FBgn0030592\t6\n+FBgn0030593\t3\n+FBgn0030594\t3\n+FBgn0030595\t1\n+FBgn0030596\t10\n+FBgn0030597\t4\n+FBgn0030598\t4\n+FBgn0030599\t3\n+FBgn0030600\t485\n+FBgn0030603\t151\n+FBgn0030605\t159\n+FBgn0030606\t113\n+FBgn0030607\t4\n+FBgn0030608\t0\n+FBgn0030610\t83\n+FBgn0030611\t26\n+FBgn0030612\t74\n+FBgn0030613\t2\n+FBgn0030614\t0\n+FBgn0030615\t14\n+FBgn0030616\t6872\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t58\n+FBgn0030626\t135\n+FBgn0030627\t161\n+FBgn0030628\t141\n+FBgn0030629\t31\n+FBgn0030630\t108\n+FBgn0030631\t274\n+FBgn0030634\t4\n+FBgn0030636\t4\n+FBgn0030638\t154\n+FBgn0030640\t0\n+FBgn0030641\t5\n+FBgn0030642\t5\n+FBgn0030643\t1\n+FBgn0030645\t23\n+FBgn0030646\t51\n+FBgn0030647\t3\n+FBgn0030648\t81\n+FBgn0030653\t44\n+FBgn0030654\t27\n+FBgn0030655\t65\n+FBgn0030657\t22\n+FBgn0030658\t245\n+FBgn0030659\t111\n+FBgn0030660\t30\n+FBgn0030661\t4\n+FBgn0030662\t135\n+FBgn0030663\t0\n+FBgn0030664\t5\n+FBgn0030665\t2\n+FBgn0030666\t5\n+FBgn0030667\t33\n+FBgn0030668\t65\n+FBgn0030669\t54\n+FBgn0030670\t151\n+FBgn0030671\t66\n+FBgn0030672\t1376\n+FBgn0030673\t22\n+FBgn0030674\t2023\n+FBgn0030675\t14\n+FBgn0030676\t4\n+FBgn0030678\t45\n+FBgn0030679\t119\n+FBgn0030680\t136\n+FBgn0030683\t45\n+FBgn0030684\t0\n+FBgn0030685\t663\n+FBgn0030686\t126\n+FBgn0030687\t146\n+FBgn0030688\t0\n+FBgn0030691\t7\n+FBgn0030692\t186\n+FBgn0030693\t95\n+FBgn0030694\t59\n+no_feature\t172410\n+ambiguous\t33519\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t8666693\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461177_untreat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461177_untreat_paired.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\tuntreat2\n+FBgn0000003\t0\n+FBgn0000008\t73\n+FBgn0000014\t4\n+FBgn0000015\t0\n+FBgn0000017\t3526\n+FBgn0000018\t235\n+FBgn0000022\t0\n+FBgn0000024\t3\n+FBgn0000028\t0\n+FBgn0000032\t593\n+FBgn0000036\t0\n+FBgn0000037\t7\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t45676\n+FBgn0000043\t15729\n+FBgn0000044\t14\n+FBgn0000045\t4\n+FBgn0000046\t5\n+FBgn0000047\t2\n+FBgn0000052\t1612\n+FBgn0000053\t1251\n+FBgn0000054\t455\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t437\n+FBgn0000061\t0\n+FBgn0000063\t210\n+FBgn0000064\t4891\n+FBgn0000071\t76\n+FBgn0000075\t0\n+FBgn0000077\t110\n+FBgn0000078\t20\n+FBgn0000079\t196\n+FBgn0000083\t3575\n+FBgn0000084\t1302\n+FBgn0000092\t10\n+FBgn0000094\t13\n+FBgn0000097\t2164\n+FBgn0000099\t2\n+FBgn0000100\t17109\n+FBgn0000108\t37\n+FBgn0000109\t73\n+FBgn0000114\t2\n+FBgn0000115\t355\n+FBgn0000116\t273\n+FBgn0000117\t6833\n+FBgn0000119\t450\n+FBgn0000120\t0\n+FBgn0000121\t2\n+FBgn0000137\t0\n+FBgn0000139\t343\n+FBgn0000140\t625\n+FBgn0000142\t1333\n+FBgn0000146\t844\n+FBgn0000147\t188\n+FBgn0000150\t5092\n+FBgn0000152\t316\n+FBgn0000153\t8\n+FBgn0000157\t0\n+FBgn0000158\t2\n+FBgn0000163\t719\n+FBgn0000166\t0\n+FBgn0000171\t5320\n+FBgn0000173\t833\n+FBgn0000179\t0\n+FBgn0000180\t17\n+FBgn0000181\t8601\n+FBgn0000182\t1\n+FBgn0000183\t1645\n+FBgn0000206\t0\n+FBgn0000210\t1134\n+FBgn0000212\t2059\n+FBgn0000216\t0\n+FBgn0000221\t141\n+FBgn0000227\t0\n+FBgn0000228\t565\n+FBgn0000229\t509\n+FBgn0000233\t3\n+FBgn0000239\t1654\n+FBgn0000241\t1\n+FBgn0000242\t102\n+FBgn0000244\t362\n+FBgn0000246\t77\n+FBgn0000247\t1926\n+FBgn0000250\t1437\n+FBgn0000251\t1\n+FBgn0000253\t5708\n+FBgn0000256\t1636\n+FBgn0000257\t527\n+FBgn0000258\t558\n+FBgn0000259\t1066\n+FBgn0000261\t1454\n+FBgn0000273\t1532\n+FBgn0000274\t0\n+FBgn0000276\t21\n+FBgn0000277\t7\n+FBgn0000278\t26\n+FBgn0000279\t15\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2214\n+FBgn0000286\t368\n+FBgn0000287\t0\n+FBgn0000289\t2368\n+FBgn0000299\t30451\n+FBgn0000303\t1\n+FBgn0000307\t1124\n+FBgn0000308\t8969\n+FBgn0000313\t27\n+FBgn0000316\t1\n+FBgn0000317\t848\n+FBgn0000318\t505\n+FBgn0000319\t9273\n+FBgn0000320\t0\n+FBgn0000326\t187\n+FBgn0000330\t183\n+FBgn0000337\t15\n+FBgn0000338\t1328\n+FBgn0000339\t275\n+FBgn0000346\t53\n+FBgn0000351\t25\n+FBgn0000352\t584\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t0\n+FBgn0000370\t6689\n+FBgn0000376\t832\n+FBgn0000377\t592\n+FBgn0000382\t555\n+FBgn0000384\t386\n+FBgn0000392\t604\n+FBgn0000394\t412\n+FBgn0000395\t426\n+FBgn0000404\t1453\n+FBgn0000405\t1293\n+FBgn0000406\t237\n+FBgn0000409\t2478\n+FBgn0000411\t0\n+FBgn0000412\t1638\n+FBgn0000413\t2088\n+FBgn0000414\t1642\n+FBgn0000416\t28244\n+FBgn0000422\t3\n+FBgn0000426\t390\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t1\n+FBgn0000447\t306\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1808\n+FBgn0000455\t397\n+FBgn0000459\t2\n+FBgn0000463\t0\n+FBgn0000464\t1018\n+FBgn0000472\t1960\n+FBgn0000473\t8\n+FBgn0000477\t0\n+FBgn0000479\t545\n+FBgn0000482\t678\n+FBgn0000489\t74\n+FBgn0000490\t109\n+FBgn0000492\t0\n+FBgn0000497\t1\n+FBgn0000499\t692\n+FBgn0000500\t0\n+FBgn0000504\t0\n+FBgn0000520\t415\n+FBgn0000524\t520\n+FBgn0000527\t115\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t158\n+FBgn0000536\t484\n+FBgn0000541\t3203\n+FBgn0000542\t132\n+FBgn0000543\t423\n+FBgn0000546\t749\n+FBgn0000547\t220\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t130033\n+FBgn0000557\t27\n+FBgn0000559\t68894\n+FBgn0000560\t0\n+FBgn0000562\t1017\n+FBgn0000564\t0\n+FBgn0000565\t307\n+FBgn0000566\t407\n+FBgn0000567\t250\n+FBgn0000568\t3260\n+FBgn0000575\t874\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t4155\n+FBgn0000579\t5142\n+FBgn0000581\t2592\n+FBgn0000588\t223\n+FBgn0000591\t0\n+FBgn0000592\t0\n+FBgn0000594\t18\n+FBgn0000606\t0\n+FBgn0000611\t826\n+FBgn0000615\t197\n+FBgn0000617\t521\n+FBgn0000618\t58\n+FBgn0000625\t0\n+FBgn0000629\t741\n+FBgn0000630\t24\n+FBgn0000633\t5\n+FBgn0000634\t179\n+FBgn0000635\t108\n+FBgn0000636\t22\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t2\n+FBgn0000659\t0\n+FBgn0000662\t801\n+FBgn0000667\t1080\n+FBgn0000709\t1794\n+FBgn0000711\t564\n+FBgn0000715\t0\n+FBgn0000719\t1500\n+FBgn0000721\t613\n+FBgn0000723\t1372\n+FBgn0000808\t80\n+FBgn0000810\t159\n+FBgn0000826\t63\n+FBgn0000927\t20\n+FBgn0000928\t384\n+FBgn0000964\t0\n+FBgn0000986\t1596\n+FBgn0000996\t801\n+FBgn0001075\t2'..b'+FBgn0030349\t1367\n+FBgn0030350\t443\n+FBgn0030351\t52\n+FBgn0030352\t149\n+FBgn0030354\t1399\n+FBgn0030356\t0\n+FBgn0030357\t41\n+FBgn0030358\t143\n+FBgn0030359\t5\n+FBgn0030360\t14\n+FBgn0030361\t48\n+FBgn0030362\t4486\n+FBgn0030364\t241\n+FBgn0030365\t534\n+FBgn0030366\t2648\n+FBgn0030367\t32\n+FBgn0030369\t20\n+FBgn0030370\t0\n+FBgn0030373\t137\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t25\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t175\n+FBgn0030394\t6\n+FBgn0030395\t0\n+FBgn0030396\t14\n+FBgn0030398\t1\n+FBgn0030399\t3\n+FBgn0030400\t1048\n+FBgn0030403\t750\n+FBgn0030406\t131\n+FBgn0030407\t23\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t67\n+FBgn0030411\t74\n+FBgn0030412\t821\n+FBgn0030417\t81\n+FBgn0030418\t220\n+FBgn0030420\t739\n+FBgn0030421\t81\n+FBgn0030425\t4\n+FBgn0030429\t1\n+FBgn0030431\t301\n+FBgn0030432\t28\n+FBgn0030433\t246\n+FBgn0030434\t593\n+FBgn0030435\t425\n+FBgn0030437\t0\n+FBgn0030438\t5\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t311\n+FBgn0030448\t446\n+FBgn0030449\t0\n+FBgn0030451\t660\n+FBgn0030452\t666\n+FBgn0030455\t6\n+FBgn0030456\t364\n+FBgn0030457\t299\n+FBgn0030459\t3\n+FBgn0030460\t230\n+FBgn0030462\t0\n+FBgn0030465\t414\n+FBgn0030466\t1718\n+FBgn0030467\t437\n+FBgn0030468\t1151\n+FBgn0030469\t1579\n+FBgn0030474\t564\n+FBgn0030477\t3\n+FBgn0030478\t936\n+FBgn0030479\t159\n+FBgn0030480\t120\n+FBgn0030481\t265\n+FBgn0030482\t3006\n+FBgn0030483\t3\n+FBgn0030484\t747\n+FBgn0030485\t155\n+FBgn0030486\t1549\n+FBgn0030491\t3\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t573\n+FBgn0030500\t446\n+FBgn0030501\t766\n+FBgn0030502\t1894\n+FBgn0030503\t94\n+FBgn0030504\t1883\n+FBgn0030505\t1329\n+FBgn0030506\t203\n+FBgn0030507\t190\n+FBgn0030508\t5\n+FBgn0030509\t0\n+FBgn0030510\t281\n+FBgn0030511\t96\n+FBgn0030512\t870\n+FBgn0030514\t1092\n+FBgn0030518\t137\n+FBgn0030519\t662\n+FBgn0030520\t3457\n+FBgn0030521\t3478\n+FBgn0030522\t147\n+FBgn0030524\t5\n+FBgn0030525\t2\n+FBgn0030528\t101\n+FBgn0030529\t6362\n+FBgn0030530\t1197\n+FBgn0030532\t1942\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t1\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t143\n+FBgn0030551\t0\n+FBgn0030552\t342\n+FBgn0030554\t212\n+FBgn0030555\t148\n+FBgn0030556\t986\n+FBgn0030558\t1\n+FBgn0030559\t7\n+FBgn0030562\t21\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t153\n+FBgn0030572\t187\n+FBgn0030573\t24\n+FBgn0030574\t10\n+FBgn0030575\t22\n+FBgn0030576\t203\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t365\n+FBgn0030582\t525\n+FBgn0030583\t17\n+FBgn0030584\t129\n+FBgn0030586\t5\n+FBgn0030587\t4\n+FBgn0030588\t91\n+FBgn0030589\t2\n+FBgn0030590\t17\n+FBgn0030591\t2\n+FBgn0030592\t1\n+FBgn0030593\t8\n+FBgn0030594\t4\n+FBgn0030595\t0\n+FBgn0030596\t19\n+FBgn0030597\t2\n+FBgn0030598\t6\n+FBgn0030599\t1\n+FBgn0030600\t1872\n+FBgn0030603\t411\n+FBgn0030605\t422\n+FBgn0030606\t326\n+FBgn0030607\t21\n+FBgn0030608\t0\n+FBgn0030610\t175\n+FBgn0030611\t64\n+FBgn0030612\t271\n+FBgn0030613\t6\n+FBgn0030614\t0\n+FBgn0030615\t43\n+FBgn0030616\t16177\n+FBgn0030617\t0\n+FBgn0030618\t1\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t183\n+FBgn0030626\t325\n+FBgn0030627\t743\n+FBgn0030628\t316\n+FBgn0030629\t71\n+FBgn0030630\t348\n+FBgn0030631\t958\n+FBgn0030634\t4\n+FBgn0030636\t8\n+FBgn0030638\t582\n+FBgn0030640\t0\n+FBgn0030641\t8\n+FBgn0030642\t20\n+FBgn0030643\t6\n+FBgn0030645\t55\n+FBgn0030646\t108\n+FBgn0030647\t11\n+FBgn0030648\t246\n+FBgn0030653\t135\n+FBgn0030654\t99\n+FBgn0030655\t185\n+FBgn0030657\t43\n+FBgn0030658\t760\n+FBgn0030659\t281\n+FBgn0030660\t88\n+FBgn0030661\t22\n+FBgn0030662\t455\n+FBgn0030663\t5\n+FBgn0030664\t4\n+FBgn0030665\t4\n+FBgn0030666\t15\n+FBgn0030667\t29\n+FBgn0030668\t137\n+FBgn0030669\t145\n+FBgn0030670\t385\n+FBgn0030671\t222\n+FBgn0030672\t4354\n+FBgn0030673\t41\n+FBgn0030674\t7263\n+FBgn0030675\t48\n+FBgn0030676\t9\n+FBgn0030678\t172\n+FBgn0030679\t245\n+FBgn0030680\t376\n+FBgn0030683\t141\n+FBgn0030684\t8\n+FBgn0030685\t1403\n+FBgn0030686\t268\n+FBgn0030687\t521\n+FBgn0030688\t1\n+FBgn0030691\t16\n+FBgn0030692\t488\n+FBgn0030693\t182\n+FBgn0030694\t142\n+no_feature\t349912\n+ambiguous\t83890\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t13300038\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461177_untreat_paired.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461177_untreat_paired.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t73\n+FBgn0000014\t4\n+FBgn0000015\t0\n+FBgn0000017\t3526\n+FBgn0000018\t235\n+FBgn0000022\t0\n+FBgn0000024\t3\n+FBgn0000028\t0\n+FBgn0000032\t593\n+FBgn0000036\t0\n+FBgn0000037\t7\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t45676\n+FBgn0000043\t15729\n+FBgn0000044\t14\n+FBgn0000045\t4\n+FBgn0000046\t5\n+FBgn0000047\t2\n+FBgn0000052\t1612\n+FBgn0000053\t1251\n+FBgn0000054\t455\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t437\n+FBgn0000061\t0\n+FBgn0000063\t210\n+FBgn0000064\t4891\n+FBgn0000071\t76\n+FBgn0000075\t0\n+FBgn0000077\t110\n+FBgn0000078\t20\n+FBgn0000079\t196\n+FBgn0000083\t3575\n+FBgn0000084\t1302\n+FBgn0000092\t10\n+FBgn0000094\t13\n+FBgn0000097\t2164\n+FBgn0000099\t2\n+FBgn0000100\t17109\n+FBgn0000108\t37\n+FBgn0000109\t73\n+FBgn0000114\t2\n+FBgn0000115\t355\n+FBgn0000116\t273\n+FBgn0000117\t6833\n+FBgn0000119\t450\n+FBgn0000120\t0\n+FBgn0000121\t2\n+FBgn0000137\t0\n+FBgn0000139\t343\n+FBgn0000140\t625\n+FBgn0000142\t1333\n+FBgn0000146\t844\n+FBgn0000147\t188\n+FBgn0000150\t5092\n+FBgn0000152\t316\n+FBgn0000153\t8\n+FBgn0000157\t0\n+FBgn0000158\t2\n+FBgn0000163\t719\n+FBgn0000166\t0\n+FBgn0000171\t5320\n+FBgn0000173\t833\n+FBgn0000179\t0\n+FBgn0000180\t17\n+FBgn0000181\t8601\n+FBgn0000182\t1\n+FBgn0000183\t1645\n+FBgn0000206\t0\n+FBgn0000210\t1134\n+FBgn0000212\t2059\n+FBgn0000216\t0\n+FBgn0000221\t141\n+FBgn0000227\t0\n+FBgn0000228\t565\n+FBgn0000229\t509\n+FBgn0000233\t3\n+FBgn0000239\t1654\n+FBgn0000241\t1\n+FBgn0000242\t102\n+FBgn0000244\t362\n+FBgn0000246\t77\n+FBgn0000247\t1926\n+FBgn0000250\t1437\n+FBgn0000251\t1\n+FBgn0000253\t5708\n+FBgn0000256\t1636\n+FBgn0000257\t527\n+FBgn0000258\t558\n+FBgn0000259\t1066\n+FBgn0000261\t1454\n+FBgn0000273\t1532\n+FBgn0000274\t0\n+FBgn0000276\t21\n+FBgn0000277\t7\n+FBgn0000278\t26\n+FBgn0000279\t15\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2214\n+FBgn0000286\t368\n+FBgn0000287\t0\n+FBgn0000289\t2368\n+FBgn0000299\t30451\n+FBgn0000303\t1\n+FBgn0000307\t1124\n+FBgn0000308\t8969\n+FBgn0000313\t27\n+FBgn0000316\t1\n+FBgn0000317\t848\n+FBgn0000318\t505\n+FBgn0000319\t9273\n+FBgn0000320\t0\n+FBgn0000326\t187\n+FBgn0000330\t183\n+FBgn0000337\t15\n+FBgn0000338\t1328\n+FBgn0000339\t275\n+FBgn0000346\t53\n+FBgn0000351\t25\n+FBgn0000352\t584\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t0\n+FBgn0000370\t6689\n+FBgn0000376\t832\n+FBgn0000377\t592\n+FBgn0000382\t555\n+FBgn0000384\t386\n+FBgn0000392\t604\n+FBgn0000394\t412\n+FBgn0000395\t426\n+FBgn0000404\t1453\n+FBgn0000405\t1293\n+FBgn0000406\t237\n+FBgn0000409\t2478\n+FBgn0000411\t0\n+FBgn0000412\t1638\n+FBgn0000413\t2088\n+FBgn0000414\t1642\n+FBgn0000416\t28244\n+FBgn0000422\t3\n+FBgn0000426\t390\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t1\n+FBgn0000447\t306\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1808\n+FBgn0000455\t397\n+FBgn0000459\t2\n+FBgn0000463\t0\n+FBgn0000464\t1018\n+FBgn0000472\t1960\n+FBgn0000473\t8\n+FBgn0000477\t0\n+FBgn0000479\t545\n+FBgn0000482\t678\n+FBgn0000489\t74\n+FBgn0000490\t109\n+FBgn0000492\t0\n+FBgn0000497\t1\n+FBgn0000499\t692\n+FBgn0000500\t0\n+FBgn0000504\t0\n+FBgn0000520\t415\n+FBgn0000524\t520\n+FBgn0000527\t115\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t158\n+FBgn0000536\t484\n+FBgn0000541\t3203\n+FBgn0000542\t132\n+FBgn0000543\t423\n+FBgn0000546\t749\n+FBgn0000547\t220\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t130033\n+FBgn0000557\t27\n+FBgn0000559\t68894\n+FBgn0000560\t0\n+FBgn0000562\t1017\n+FBgn0000564\t0\n+FBgn0000565\t307\n+FBgn0000566\t407\n+FBgn0000567\t250\n+FBgn0000568\t3260\n+FBgn0000575\t874\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t4155\n+FBgn0000579\t5142\n+FBgn0000581\t2592\n+FBgn0000588\t223\n+FBgn0000591\t0\n+FBgn0000592\t0\n+FBgn0000594\t18\n+FBgn0000606\t0\n+FBgn0000611\t826\n+FBgn0000615\t197\n+FBgn0000617\t521\n+FBgn0000618\t58\n+FBgn0000625\t0\n+FBgn0000629\t741\n+FBgn0000630\t24\n+FBgn0000633\t5\n+FBgn0000634\t179\n+FBgn0000635\t108\n+FBgn0000636\t22\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t2\n+FBgn0000659\t0\n+FBgn0000662\t801\n+FBgn0000667\t1080\n+FBgn0000709\t1794\n+FBgn0000711\t564\n+FBgn0000715\t0\n+FBgn0000719\t1500\n+FBgn0000721\t613\n+FBgn0000723\t1372\n+FBgn0000808\t80\n+FBgn0000810\t159\n+FBgn0000826\t63\n+FBgn0000927\t20\n+FBgn0000928\t384\n+FBgn0000964\t0\n+FBgn0000986\t1596\n+FBgn0000996\t801\n+FBgn0001075\t27\n+FBgn0001077\t0\n'..b'+FBgn0030349\t1367\n+FBgn0030350\t443\n+FBgn0030351\t52\n+FBgn0030352\t149\n+FBgn0030354\t1399\n+FBgn0030356\t0\n+FBgn0030357\t41\n+FBgn0030358\t143\n+FBgn0030359\t5\n+FBgn0030360\t14\n+FBgn0030361\t48\n+FBgn0030362\t4486\n+FBgn0030364\t241\n+FBgn0030365\t534\n+FBgn0030366\t2648\n+FBgn0030367\t32\n+FBgn0030369\t20\n+FBgn0030370\t0\n+FBgn0030373\t137\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t25\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t175\n+FBgn0030394\t6\n+FBgn0030395\t0\n+FBgn0030396\t14\n+FBgn0030398\t1\n+FBgn0030399\t3\n+FBgn0030400\t1048\n+FBgn0030403\t750\n+FBgn0030406\t131\n+FBgn0030407\t23\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t67\n+FBgn0030411\t74\n+FBgn0030412\t821\n+FBgn0030417\t81\n+FBgn0030418\t220\n+FBgn0030420\t739\n+FBgn0030421\t81\n+FBgn0030425\t4\n+FBgn0030429\t1\n+FBgn0030431\t301\n+FBgn0030432\t28\n+FBgn0030433\t246\n+FBgn0030434\t593\n+FBgn0030435\t425\n+FBgn0030437\t0\n+FBgn0030438\t5\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t311\n+FBgn0030448\t446\n+FBgn0030449\t0\n+FBgn0030451\t660\n+FBgn0030452\t666\n+FBgn0030455\t6\n+FBgn0030456\t364\n+FBgn0030457\t299\n+FBgn0030459\t3\n+FBgn0030460\t230\n+FBgn0030462\t0\n+FBgn0030465\t414\n+FBgn0030466\t1718\n+FBgn0030467\t437\n+FBgn0030468\t1151\n+FBgn0030469\t1579\n+FBgn0030474\t564\n+FBgn0030477\t3\n+FBgn0030478\t936\n+FBgn0030479\t159\n+FBgn0030480\t120\n+FBgn0030481\t265\n+FBgn0030482\t3006\n+FBgn0030483\t3\n+FBgn0030484\t747\n+FBgn0030485\t155\n+FBgn0030486\t1549\n+FBgn0030491\t3\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t573\n+FBgn0030500\t446\n+FBgn0030501\t766\n+FBgn0030502\t1894\n+FBgn0030503\t94\n+FBgn0030504\t1883\n+FBgn0030505\t1329\n+FBgn0030506\t203\n+FBgn0030507\t190\n+FBgn0030508\t5\n+FBgn0030509\t0\n+FBgn0030510\t281\n+FBgn0030511\t96\n+FBgn0030512\t870\n+FBgn0030514\t1092\n+FBgn0030518\t137\n+FBgn0030519\t662\n+FBgn0030520\t3457\n+FBgn0030521\t3478\n+FBgn0030522\t147\n+FBgn0030524\t5\n+FBgn0030525\t2\n+FBgn0030528\t101\n+FBgn0030529\t6362\n+FBgn0030530\t1197\n+FBgn0030532\t1942\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t1\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t143\n+FBgn0030551\t0\n+FBgn0030552\t342\n+FBgn0030554\t212\n+FBgn0030555\t148\n+FBgn0030556\t986\n+FBgn0030558\t1\n+FBgn0030559\t7\n+FBgn0030562\t21\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t153\n+FBgn0030572\t187\n+FBgn0030573\t24\n+FBgn0030574\t10\n+FBgn0030575\t22\n+FBgn0030576\t203\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t365\n+FBgn0030582\t525\n+FBgn0030583\t17\n+FBgn0030584\t129\n+FBgn0030586\t5\n+FBgn0030587\t4\n+FBgn0030588\t91\n+FBgn0030589\t2\n+FBgn0030590\t17\n+FBgn0030591\t2\n+FBgn0030592\t1\n+FBgn0030593\t8\n+FBgn0030594\t4\n+FBgn0030595\t0\n+FBgn0030596\t19\n+FBgn0030597\t2\n+FBgn0030598\t6\n+FBgn0030599\t1\n+FBgn0030600\t1872\n+FBgn0030603\t411\n+FBgn0030605\t422\n+FBgn0030606\t326\n+FBgn0030607\t21\n+FBgn0030608\t0\n+FBgn0030610\t175\n+FBgn0030611\t64\n+FBgn0030612\t271\n+FBgn0030613\t6\n+FBgn0030614\t0\n+FBgn0030615\t43\n+FBgn0030616\t16177\n+FBgn0030617\t0\n+FBgn0030618\t1\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t183\n+FBgn0030626\t325\n+FBgn0030627\t743\n+FBgn0030628\t316\n+FBgn0030629\t71\n+FBgn0030630\t348\n+FBgn0030631\t958\n+FBgn0030634\t4\n+FBgn0030636\t8\n+FBgn0030638\t582\n+FBgn0030640\t0\n+FBgn0030641\t8\n+FBgn0030642\t20\n+FBgn0030643\t6\n+FBgn0030645\t55\n+FBgn0030646\t108\n+FBgn0030647\t11\n+FBgn0030648\t246\n+FBgn0030653\t135\n+FBgn0030654\t99\n+FBgn0030655\t185\n+FBgn0030657\t43\n+FBgn0030658\t760\n+FBgn0030659\t281\n+FBgn0030660\t88\n+FBgn0030661\t22\n+FBgn0030662\t455\n+FBgn0030663\t5\n+FBgn0030664\t4\n+FBgn0030665\t4\n+FBgn0030666\t15\n+FBgn0030667\t29\n+FBgn0030668\t137\n+FBgn0030669\t145\n+FBgn0030670\t385\n+FBgn0030671\t222\n+FBgn0030672\t4354\n+FBgn0030673\t41\n+FBgn0030674\t7263\n+FBgn0030675\t48\n+FBgn0030676\t9\n+FBgn0030678\t172\n+FBgn0030679\t245\n+FBgn0030680\t376\n+FBgn0030683\t141\n+FBgn0030684\t8\n+FBgn0030685\t1403\n+FBgn0030686\t268\n+FBgn0030687\t521\n+FBgn0030688\t1\n+FBgn0030691\t16\n+FBgn0030692\t488\n+FBgn0030693\t182\n+FBgn0030694\t142\n+no_feature\t349912\n+ambiguous\t83890\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t13300038\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461178_untreat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461178_untreat_paired.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\tuntreat3\n+FBgn0000003\t0\n+FBgn0000008\t57\n+FBgn0000014\t0\n+FBgn0000015\t1\n+FBgn0000017\t2834\n+FBgn0000018\t273\n+FBgn0000022\t0\n+FBgn0000024\t2\n+FBgn0000028\t0\n+FBgn0000032\t648\n+FBgn0000036\t0\n+FBgn0000037\t0\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t50543\n+FBgn0000043\t17159\n+FBgn0000044\t14\n+FBgn0000045\t6\n+FBgn0000046\t5\n+FBgn0000047\t3\n+FBgn0000052\t1808\n+FBgn0000053\t1386\n+FBgn0000054\t427\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t531\n+FBgn0000061\t1\n+FBgn0000063\t233\n+FBgn0000064\t5205\n+FBgn0000071\t84\n+FBgn0000075\t1\n+FBgn0000077\t156\n+FBgn0000078\t30\n+FBgn0000079\t201\n+FBgn0000083\t4230\n+FBgn0000084\t1456\n+FBgn0000092\t10\n+FBgn0000094\t4\n+FBgn0000097\t1890\n+FBgn0000099\t1\n+FBgn0000100\t21320\n+FBgn0000108\t32\n+FBgn0000109\t99\n+FBgn0000114\t0\n+FBgn0000115\t403\n+FBgn0000116\t258\n+FBgn0000117\t7410\n+FBgn0000119\t461\n+FBgn0000120\t0\n+FBgn0000121\t1\n+FBgn0000137\t0\n+FBgn0000139\t546\n+FBgn0000140\t493\n+FBgn0000142\t1224\n+FBgn0000146\t903\n+FBgn0000147\t286\n+FBgn0000150\t6269\n+FBgn0000152\t353\n+FBgn0000153\t19\n+FBgn0000157\t0\n+FBgn0000158\t1\n+FBgn0000163\t645\n+FBgn0000166\t0\n+FBgn0000171\t4539\n+FBgn0000173\t1169\n+FBgn0000179\t0\n+FBgn0000180\t13\n+FBgn0000181\t10139\n+FBgn0000182\t4\n+FBgn0000183\t1795\n+FBgn0000206\t0\n+FBgn0000210\t904\n+FBgn0000212\t2093\n+FBgn0000216\t0\n+FBgn0000221\t188\n+FBgn0000227\t0\n+FBgn0000228\t544\n+FBgn0000229\t550\n+FBgn0000233\t6\n+FBgn0000239\t1691\n+FBgn0000241\t2\n+FBgn0000242\t105\n+FBgn0000244\t332\n+FBgn0000246\t68\n+FBgn0000247\t1835\n+FBgn0000250\t1640\n+FBgn0000251\t1\n+FBgn0000253\t6073\n+FBgn0000256\t1607\n+FBgn0000257\t558\n+FBgn0000258\t557\n+FBgn0000259\t1174\n+FBgn0000261\t1350\n+FBgn0000273\t1265\n+FBgn0000274\t0\n+FBgn0000276\t30\n+FBgn0000277\t17\n+FBgn0000278\t24\n+FBgn0000279\t24\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2302\n+FBgn0000286\t325\n+FBgn0000287\t1\n+FBgn0000289\t2375\n+FBgn0000299\t28552\n+FBgn0000303\t0\n+FBgn0000307\t968\n+FBgn0000308\t10605\n+FBgn0000313\t32\n+FBgn0000316\t1\n+FBgn0000317\t853\n+FBgn0000318\t709\n+FBgn0000319\t9571\n+FBgn0000320\t0\n+FBgn0000326\t144\n+FBgn0000330\t180\n+FBgn0000337\t16\n+FBgn0000338\t1070\n+FBgn0000339\t366\n+FBgn0000346\t39\n+FBgn0000351\t29\n+FBgn0000352\t533\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t3\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t1\n+FBgn0000363\t7\n+FBgn0000370\t8048\n+FBgn0000376\t926\n+FBgn0000377\t609\n+FBgn0000382\t499\n+FBgn0000384\t436\n+FBgn0000392\t625\n+FBgn0000394\t452\n+FBgn0000395\t354\n+FBgn0000404\t1584\n+FBgn0000405\t1238\n+FBgn0000406\t382\n+FBgn0000409\t3223\n+FBgn0000411\t0\n+FBgn0000412\t1798\n+FBgn0000413\t1829\n+FBgn0000414\t1525\n+FBgn0000416\t31544\n+FBgn0000422\t2\n+FBgn0000426\t467\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t2\n+FBgn0000447\t388\n+FBgn0000448\t2\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1946\n+FBgn0000455\t512\n+FBgn0000459\t3\n+FBgn0000463\t1\n+FBgn0000464\t961\n+FBgn0000472\t1706\n+FBgn0000473\t12\n+FBgn0000477\t1\n+FBgn0000479\t624\n+FBgn0000482\t751\n+FBgn0000489\t67\n+FBgn0000490\t97\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t682\n+FBgn0000500\t5\n+FBgn0000504\t3\n+FBgn0000520\t425\n+FBgn0000524\t519\n+FBgn0000527\t119\n+FBgn0000529\t0\n+FBgn0000533\t8\n+FBgn0000535\t133\n+FBgn0000536\t557\n+FBgn0000541\t2697\n+FBgn0000542\t110\n+FBgn0000543\t517\n+FBgn0000546\t562\n+FBgn0000547\t182\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t153364\n+FBgn0000557\t24\n+FBgn0000559\t81476\n+FBgn0000560\t0\n+FBgn0000562\t981\n+FBgn0000564\t0\n+FBgn0000565\t352\n+FBgn0000566\t593\n+FBgn0000567\t212\n+FBgn0000568\t2567\n+FBgn0000575\t785\n+FBgn0000576\t0\n+FBgn0000577\t2\n+FBgn0000578\t3649\n+FBgn0000579\t5543\n+FBgn0000581\t2256\n+FBgn0000588\t270\n+FBgn0000591\t0\n+FBgn0000592\t2\n+FBgn0000594\t19\n+FBgn0000606\t0\n+FBgn0000611\t1005\n+FBgn0000615\t250\n+FBgn0000617\t641\n+FBgn0000618\t112\n+FBgn0000625\t0\n+FBgn0000629\t744\n+FBgn0000630\t8\n+FBgn0000633\t11\n+FBgn0000634\t200\n+FBgn0000635\t102\n+FBgn0000636\t34\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t3\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t764\n+FBgn0000667\t1247\n+FBgn0000709\t1605\n+FBgn0000711\t688\n+FBgn0000715\t0\n+FBgn0000719\t1351\n+FBgn0000721\t578\n+FBgn0000723\t1436\n+FBgn0000808\t103\n+FBgn0000810\t152\n+FBgn0000826\t68\n+FBgn0000927\t23\n+FBgn0000928\t423\n+FBgn0000964\t1\n+FBgn0000986\t1394\n+FBgn0000996\t848\n+FBgn000107'..b'0030349\t1431\n+FBgn0030350\t564\n+FBgn0030351\t76\n+FBgn0030352\t202\n+FBgn0030354\t1343\n+FBgn0030356\t0\n+FBgn0030357\t55\n+FBgn0030358\t208\n+FBgn0030359\t1\n+FBgn0030360\t18\n+FBgn0030361\t84\n+FBgn0030362\t6022\n+FBgn0030364\t423\n+FBgn0030365\t582\n+FBgn0030366\t2600\n+FBgn0030367\t64\n+FBgn0030369\t35\n+FBgn0030370\t0\n+FBgn0030373\t184\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t41\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t239\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t25\n+FBgn0030398\t2\n+FBgn0030399\t0\n+FBgn0030400\t864\n+FBgn0030403\t867\n+FBgn0030406\t123\n+FBgn0030407\t35\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t59\n+FBgn0030411\t77\n+FBgn0030412\t921\n+FBgn0030417\t63\n+FBgn0030418\t270\n+FBgn0030420\t685\n+FBgn0030421\t100\n+FBgn0030425\t4\n+FBgn0030429\t1\n+FBgn0030431\t379\n+FBgn0030432\t22\n+FBgn0030433\t300\n+FBgn0030434\t593\n+FBgn0030435\t515\n+FBgn0030437\t0\n+FBgn0030438\t0\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t454\n+FBgn0030448\t319\n+FBgn0030449\t1\n+FBgn0030451\t871\n+FBgn0030452\t808\n+FBgn0030455\t1\n+FBgn0030456\t408\n+FBgn0030457\t331\n+FBgn0030459\t3\n+FBgn0030460\t350\n+FBgn0030462\t1\n+FBgn0030465\t542\n+FBgn0030466\t1593\n+FBgn0030467\t519\n+FBgn0030468\t1136\n+FBgn0030469\t1506\n+FBgn0030474\t606\n+FBgn0030477\t1\n+FBgn0030478\t1231\n+FBgn0030479\t165\n+FBgn0030480\t188\n+FBgn0030481\t310\n+FBgn0030482\t3044\n+FBgn0030483\t0\n+FBgn0030484\t831\n+FBgn0030485\t198\n+FBgn0030486\t1432\n+FBgn0030491\t2\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t525\n+FBgn0030500\t412\n+FBgn0030501\t951\n+FBgn0030502\t1806\n+FBgn0030503\t107\n+FBgn0030504\t2049\n+FBgn0030505\t1152\n+FBgn0030506\t329\n+FBgn0030507\t324\n+FBgn0030508\t6\n+FBgn0030509\t0\n+FBgn0030510\t334\n+FBgn0030511\t116\n+FBgn0030512\t897\n+FBgn0030514\t1188\n+FBgn0030518\t182\n+FBgn0030519\t1023\n+FBgn0030520\t3494\n+FBgn0030521\t3998\n+FBgn0030522\t199\n+FBgn0030524\t4\n+FBgn0030525\t2\n+FBgn0030528\t120\n+FBgn0030529\t7019\n+FBgn0030530\t1220\n+FBgn0030532\t1496\n+FBgn0030536\t0\n+FBgn0030537\t1\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t187\n+FBgn0030551\t2\n+FBgn0030552\t365\n+FBgn0030554\t242\n+FBgn0030555\t137\n+FBgn0030556\t1131\n+FBgn0030558\t0\n+FBgn0030559\t4\n+FBgn0030562\t17\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t167\n+FBgn0030572\t228\n+FBgn0030573\t22\n+FBgn0030574\t8\n+FBgn0030575\t31\n+FBgn0030576\t182\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t342\n+FBgn0030582\t587\n+FBgn0030583\t33\n+FBgn0030584\t183\n+FBgn0030586\t2\n+FBgn0030587\t3\n+FBgn0030588\t121\n+FBgn0030589\t0\n+FBgn0030590\t11\n+FBgn0030591\t2\n+FBgn0030592\t11\n+FBgn0030593\t9\n+FBgn0030594\t5\n+FBgn0030595\t0\n+FBgn0030596\t10\n+FBgn0030597\t1\n+FBgn0030598\t7\n+FBgn0030599\t2\n+FBgn0030600\t1776\n+FBgn0030603\t408\n+FBgn0030605\t536\n+FBgn0030606\t345\n+FBgn0030607\t11\n+FBgn0030608\t0\n+FBgn0030610\t201\n+FBgn0030611\t88\n+FBgn0030612\t348\n+FBgn0030613\t8\n+FBgn0030614\t0\n+FBgn0030615\t47\n+FBgn0030616\t21615\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t189\n+FBgn0030626\t266\n+FBgn0030627\t681\n+FBgn0030628\t325\n+FBgn0030629\t90\n+FBgn0030630\t439\n+FBgn0030631\t949\n+FBgn0030634\t3\n+FBgn0030636\t6\n+FBgn0030638\t658\n+FBgn0030640\t0\n+FBgn0030641\t2\n+FBgn0030642\t10\n+FBgn0030643\t7\n+FBgn0030645\t55\n+FBgn0030646\t155\n+FBgn0030647\t1\n+FBgn0030648\t269\n+FBgn0030653\t143\n+FBgn0030654\t58\n+FBgn0030655\t204\n+FBgn0030657\t54\n+FBgn0030658\t858\n+FBgn0030659\t320\n+FBgn0030660\t90\n+FBgn0030661\t10\n+FBgn0030662\t416\n+FBgn0030663\t1\n+FBgn0030664\t13\n+FBgn0030665\t3\n+FBgn0030666\t16\n+FBgn0030667\t60\n+FBgn0030668\t198\n+FBgn0030669\t183\n+FBgn0030670\t475\n+FBgn0030671\t239\n+FBgn0030672\t4892\n+FBgn0030673\t60\n+FBgn0030674\t5990\n+FBgn0030675\t73\n+FBgn0030676\t6\n+FBgn0030678\t139\n+FBgn0030679\t346\n+FBgn0030680\t355\n+FBgn0030683\t174\n+FBgn0030684\t1\n+FBgn0030685\t1414\n+FBgn0030686\t339\n+FBgn0030687\t532\n+FBgn0030688\t1\n+FBgn0030691\t8\n+FBgn0030692\t538\n+FBgn0030693\t242\n+FBgn0030694\t168\n+no_feature\t284334\n+ambiguous\t96881\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t11365569\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461178_untreat_paired.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461178_untreat_paired.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t57\n+FBgn0000014\t0\n+FBgn0000015\t1\n+FBgn0000017\t2834\n+FBgn0000018\t273\n+FBgn0000022\t0\n+FBgn0000024\t2\n+FBgn0000028\t0\n+FBgn0000032\t648\n+FBgn0000036\t0\n+FBgn0000037\t0\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t50543\n+FBgn0000043\t17159\n+FBgn0000044\t14\n+FBgn0000045\t6\n+FBgn0000046\t5\n+FBgn0000047\t3\n+FBgn0000052\t1808\n+FBgn0000053\t1386\n+FBgn0000054\t427\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t531\n+FBgn0000061\t1\n+FBgn0000063\t233\n+FBgn0000064\t5205\n+FBgn0000071\t84\n+FBgn0000075\t1\n+FBgn0000077\t156\n+FBgn0000078\t30\n+FBgn0000079\t201\n+FBgn0000083\t4230\n+FBgn0000084\t1456\n+FBgn0000092\t10\n+FBgn0000094\t4\n+FBgn0000097\t1890\n+FBgn0000099\t1\n+FBgn0000100\t21320\n+FBgn0000108\t32\n+FBgn0000109\t99\n+FBgn0000114\t0\n+FBgn0000115\t403\n+FBgn0000116\t258\n+FBgn0000117\t7410\n+FBgn0000119\t461\n+FBgn0000120\t0\n+FBgn0000121\t1\n+FBgn0000137\t0\n+FBgn0000139\t546\n+FBgn0000140\t493\n+FBgn0000142\t1224\n+FBgn0000146\t903\n+FBgn0000147\t286\n+FBgn0000150\t6269\n+FBgn0000152\t353\n+FBgn0000153\t19\n+FBgn0000157\t0\n+FBgn0000158\t1\n+FBgn0000163\t645\n+FBgn0000166\t0\n+FBgn0000171\t4539\n+FBgn0000173\t1169\n+FBgn0000179\t0\n+FBgn0000180\t13\n+FBgn0000181\t10139\n+FBgn0000182\t4\n+FBgn0000183\t1795\n+FBgn0000206\t0\n+FBgn0000210\t904\n+FBgn0000212\t2093\n+FBgn0000216\t0\n+FBgn0000221\t188\n+FBgn0000227\t0\n+FBgn0000228\t544\n+FBgn0000229\t550\n+FBgn0000233\t6\n+FBgn0000239\t1691\n+FBgn0000241\t2\n+FBgn0000242\t105\n+FBgn0000244\t332\n+FBgn0000246\t68\n+FBgn0000247\t1835\n+FBgn0000250\t1640\n+FBgn0000251\t1\n+FBgn0000253\t6073\n+FBgn0000256\t1607\n+FBgn0000257\t558\n+FBgn0000258\t557\n+FBgn0000259\t1174\n+FBgn0000261\t1350\n+FBgn0000273\t1265\n+FBgn0000274\t0\n+FBgn0000276\t30\n+FBgn0000277\t17\n+FBgn0000278\t24\n+FBgn0000279\t24\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2302\n+FBgn0000286\t325\n+FBgn0000287\t1\n+FBgn0000289\t2375\n+FBgn0000299\t28552\n+FBgn0000303\t0\n+FBgn0000307\t968\n+FBgn0000308\t10605\n+FBgn0000313\t32\n+FBgn0000316\t1\n+FBgn0000317\t853\n+FBgn0000318\t709\n+FBgn0000319\t9571\n+FBgn0000320\t0\n+FBgn0000326\t144\n+FBgn0000330\t180\n+FBgn0000337\t16\n+FBgn0000338\t1070\n+FBgn0000339\t366\n+FBgn0000346\t39\n+FBgn0000351\t29\n+FBgn0000352\t533\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t3\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t1\n+FBgn0000363\t7\n+FBgn0000370\t8048\n+FBgn0000376\t926\n+FBgn0000377\t609\n+FBgn0000382\t499\n+FBgn0000384\t436\n+FBgn0000392\t625\n+FBgn0000394\t452\n+FBgn0000395\t354\n+FBgn0000404\t1584\n+FBgn0000405\t1238\n+FBgn0000406\t382\n+FBgn0000409\t3223\n+FBgn0000411\t0\n+FBgn0000412\t1798\n+FBgn0000413\t1829\n+FBgn0000414\t1525\n+FBgn0000416\t31544\n+FBgn0000422\t2\n+FBgn0000426\t467\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t2\n+FBgn0000447\t388\n+FBgn0000448\t2\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1946\n+FBgn0000455\t512\n+FBgn0000459\t3\n+FBgn0000463\t1\n+FBgn0000464\t961\n+FBgn0000472\t1706\n+FBgn0000473\t12\n+FBgn0000477\t1\n+FBgn0000479\t624\n+FBgn0000482\t751\n+FBgn0000489\t67\n+FBgn0000490\t97\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t682\n+FBgn0000500\t5\n+FBgn0000504\t3\n+FBgn0000520\t425\n+FBgn0000524\t519\n+FBgn0000527\t119\n+FBgn0000529\t0\n+FBgn0000533\t8\n+FBgn0000535\t133\n+FBgn0000536\t557\n+FBgn0000541\t2697\n+FBgn0000542\t110\n+FBgn0000543\t517\n+FBgn0000546\t562\n+FBgn0000547\t182\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t153364\n+FBgn0000557\t24\n+FBgn0000559\t81476\n+FBgn0000560\t0\n+FBgn0000562\t981\n+FBgn0000564\t0\n+FBgn0000565\t352\n+FBgn0000566\t593\n+FBgn0000567\t212\n+FBgn0000568\t2567\n+FBgn0000575\t785\n+FBgn0000576\t0\n+FBgn0000577\t2\n+FBgn0000578\t3649\n+FBgn0000579\t5543\n+FBgn0000581\t2256\n+FBgn0000588\t270\n+FBgn0000591\t0\n+FBgn0000592\t2\n+FBgn0000594\t19\n+FBgn0000606\t0\n+FBgn0000611\t1005\n+FBgn0000615\t250\n+FBgn0000617\t641\n+FBgn0000618\t112\n+FBgn0000625\t0\n+FBgn0000629\t744\n+FBgn0000630\t8\n+FBgn0000633\t11\n+FBgn0000634\t200\n+FBgn0000635\t102\n+FBgn0000636\t34\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t3\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t764\n+FBgn0000667\t1247\n+FBgn0000709\t1605\n+FBgn0000711\t688\n+FBgn0000715\t0\n+FBgn0000719\t1351\n+FBgn0000721\t578\n+FBgn0000723\t1436\n+FBgn0000808\t103\n+FBgn0000810\t152\n+FBgn0000826\t68\n+FBgn0000927\t23\n+FBgn0000928\t423\n+FBgn0000964\t1\n+FBgn0000986\t1394\n+FBgn0000996\t848\n+FBgn0001075\t17\n+FBgn0001077'..b'0030349\t1431\n+FBgn0030350\t564\n+FBgn0030351\t76\n+FBgn0030352\t202\n+FBgn0030354\t1343\n+FBgn0030356\t0\n+FBgn0030357\t55\n+FBgn0030358\t208\n+FBgn0030359\t1\n+FBgn0030360\t18\n+FBgn0030361\t84\n+FBgn0030362\t6022\n+FBgn0030364\t423\n+FBgn0030365\t582\n+FBgn0030366\t2600\n+FBgn0030367\t64\n+FBgn0030369\t35\n+FBgn0030370\t0\n+FBgn0030373\t184\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t41\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t239\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t25\n+FBgn0030398\t2\n+FBgn0030399\t0\n+FBgn0030400\t864\n+FBgn0030403\t867\n+FBgn0030406\t123\n+FBgn0030407\t35\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t59\n+FBgn0030411\t77\n+FBgn0030412\t921\n+FBgn0030417\t63\n+FBgn0030418\t270\n+FBgn0030420\t685\n+FBgn0030421\t100\n+FBgn0030425\t4\n+FBgn0030429\t1\n+FBgn0030431\t379\n+FBgn0030432\t22\n+FBgn0030433\t300\n+FBgn0030434\t593\n+FBgn0030435\t515\n+FBgn0030437\t0\n+FBgn0030438\t0\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t454\n+FBgn0030448\t319\n+FBgn0030449\t1\n+FBgn0030451\t871\n+FBgn0030452\t808\n+FBgn0030455\t1\n+FBgn0030456\t408\n+FBgn0030457\t331\n+FBgn0030459\t3\n+FBgn0030460\t350\n+FBgn0030462\t1\n+FBgn0030465\t542\n+FBgn0030466\t1593\n+FBgn0030467\t519\n+FBgn0030468\t1136\n+FBgn0030469\t1506\n+FBgn0030474\t606\n+FBgn0030477\t1\n+FBgn0030478\t1231\n+FBgn0030479\t165\n+FBgn0030480\t188\n+FBgn0030481\t310\n+FBgn0030482\t3044\n+FBgn0030483\t0\n+FBgn0030484\t831\n+FBgn0030485\t198\n+FBgn0030486\t1432\n+FBgn0030491\t2\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t525\n+FBgn0030500\t412\n+FBgn0030501\t951\n+FBgn0030502\t1806\n+FBgn0030503\t107\n+FBgn0030504\t2049\n+FBgn0030505\t1152\n+FBgn0030506\t329\n+FBgn0030507\t324\n+FBgn0030508\t6\n+FBgn0030509\t0\n+FBgn0030510\t334\n+FBgn0030511\t116\n+FBgn0030512\t897\n+FBgn0030514\t1188\n+FBgn0030518\t182\n+FBgn0030519\t1023\n+FBgn0030520\t3494\n+FBgn0030521\t3998\n+FBgn0030522\t199\n+FBgn0030524\t4\n+FBgn0030525\t2\n+FBgn0030528\t120\n+FBgn0030529\t7019\n+FBgn0030530\t1220\n+FBgn0030532\t1496\n+FBgn0030536\t0\n+FBgn0030537\t1\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t187\n+FBgn0030551\t2\n+FBgn0030552\t365\n+FBgn0030554\t242\n+FBgn0030555\t137\n+FBgn0030556\t1131\n+FBgn0030558\t0\n+FBgn0030559\t4\n+FBgn0030562\t17\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t167\n+FBgn0030572\t228\n+FBgn0030573\t22\n+FBgn0030574\t8\n+FBgn0030575\t31\n+FBgn0030576\t182\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t342\n+FBgn0030582\t587\n+FBgn0030583\t33\n+FBgn0030584\t183\n+FBgn0030586\t2\n+FBgn0030587\t3\n+FBgn0030588\t121\n+FBgn0030589\t0\n+FBgn0030590\t11\n+FBgn0030591\t2\n+FBgn0030592\t11\n+FBgn0030593\t9\n+FBgn0030594\t5\n+FBgn0030595\t0\n+FBgn0030596\t10\n+FBgn0030597\t1\n+FBgn0030598\t7\n+FBgn0030599\t2\n+FBgn0030600\t1776\n+FBgn0030603\t408\n+FBgn0030605\t536\n+FBgn0030606\t345\n+FBgn0030607\t11\n+FBgn0030608\t0\n+FBgn0030610\t201\n+FBgn0030611\t88\n+FBgn0030612\t348\n+FBgn0030613\t8\n+FBgn0030614\t0\n+FBgn0030615\t47\n+FBgn0030616\t21615\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t189\n+FBgn0030626\t266\n+FBgn0030627\t681\n+FBgn0030628\t325\n+FBgn0030629\t90\n+FBgn0030630\t439\n+FBgn0030631\t949\n+FBgn0030634\t3\n+FBgn0030636\t6\n+FBgn0030638\t658\n+FBgn0030640\t0\n+FBgn0030641\t2\n+FBgn0030642\t10\n+FBgn0030643\t7\n+FBgn0030645\t55\n+FBgn0030646\t155\n+FBgn0030647\t1\n+FBgn0030648\t269\n+FBgn0030653\t143\n+FBgn0030654\t58\n+FBgn0030655\t204\n+FBgn0030657\t54\n+FBgn0030658\t858\n+FBgn0030659\t320\n+FBgn0030660\t90\n+FBgn0030661\t10\n+FBgn0030662\t416\n+FBgn0030663\t1\n+FBgn0030664\t13\n+FBgn0030665\t3\n+FBgn0030666\t16\n+FBgn0030667\t60\n+FBgn0030668\t198\n+FBgn0030669\t183\n+FBgn0030670\t475\n+FBgn0030671\t239\n+FBgn0030672\t4892\n+FBgn0030673\t60\n+FBgn0030674\t5990\n+FBgn0030675\t73\n+FBgn0030676\t6\n+FBgn0030678\t139\n+FBgn0030679\t346\n+FBgn0030680\t355\n+FBgn0030683\t174\n+FBgn0030684\t1\n+FBgn0030685\t1414\n+FBgn0030686\t339\n+FBgn0030687\t532\n+FBgn0030688\t1\n+FBgn0030691\t8\n+FBgn0030692\t538\n+FBgn0030693\t242\n+FBgn0030694\t168\n+no_feature\t284334\n+ambiguous\t96881\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t11365569\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461179_treat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461179_treat_single.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\ttreat1\n+FBgn0000003\t0\n+FBgn0000008\t19\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t980\n+FBgn0000018\t107\n+FBgn0000022\t0\n+FBgn0000024\t1\n+FBgn0000028\t0\n+FBgn0000032\t275\n+FBgn0000036\t0\n+FBgn0000037\t4\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t20725\n+FBgn0000043\t9231\n+FBgn0000044\t10\n+FBgn0000045\t0\n+FBgn0000046\t9\n+FBgn0000047\t2\n+FBgn0000052\t522\n+FBgn0000053\t529\n+FBgn0000054\t154\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t156\n+FBgn0000061\t1\n+FBgn0000063\t101\n+FBgn0000064\t2216\n+FBgn0000071\t146\n+FBgn0000075\t0\n+FBgn0000077\t43\n+FBgn0000078\t2\n+FBgn0000079\t9\n+FBgn0000083\t1304\n+FBgn0000084\t331\n+FBgn0000092\t2\n+FBgn0000094\t8\n+FBgn0000097\t814\n+FBgn0000099\t0\n+FBgn0000100\t5774\n+FBgn0000108\t17\n+FBgn0000109\t46\n+FBgn0000114\t2\n+FBgn0000115\t145\n+FBgn0000116\t179\n+FBgn0000117\t2678\n+FBgn0000119\t162\n+FBgn0000120\t0\n+FBgn0000121\t2\n+FBgn0000137\t0\n+FBgn0000139\t118\n+FBgn0000140\t284\n+FBgn0000142\t435\n+FBgn0000146\t556\n+FBgn0000147\t116\n+FBgn0000150\t2382\n+FBgn0000152\t125\n+FBgn0000153\t4\n+FBgn0000157\t0\n+FBgn0000158\t1\n+FBgn0000163\t232\n+FBgn0000166\t0\n+FBgn0000171\t1393\n+FBgn0000173\t435\n+FBgn0000179\t0\n+FBgn0000180\t3\n+FBgn0000181\t3287\n+FBgn0000182\t1\n+FBgn0000183\t728\n+FBgn0000206\t0\n+FBgn0000210\t359\n+FBgn0000212\t843\n+FBgn0000216\t0\n+FBgn0000221\t54\n+FBgn0000227\t0\n+FBgn0000228\t180\n+FBgn0000229\t276\n+FBgn0000233\t1\n+FBgn0000239\t687\n+FBgn0000241\t3\n+FBgn0000242\t19\n+FBgn0000244\t121\n+FBgn0000246\t67\n+FBgn0000247\t609\n+FBgn0000250\t555\n+FBgn0000251\t0\n+FBgn0000253\t3421\n+FBgn0000256\t433\n+FBgn0000257\t186\n+FBgn0000258\t463\n+FBgn0000259\t684\n+FBgn0000261\t399\n+FBgn0000273\t516\n+FBgn0000274\t0\n+FBgn0000276\t26\n+FBgn0000277\t7\n+FBgn0000278\t3\n+FBgn0000279\t32\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t896\n+FBgn0000286\t106\n+FBgn0000287\t0\n+FBgn0000289\t789\n+FBgn0000299\t15690\n+FBgn0000303\t3\n+FBgn0000307\t530\n+FBgn0000308\t5161\n+FBgn0000313\t9\n+FBgn0000316\t1\n+FBgn0000317\t384\n+FBgn0000318\t266\n+FBgn0000319\t3577\n+FBgn0000320\t0\n+FBgn0000326\t79\n+FBgn0000330\t43\n+FBgn0000337\t4\n+FBgn0000338\t562\n+FBgn0000339\t218\n+FBgn0000346\t28\n+FBgn0000351\t12\n+FBgn0000352\t221\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t2\n+FBgn0000358\t0\n+FBgn0000359\t1\n+FBgn0000360\t0\n+FBgn0000363\t1\n+FBgn0000370\t3310\n+FBgn0000376\t299\n+FBgn0000377\t226\n+FBgn0000382\t191\n+FBgn0000384\t143\n+FBgn0000392\t287\n+FBgn0000394\t125\n+FBgn0000395\t125\n+FBgn0000404\t723\n+FBgn0000405\t736\n+FBgn0000406\t20\n+FBgn0000409\t1010\n+FBgn0000411\t0\n+FBgn0000412\t876\n+FBgn0000413\t578\n+FBgn0000414\t513\n+FBgn0000416\t8816\n+FBgn0000422\t1\n+FBgn0000426\t198\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t2\n+FBgn0000447\t210\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t582\n+FBgn0000455\t138\n+FBgn0000459\t2\n+FBgn0000463\t1\n+FBgn0000464\t425\n+FBgn0000472\t726\n+FBgn0000473\t3\n+FBgn0000477\t0\n+FBgn0000479\t194\n+FBgn0000482\t211\n+FBgn0000489\t27\n+FBgn0000490\t73\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t210\n+FBgn0000500\t0\n+FBgn0000504\t7\n+FBgn0000520\t118\n+FBgn0000524\t212\n+FBgn0000527\t22\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t39\n+FBgn0000536\t279\n+FBgn0000541\t1597\n+FBgn0000542\t34\n+FBgn0000543\t183\n+FBgn0000546\t256\n+FBgn0000547\t109\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t42057\n+FBgn0000557\t16\n+FBgn0000559\t26239\n+FBgn0000560\t0\n+FBgn0000562\t323\n+FBgn0000564\t0\n+FBgn0000565\t190\n+FBgn0000566\t210\n+FBgn0000567\t35\n+FBgn0000568\t865\n+FBgn0000575\t495\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t1201\n+FBgn0000579\t2351\n+FBgn0000581\t816\n+FBgn0000588\t70\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t9\n+FBgn0000606\t0\n+FBgn0000611\t345\n+FBgn0000615\t123\n+FBgn0000617\t186\n+FBgn0000618\t38\n+FBgn0000625\t0\n+FBgn0000629\t238\n+FBgn0000630\t4\n+FBgn0000633\t10\n+FBgn0000634\t99\n+FBgn0000635\t37\n+FBgn0000636\t18\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t1\n+FBgn0000659\t1\n+FBgn0000662\t292\n+FBgn0000667\t335\n+FBgn0000709\t589\n+FBgn0000711\t339\n+FBgn0000715\t0\n+FBgn0000719\t490\n+FBgn0000721\t257\n+FBgn0000723\t504\n+FBgn0000808\t38\n+FBgn0000810\t89\n+FBgn0000826\t38\n+FBgn0000927\t8\n+FBgn0000928\t228\n+FBgn0000964\t0\n+FBgn0000986\t642\n+FBgn0000996\t308\n+FBgn0001075\t15\n+FBgn0001077\t0\n+FBgn0001078\t274\n+FBgn0001079\t104\n+FBgn0001083\t46\n'..b'gn0030345\t69\n+FBgn0030346\t36\n+FBgn0030347\t50\n+FBgn0030348\t2\n+FBgn0030349\t361\n+FBgn0030350\t252\n+FBgn0030351\t59\n+FBgn0030352\t74\n+FBgn0030354\t440\n+FBgn0030356\t1\n+FBgn0030357\t32\n+FBgn0030358\t47\n+FBgn0030359\t2\n+FBgn0030360\t6\n+FBgn0030361\t40\n+FBgn0030362\t1341\n+FBgn0030364\t157\n+FBgn0030365\t200\n+FBgn0030366\t1123\n+FBgn0030367\t17\n+FBgn0030369\t12\n+FBgn0030370\t0\n+FBgn0030373\t72\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t12\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t83\n+FBgn0030394\t1\n+FBgn0030395\t0\n+FBgn0030396\t6\n+FBgn0030398\t0\n+FBgn0030399\t0\n+FBgn0030400\t326\n+FBgn0030403\t205\n+FBgn0030406\t50\n+FBgn0030407\t10\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t23\n+FBgn0030411\t34\n+FBgn0030412\t326\n+FBgn0030417\t34\n+FBgn0030418\t94\n+FBgn0030420\t321\n+FBgn0030421\t68\n+FBgn0030425\t2\n+FBgn0030429\t1\n+FBgn0030431\t110\n+FBgn0030432\t5\n+FBgn0030433\t127\n+FBgn0030434\t176\n+FBgn0030435\t199\n+FBgn0030437\t0\n+FBgn0030438\t1\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t131\n+FBgn0030448\t101\n+FBgn0030449\t0\n+FBgn0030451\t212\n+FBgn0030452\t149\n+FBgn0030455\t1\n+FBgn0030456\t226\n+FBgn0030457\t126\n+FBgn0030459\t2\n+FBgn0030460\t122\n+FBgn0030462\t0\n+FBgn0030465\t123\n+FBgn0030466\t704\n+FBgn0030467\t237\n+FBgn0030468\t369\n+FBgn0030469\t471\n+FBgn0030474\t250\n+FBgn0030477\t0\n+FBgn0030478\t337\n+FBgn0030479\t59\n+FBgn0030480\t83\n+FBgn0030481\t108\n+FBgn0030482\t967\n+FBgn0030483\t0\n+FBgn0030484\t329\n+FBgn0030485\t85\n+FBgn0030486\t579\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t164\n+FBgn0030500\t176\n+FBgn0030501\t383\n+FBgn0030502\t679\n+FBgn0030503\t36\n+FBgn0030504\t668\n+FBgn0030505\t348\n+FBgn0030506\t105\n+FBgn0030507\t78\n+FBgn0030508\t0\n+FBgn0030509\t0\n+FBgn0030510\t84\n+FBgn0030511\t58\n+FBgn0030512\t333\n+FBgn0030514\t375\n+FBgn0030518\t87\n+FBgn0030519\t242\n+FBgn0030520\t1378\n+FBgn0030521\t1203\n+FBgn0030522\t60\n+FBgn0030524\t2\n+FBgn0030525\t2\n+FBgn0030528\t35\n+FBgn0030529\t1901\n+FBgn0030530\t337\n+FBgn0030532\t345\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t1\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t78\n+FBgn0030551\t0\n+FBgn0030552\t110\n+FBgn0030554\t54\n+FBgn0030555\t53\n+FBgn0030556\t293\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t9\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t63\n+FBgn0030572\t86\n+FBgn0030573\t13\n+FBgn0030574\t4\n+FBgn0030575\t11\n+FBgn0030576\t58\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t118\n+FBgn0030582\t259\n+FBgn0030583\t12\n+FBgn0030584\t77\n+FBgn0030586\t2\n+FBgn0030587\t2\n+FBgn0030588\t72\n+FBgn0030589\t2\n+FBgn0030590\t12\n+FBgn0030591\t0\n+FBgn0030592\t1\n+FBgn0030593\t3\n+FBgn0030594\t2\n+FBgn0030595\t1\n+FBgn0030596\t4\n+FBgn0030597\t4\n+FBgn0030598\t15\n+FBgn0030599\t1\n+FBgn0030600\t570\n+FBgn0030603\t132\n+FBgn0030605\t148\n+FBgn0030606\t118\n+FBgn0030607\t10\n+FBgn0030608\t0\n+FBgn0030610\t79\n+FBgn0030611\t28\n+FBgn0030612\t92\n+FBgn0030613\t2\n+FBgn0030614\t0\n+FBgn0030615\t22\n+FBgn0030616\t5539\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t96\n+FBgn0030626\t124\n+FBgn0030627\t175\n+FBgn0030628\t107\n+FBgn0030629\t34\n+FBgn0030630\t153\n+FBgn0030631\t273\n+FBgn0030634\t2\n+FBgn0030636\t1\n+FBgn0030638\t234\n+FBgn0030640\t0\n+FBgn0030641\t3\n+FBgn0030642\t2\n+FBgn0030643\t2\n+FBgn0030645\t27\n+FBgn0030646\t54\n+FBgn0030647\t1\n+FBgn0030648\t101\n+FBgn0030653\t57\n+FBgn0030654\t26\n+FBgn0030655\t76\n+FBgn0030657\t21\n+FBgn0030658\t261\n+FBgn0030659\t108\n+FBgn0030660\t47\n+FBgn0030661\t11\n+FBgn0030662\t176\n+FBgn0030663\t0\n+FBgn0030664\t5\n+FBgn0030665\t1\n+FBgn0030666\t1\n+FBgn0030667\t46\n+FBgn0030668\t49\n+FBgn0030669\t57\n+FBgn0030670\t154\n+FBgn0030671\t102\n+FBgn0030672\t1197\n+FBgn0030673\t21\n+FBgn0030674\t2108\n+FBgn0030675\t18\n+FBgn0030676\t7\n+FBgn0030678\t34\n+FBgn0030679\t72\n+FBgn0030680\t126\n+FBgn0030683\t61\n+FBgn0030684\t0\n+FBgn0030685\t443\n+FBgn0030686\t86\n+FBgn0030687\t162\n+FBgn0030688\t1\n+FBgn0030691\t7\n+FBgn0030692\t170\n+FBgn0030693\t125\n+FBgn0030694\t60\n+no_feature\t239081\n+ambiguous\t43070\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t14421559\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461179_treat_single.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461179_treat_single.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t19\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t980\n+FBgn0000018\t107\n+FBgn0000022\t0\n+FBgn0000024\t1\n+FBgn0000028\t0\n+FBgn0000032\t275\n+FBgn0000036\t0\n+FBgn0000037\t4\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t20725\n+FBgn0000043\t9231\n+FBgn0000044\t10\n+FBgn0000045\t0\n+FBgn0000046\t9\n+FBgn0000047\t2\n+FBgn0000052\t522\n+FBgn0000053\t529\n+FBgn0000054\t154\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t156\n+FBgn0000061\t1\n+FBgn0000063\t101\n+FBgn0000064\t2216\n+FBgn0000071\t146\n+FBgn0000075\t0\n+FBgn0000077\t43\n+FBgn0000078\t2\n+FBgn0000079\t9\n+FBgn0000083\t1304\n+FBgn0000084\t331\n+FBgn0000092\t2\n+FBgn0000094\t8\n+FBgn0000097\t814\n+FBgn0000099\t0\n+FBgn0000100\t5774\n+FBgn0000108\t17\n+FBgn0000109\t46\n+FBgn0000114\t2\n+FBgn0000115\t145\n+FBgn0000116\t179\n+FBgn0000117\t2678\n+FBgn0000119\t162\n+FBgn0000120\t0\n+FBgn0000121\t2\n+FBgn0000137\t0\n+FBgn0000139\t118\n+FBgn0000140\t284\n+FBgn0000142\t435\n+FBgn0000146\t556\n+FBgn0000147\t116\n+FBgn0000150\t2382\n+FBgn0000152\t125\n+FBgn0000153\t4\n+FBgn0000157\t0\n+FBgn0000158\t1\n+FBgn0000163\t232\n+FBgn0000166\t0\n+FBgn0000171\t1393\n+FBgn0000173\t435\n+FBgn0000179\t0\n+FBgn0000180\t3\n+FBgn0000181\t3287\n+FBgn0000182\t1\n+FBgn0000183\t728\n+FBgn0000206\t0\n+FBgn0000210\t359\n+FBgn0000212\t843\n+FBgn0000216\t0\n+FBgn0000221\t54\n+FBgn0000227\t0\n+FBgn0000228\t180\n+FBgn0000229\t276\n+FBgn0000233\t1\n+FBgn0000239\t687\n+FBgn0000241\t3\n+FBgn0000242\t19\n+FBgn0000244\t121\n+FBgn0000246\t67\n+FBgn0000247\t609\n+FBgn0000250\t555\n+FBgn0000251\t0\n+FBgn0000253\t3421\n+FBgn0000256\t433\n+FBgn0000257\t186\n+FBgn0000258\t463\n+FBgn0000259\t684\n+FBgn0000261\t399\n+FBgn0000273\t516\n+FBgn0000274\t0\n+FBgn0000276\t26\n+FBgn0000277\t7\n+FBgn0000278\t3\n+FBgn0000279\t32\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t896\n+FBgn0000286\t106\n+FBgn0000287\t0\n+FBgn0000289\t789\n+FBgn0000299\t15690\n+FBgn0000303\t3\n+FBgn0000307\t530\n+FBgn0000308\t5161\n+FBgn0000313\t9\n+FBgn0000316\t1\n+FBgn0000317\t384\n+FBgn0000318\t266\n+FBgn0000319\t3577\n+FBgn0000320\t0\n+FBgn0000326\t79\n+FBgn0000330\t43\n+FBgn0000337\t4\n+FBgn0000338\t562\n+FBgn0000339\t218\n+FBgn0000346\t28\n+FBgn0000351\t12\n+FBgn0000352\t221\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t2\n+FBgn0000358\t0\n+FBgn0000359\t1\n+FBgn0000360\t0\n+FBgn0000363\t1\n+FBgn0000370\t3310\n+FBgn0000376\t299\n+FBgn0000377\t226\n+FBgn0000382\t191\n+FBgn0000384\t143\n+FBgn0000392\t287\n+FBgn0000394\t125\n+FBgn0000395\t125\n+FBgn0000404\t723\n+FBgn0000405\t736\n+FBgn0000406\t20\n+FBgn0000409\t1010\n+FBgn0000411\t0\n+FBgn0000412\t876\n+FBgn0000413\t578\n+FBgn0000414\t513\n+FBgn0000416\t8816\n+FBgn0000422\t1\n+FBgn0000426\t198\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t2\n+FBgn0000447\t210\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t582\n+FBgn0000455\t138\n+FBgn0000459\t2\n+FBgn0000463\t1\n+FBgn0000464\t425\n+FBgn0000472\t726\n+FBgn0000473\t3\n+FBgn0000477\t0\n+FBgn0000479\t194\n+FBgn0000482\t211\n+FBgn0000489\t27\n+FBgn0000490\t73\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t210\n+FBgn0000500\t0\n+FBgn0000504\t7\n+FBgn0000520\t118\n+FBgn0000524\t212\n+FBgn0000527\t22\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t39\n+FBgn0000536\t279\n+FBgn0000541\t1597\n+FBgn0000542\t34\n+FBgn0000543\t183\n+FBgn0000546\t256\n+FBgn0000547\t109\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t42057\n+FBgn0000557\t16\n+FBgn0000559\t26239\n+FBgn0000560\t0\n+FBgn0000562\t323\n+FBgn0000564\t0\n+FBgn0000565\t190\n+FBgn0000566\t210\n+FBgn0000567\t35\n+FBgn0000568\t865\n+FBgn0000575\t495\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t1201\n+FBgn0000579\t2351\n+FBgn0000581\t816\n+FBgn0000588\t70\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t9\n+FBgn0000606\t0\n+FBgn0000611\t345\n+FBgn0000615\t123\n+FBgn0000617\t186\n+FBgn0000618\t38\n+FBgn0000625\t0\n+FBgn0000629\t238\n+FBgn0000630\t4\n+FBgn0000633\t10\n+FBgn0000634\t99\n+FBgn0000635\t37\n+FBgn0000636\t18\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t1\n+FBgn0000659\t1\n+FBgn0000662\t292\n+FBgn0000667\t335\n+FBgn0000709\t589\n+FBgn0000711\t339\n+FBgn0000715\t0\n+FBgn0000719\t490\n+FBgn0000721\t257\n+FBgn0000723\t504\n+FBgn0000808\t38\n+FBgn0000810\t89\n+FBgn0000826\t38\n+FBgn0000927\t8\n+FBgn0000928\t228\n+FBgn0000964\t0\n+FBgn0000986\t642\n+FBgn0000996\t308\n+FBgn0001075\t15\n+FBgn0001077\t0\n+FBgn0001078\t274\n+FBgn0001079\t104\n+FBgn0001083\t46\n+FBgn0001084\t21'..b'gn0030345\t69\n+FBgn0030346\t36\n+FBgn0030347\t50\n+FBgn0030348\t2\n+FBgn0030349\t361\n+FBgn0030350\t252\n+FBgn0030351\t59\n+FBgn0030352\t74\n+FBgn0030354\t440\n+FBgn0030356\t1\n+FBgn0030357\t32\n+FBgn0030358\t47\n+FBgn0030359\t2\n+FBgn0030360\t6\n+FBgn0030361\t40\n+FBgn0030362\t1341\n+FBgn0030364\t157\n+FBgn0030365\t200\n+FBgn0030366\t1123\n+FBgn0030367\t17\n+FBgn0030369\t12\n+FBgn0030370\t0\n+FBgn0030373\t72\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t12\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t83\n+FBgn0030394\t1\n+FBgn0030395\t0\n+FBgn0030396\t6\n+FBgn0030398\t0\n+FBgn0030399\t0\n+FBgn0030400\t326\n+FBgn0030403\t205\n+FBgn0030406\t50\n+FBgn0030407\t10\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t23\n+FBgn0030411\t34\n+FBgn0030412\t326\n+FBgn0030417\t34\n+FBgn0030418\t94\n+FBgn0030420\t321\n+FBgn0030421\t68\n+FBgn0030425\t2\n+FBgn0030429\t1\n+FBgn0030431\t110\n+FBgn0030432\t5\n+FBgn0030433\t127\n+FBgn0030434\t176\n+FBgn0030435\t199\n+FBgn0030437\t0\n+FBgn0030438\t1\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t131\n+FBgn0030448\t101\n+FBgn0030449\t0\n+FBgn0030451\t212\n+FBgn0030452\t149\n+FBgn0030455\t1\n+FBgn0030456\t226\n+FBgn0030457\t126\n+FBgn0030459\t2\n+FBgn0030460\t122\n+FBgn0030462\t0\n+FBgn0030465\t123\n+FBgn0030466\t704\n+FBgn0030467\t237\n+FBgn0030468\t369\n+FBgn0030469\t471\n+FBgn0030474\t250\n+FBgn0030477\t0\n+FBgn0030478\t337\n+FBgn0030479\t59\n+FBgn0030480\t83\n+FBgn0030481\t108\n+FBgn0030482\t967\n+FBgn0030483\t0\n+FBgn0030484\t329\n+FBgn0030485\t85\n+FBgn0030486\t579\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t164\n+FBgn0030500\t176\n+FBgn0030501\t383\n+FBgn0030502\t679\n+FBgn0030503\t36\n+FBgn0030504\t668\n+FBgn0030505\t348\n+FBgn0030506\t105\n+FBgn0030507\t78\n+FBgn0030508\t0\n+FBgn0030509\t0\n+FBgn0030510\t84\n+FBgn0030511\t58\n+FBgn0030512\t333\n+FBgn0030514\t375\n+FBgn0030518\t87\n+FBgn0030519\t242\n+FBgn0030520\t1378\n+FBgn0030521\t1203\n+FBgn0030522\t60\n+FBgn0030524\t2\n+FBgn0030525\t2\n+FBgn0030528\t35\n+FBgn0030529\t1901\n+FBgn0030530\t337\n+FBgn0030532\t345\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t1\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t78\n+FBgn0030551\t0\n+FBgn0030552\t110\n+FBgn0030554\t54\n+FBgn0030555\t53\n+FBgn0030556\t293\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t9\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t1\n+FBgn0030570\t0\n+FBgn0030571\t63\n+FBgn0030572\t86\n+FBgn0030573\t13\n+FBgn0030574\t4\n+FBgn0030575\t11\n+FBgn0030576\t58\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t118\n+FBgn0030582\t259\n+FBgn0030583\t12\n+FBgn0030584\t77\n+FBgn0030586\t2\n+FBgn0030587\t2\n+FBgn0030588\t72\n+FBgn0030589\t2\n+FBgn0030590\t12\n+FBgn0030591\t0\n+FBgn0030592\t1\n+FBgn0030593\t3\n+FBgn0030594\t2\n+FBgn0030595\t1\n+FBgn0030596\t4\n+FBgn0030597\t4\n+FBgn0030598\t15\n+FBgn0030599\t1\n+FBgn0030600\t570\n+FBgn0030603\t132\n+FBgn0030605\t148\n+FBgn0030606\t118\n+FBgn0030607\t10\n+FBgn0030608\t0\n+FBgn0030610\t79\n+FBgn0030611\t28\n+FBgn0030612\t92\n+FBgn0030613\t2\n+FBgn0030614\t0\n+FBgn0030615\t22\n+FBgn0030616\t5539\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t96\n+FBgn0030626\t124\n+FBgn0030627\t175\n+FBgn0030628\t107\n+FBgn0030629\t34\n+FBgn0030630\t153\n+FBgn0030631\t273\n+FBgn0030634\t2\n+FBgn0030636\t1\n+FBgn0030638\t234\n+FBgn0030640\t0\n+FBgn0030641\t3\n+FBgn0030642\t2\n+FBgn0030643\t2\n+FBgn0030645\t27\n+FBgn0030646\t54\n+FBgn0030647\t1\n+FBgn0030648\t101\n+FBgn0030653\t57\n+FBgn0030654\t26\n+FBgn0030655\t76\n+FBgn0030657\t21\n+FBgn0030658\t261\n+FBgn0030659\t108\n+FBgn0030660\t47\n+FBgn0030661\t11\n+FBgn0030662\t176\n+FBgn0030663\t0\n+FBgn0030664\t5\n+FBgn0030665\t1\n+FBgn0030666\t1\n+FBgn0030667\t46\n+FBgn0030668\t49\n+FBgn0030669\t57\n+FBgn0030670\t154\n+FBgn0030671\t102\n+FBgn0030672\t1197\n+FBgn0030673\t21\n+FBgn0030674\t2108\n+FBgn0030675\t18\n+FBgn0030676\t7\n+FBgn0030678\t34\n+FBgn0030679\t72\n+FBgn0030680\t126\n+FBgn0030683\t61\n+FBgn0030684\t0\n+FBgn0030685\t443\n+FBgn0030686\t86\n+FBgn0030687\t162\n+FBgn0030688\t1\n+FBgn0030691\t7\n+FBgn0030692\t170\n+FBgn0030693\t125\n+FBgn0030694\t60\n+no_feature\t239081\n+ambiguous\t43070\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t14421559\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461180_treat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461180_treat_paired.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\ttreat2\n+FBgn0000003\t0\n+FBgn0000008\t69\n+FBgn0000014\t2\n+FBgn0000015\t0\n+FBgn0000017\t2375\n+FBgn0000018\t235\n+FBgn0000022\t0\n+FBgn0000024\t2\n+FBgn0000028\t1\n+FBgn0000032\t553\n+FBgn0000036\t0\n+FBgn0000037\t9\n+FBgn0000038\t0\n+FBgn0000039\t1\n+FBgn0000042\t61359\n+FBgn0000043\t25056\n+FBgn0000044\t18\n+FBgn0000045\t9\n+FBgn0000046\t24\n+FBgn0000047\t12\n+FBgn0000052\t1439\n+FBgn0000053\t1594\n+FBgn0000054\t378\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t473\n+FBgn0000061\t1\n+FBgn0000063\t251\n+FBgn0000064\t5361\n+FBgn0000071\t385\n+FBgn0000075\t0\n+FBgn0000077\t112\n+FBgn0000078\t11\n+FBgn0000079\t75\n+FBgn0000083\t3552\n+FBgn0000084\t1033\n+FBgn0000092\t4\n+FBgn0000094\t5\n+FBgn0000097\t1874\n+FBgn0000099\t1\n+FBgn0000100\t16110\n+FBgn0000108\t27\n+FBgn0000109\t61\n+FBgn0000114\t1\n+FBgn0000115\t336\n+FBgn0000116\t666\n+FBgn0000117\t7588\n+FBgn0000119\t381\n+FBgn0000120\t0\n+FBgn0000121\t5\n+FBgn0000137\t0\n+FBgn0000139\t293\n+FBgn0000140\t604\n+FBgn0000142\t1115\n+FBgn0000146\t1152\n+FBgn0000147\t295\n+FBgn0000150\t6419\n+FBgn0000152\t343\n+FBgn0000153\t16\n+FBgn0000157\t0\n+FBgn0000158\t6\n+FBgn0000163\t497\n+FBgn0000166\t0\n+FBgn0000171\t4383\n+FBgn0000173\t993\n+FBgn0000179\t0\n+FBgn0000180\t23\n+FBgn0000181\t7624\n+FBgn0000182\t1\n+FBgn0000183\t1501\n+FBgn0000206\t0\n+FBgn0000210\t1080\n+FBgn0000212\t2084\n+FBgn0000216\t0\n+FBgn0000221\t119\n+FBgn0000227\t0\n+FBgn0000228\t472\n+FBgn0000229\t394\n+FBgn0000233\t2\n+FBgn0000239\t1570\n+FBgn0000241\t4\n+FBgn0000242\t92\n+FBgn0000244\t254\n+FBgn0000246\t73\n+FBgn0000247\t1659\n+FBgn0000250\t1283\n+FBgn0000251\t0\n+FBgn0000253\t5877\n+FBgn0000256\t1049\n+FBgn0000257\t494\n+FBgn0000258\t498\n+FBgn0000259\t1023\n+FBgn0000261\t1106\n+FBgn0000273\t1102\n+FBgn0000274\t0\n+FBgn0000276\t42\n+FBgn0000277\t15\n+FBgn0000278\t16\n+FBgn0000279\t34\n+FBgn0000280\t1\n+FBgn0000281\t1\n+FBgn0000283\t2196\n+FBgn0000286\t243\n+FBgn0000287\t0\n+FBgn0000289\t2072\n+FBgn0000299\t44540\n+FBgn0000303\t1\n+FBgn0000307\t866\n+FBgn0000308\t9427\n+FBgn0000313\t32\n+FBgn0000316\t2\n+FBgn0000317\t851\n+FBgn0000318\t623\n+FBgn0000319\t9250\n+FBgn0000320\t1\n+FBgn0000326\t170\n+FBgn0000330\t135\n+FBgn0000337\t12\n+FBgn0000338\t1155\n+FBgn0000339\t265\n+FBgn0000346\t44\n+FBgn0000351\t22\n+FBgn0000352\t506\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t1\n+FBgn0000363\t3\n+FBgn0000370\t6358\n+FBgn0000376\t808\n+FBgn0000377\t597\n+FBgn0000382\t426\n+FBgn0000384\t395\n+FBgn0000392\t842\n+FBgn0000394\t316\n+FBgn0000395\t267\n+FBgn0000404\t1467\n+FBgn0000405\t1809\n+FBgn0000406\t57\n+FBgn0000409\t2620\n+FBgn0000411\t0\n+FBgn0000412\t1816\n+FBgn0000413\t1650\n+FBgn0000414\t1231\n+FBgn0000416\t20885\n+FBgn0000422\t0\n+FBgn0000426\t413\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t471\n+FBgn0000448\t0\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1723\n+FBgn0000455\t356\n+FBgn0000459\t2\n+FBgn0000463\t0\n+FBgn0000464\t934\n+FBgn0000472\t1337\n+FBgn0000473\t4\n+FBgn0000477\t0\n+FBgn0000479\t541\n+FBgn0000482\t637\n+FBgn0000489\t60\n+FBgn0000490\t162\n+FBgn0000492\t1\n+FBgn0000497\t0\n+FBgn0000499\t626\n+FBgn0000500\t7\n+FBgn0000504\t4\n+FBgn0000520\t392\n+FBgn0000524\t702\n+FBgn0000527\t71\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t81\n+FBgn0000536\t528\n+FBgn0000541\t2699\n+FBgn0000542\t100\n+FBgn0000543\t506\n+FBgn0000546\t583\n+FBgn0000547\t231\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t116127\n+FBgn0000557\t29\n+FBgn0000559\t69701\n+FBgn0000560\t0\n+FBgn0000562\t891\n+FBgn0000564\t0\n+FBgn0000565\t517\n+FBgn0000566\t598\n+FBgn0000567\t85\n+FBgn0000568\t2091\n+FBgn0000575\t780\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t2813\n+FBgn0000579\t6646\n+FBgn0000581\t2111\n+FBgn0000588\t248\n+FBgn0000591\t0\n+FBgn0000592\t0\n+FBgn0000594\t10\n+FBgn0000606\t1\n+FBgn0000611\t731\n+FBgn0000615\t255\n+FBgn0000617\t500\n+FBgn0000618\t97\n+FBgn0000625\t0\n+FBgn0000629\t599\n+FBgn0000630\t4\n+FBgn0000633\t17\n+FBgn0000634\t237\n+FBgn0000635\t114\n+FBgn0000636\t18\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t0\n+FBgn0000658\t3\n+FBgn0000659\t0\n+FBgn0000662\t693\n+FBgn0000667\t905\n+FBgn0000709\t1348\n+FBgn0000711\t588\n+FBgn0000715\t0\n+FBgn0000719\t1157\n+FBgn0000721\t546\n+FBgn0000723\t1180\n+FBgn0000808\t66\n+FBgn0000810\t155\n+FBgn0000826\t84\n+FBgn0000927\t29\n+FBgn0000928\t493\n+FBgn0000964\t0\n+FBgn0000986\t1544\n+FBgn0000996\t626\n+FBgn0001075\t27\n+FBgn0'..b'\n+FBgn0030349\t918\n+FBgn0030350\t458\n+FBgn0030351\t81\n+FBgn0030352\t190\n+FBgn0030354\t1148\n+FBgn0030356\t0\n+FBgn0030357\t45\n+FBgn0030358\t117\n+FBgn0030359\t2\n+FBgn0030360\t20\n+FBgn0030361\t75\n+FBgn0030362\t3681\n+FBgn0030364\t343\n+FBgn0030365\t483\n+FBgn0030366\t2409\n+FBgn0030367\t47\n+FBgn0030369\t31\n+FBgn0030370\t0\n+FBgn0030373\t194\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t35\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t1\n+FBgn0030391\t189\n+FBgn0030394\t0\n+FBgn0030395\t0\n+FBgn0030396\t23\n+FBgn0030398\t0\n+FBgn0030399\t5\n+FBgn0030400\t827\n+FBgn0030403\t609\n+FBgn0030406\t110\n+FBgn0030407\t25\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t70\n+FBgn0030411\t66\n+FBgn0030412\t627\n+FBgn0030417\t44\n+FBgn0030418\t182\n+FBgn0030420\t477\n+FBgn0030421\t81\n+FBgn0030425\t2\n+FBgn0030429\t5\n+FBgn0030431\t271\n+FBgn0030432\t16\n+FBgn0030433\t339\n+FBgn0030434\t512\n+FBgn0030435\t459\n+FBgn0030437\t0\n+FBgn0030438\t3\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t387\n+FBgn0030448\t333\n+FBgn0030449\t0\n+FBgn0030451\t580\n+FBgn0030452\t464\n+FBgn0030455\t0\n+FBgn0030456\t513\n+FBgn0030457\t323\n+FBgn0030459\t4\n+FBgn0030460\t260\n+FBgn0030462\t0\n+FBgn0030465\t356\n+FBgn0030466\t2032\n+FBgn0030467\t547\n+FBgn0030468\t1021\n+FBgn0030469\t1509\n+FBgn0030474\t552\n+FBgn0030477\t1\n+FBgn0030478\t871\n+FBgn0030479\t108\n+FBgn0030480\t116\n+FBgn0030481\t308\n+FBgn0030482\t2385\n+FBgn0030483\t0\n+FBgn0030484\t777\n+FBgn0030485\t242\n+FBgn0030486\t1389\n+FBgn0030491\t4\n+FBgn0030492\t0\n+FBgn0030493\t1\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t496\n+FBgn0030500\t404\n+FBgn0030501\t571\n+FBgn0030502\t1309\n+FBgn0030503\t107\n+FBgn0030504\t1894\n+FBgn0030505\t983\n+FBgn0030506\t248\n+FBgn0030507\t183\n+FBgn0030508\t6\n+FBgn0030509\t1\n+FBgn0030510\t297\n+FBgn0030511\t119\n+FBgn0030512\t776\n+FBgn0030514\t927\n+FBgn0030518\t148\n+FBgn0030519\t595\n+FBgn0030520\t3149\n+FBgn0030521\t3016\n+FBgn0030522\t179\n+FBgn0030524\t2\n+FBgn0030525\t0\n+FBgn0030528\t62\n+FBgn0030529\t4060\n+FBgn0030530\t1204\n+FBgn0030532\t1224\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t216\n+FBgn0030551\t2\n+FBgn0030552\t311\n+FBgn0030554\t163\n+FBgn0030555\t136\n+FBgn0030556\t903\n+FBgn0030558\t0\n+FBgn0030559\t4\n+FBgn0030562\t22\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t0\n+FBgn0030570\t0\n+FBgn0030571\t164\n+FBgn0030572\t201\n+FBgn0030573\t16\n+FBgn0030574\t3\n+FBgn0030575\t42\n+FBgn0030576\t143\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t310\n+FBgn0030582\t610\n+FBgn0030583\t31\n+FBgn0030584\t164\n+FBgn0030586\t2\n+FBgn0030587\t3\n+FBgn0030588\t119\n+FBgn0030589\t1\n+FBgn0030590\t28\n+FBgn0030591\t1\n+FBgn0030592\t12\n+FBgn0030593\t2\n+FBgn0030594\t5\n+FBgn0030595\t0\n+FBgn0030596\t10\n+FBgn0030597\t4\n+FBgn0030598\t59\n+FBgn0030599\t1\n+FBgn0030600\t1649\n+FBgn0030603\t429\n+FBgn0030605\t388\n+FBgn0030606\t359\n+FBgn0030607\t12\n+FBgn0030608\t0\n+FBgn0030610\t163\n+FBgn0030611\t77\n+FBgn0030612\t201\n+FBgn0030613\t6\n+FBgn0030614\t2\n+FBgn0030615\t27\n+FBgn0030616\t14496\n+FBgn0030617\t1\n+FBgn0030618\t1\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t177\n+FBgn0030626\t250\n+FBgn0030627\t618\n+FBgn0030628\t300\n+FBgn0030629\t117\n+FBgn0030630\t337\n+FBgn0030631\t747\n+FBgn0030634\t0\n+FBgn0030636\t7\n+FBgn0030638\t663\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t17\n+FBgn0030643\t2\n+FBgn0030645\t64\n+FBgn0030646\t145\n+FBgn0030647\t6\n+FBgn0030648\t235\n+FBgn0030653\t156\n+FBgn0030654\t55\n+FBgn0030655\t148\n+FBgn0030657\t38\n+FBgn0030658\t710\n+FBgn0030659\t288\n+FBgn0030660\t114\n+FBgn0030661\t10\n+FBgn0030662\t570\n+FBgn0030663\t4\n+FBgn0030664\t5\n+FBgn0030665\t1\n+FBgn0030666\t1\n+FBgn0030667\t68\n+FBgn0030668\t139\n+FBgn0030669\t108\n+FBgn0030670\t323\n+FBgn0030671\t177\n+FBgn0030672\t3338\n+FBgn0030673\t44\n+FBgn0030674\t6438\n+FBgn0030675\t48\n+FBgn0030676\t1\n+FBgn0030678\t144\n+FBgn0030679\t268\n+FBgn0030680\t326\n+FBgn0030683\t171\n+FBgn0030684\t2\n+FBgn0030685\t1056\n+FBgn0030686\t269\n+FBgn0030687\t538\n+FBgn0030688\t0\n+FBgn0030691\t20\n+FBgn0030692\t499\n+FBgn0030693\t194\n+FBgn0030694\t111\n+no_feature\t252750\n+ambiguous\t83194\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t11922916\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461180_treat_paired.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461180_treat_paired.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t69\n+FBgn0000014\t2\n+FBgn0000015\t0\n+FBgn0000017\t2375\n+FBgn0000018\t235\n+FBgn0000022\t0\n+FBgn0000024\t2\n+FBgn0000028\t1\n+FBgn0000032\t553\n+FBgn0000036\t0\n+FBgn0000037\t9\n+FBgn0000038\t0\n+FBgn0000039\t1\n+FBgn0000042\t61359\n+FBgn0000043\t25056\n+FBgn0000044\t18\n+FBgn0000045\t9\n+FBgn0000046\t24\n+FBgn0000047\t12\n+FBgn0000052\t1439\n+FBgn0000053\t1594\n+FBgn0000054\t378\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t473\n+FBgn0000061\t1\n+FBgn0000063\t251\n+FBgn0000064\t5361\n+FBgn0000071\t385\n+FBgn0000075\t0\n+FBgn0000077\t112\n+FBgn0000078\t11\n+FBgn0000079\t75\n+FBgn0000083\t3552\n+FBgn0000084\t1033\n+FBgn0000092\t4\n+FBgn0000094\t5\n+FBgn0000097\t1874\n+FBgn0000099\t1\n+FBgn0000100\t16110\n+FBgn0000108\t27\n+FBgn0000109\t61\n+FBgn0000114\t1\n+FBgn0000115\t336\n+FBgn0000116\t666\n+FBgn0000117\t7588\n+FBgn0000119\t381\n+FBgn0000120\t0\n+FBgn0000121\t5\n+FBgn0000137\t0\n+FBgn0000139\t293\n+FBgn0000140\t604\n+FBgn0000142\t1115\n+FBgn0000146\t1152\n+FBgn0000147\t295\n+FBgn0000150\t6419\n+FBgn0000152\t343\n+FBgn0000153\t16\n+FBgn0000157\t0\n+FBgn0000158\t6\n+FBgn0000163\t497\n+FBgn0000166\t0\n+FBgn0000171\t4383\n+FBgn0000173\t993\n+FBgn0000179\t0\n+FBgn0000180\t23\n+FBgn0000181\t7624\n+FBgn0000182\t1\n+FBgn0000183\t1501\n+FBgn0000206\t0\n+FBgn0000210\t1080\n+FBgn0000212\t2084\n+FBgn0000216\t0\n+FBgn0000221\t119\n+FBgn0000227\t0\n+FBgn0000228\t472\n+FBgn0000229\t394\n+FBgn0000233\t2\n+FBgn0000239\t1570\n+FBgn0000241\t4\n+FBgn0000242\t92\n+FBgn0000244\t254\n+FBgn0000246\t73\n+FBgn0000247\t1659\n+FBgn0000250\t1283\n+FBgn0000251\t0\n+FBgn0000253\t5877\n+FBgn0000256\t1049\n+FBgn0000257\t494\n+FBgn0000258\t498\n+FBgn0000259\t1023\n+FBgn0000261\t1106\n+FBgn0000273\t1102\n+FBgn0000274\t0\n+FBgn0000276\t42\n+FBgn0000277\t15\n+FBgn0000278\t16\n+FBgn0000279\t34\n+FBgn0000280\t1\n+FBgn0000281\t1\n+FBgn0000283\t2196\n+FBgn0000286\t243\n+FBgn0000287\t0\n+FBgn0000289\t2072\n+FBgn0000299\t44540\n+FBgn0000303\t1\n+FBgn0000307\t866\n+FBgn0000308\t9427\n+FBgn0000313\t32\n+FBgn0000316\t2\n+FBgn0000317\t851\n+FBgn0000318\t623\n+FBgn0000319\t9250\n+FBgn0000320\t1\n+FBgn0000326\t170\n+FBgn0000330\t135\n+FBgn0000337\t12\n+FBgn0000338\t1155\n+FBgn0000339\t265\n+FBgn0000346\t44\n+FBgn0000351\t22\n+FBgn0000352\t506\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t1\n+FBgn0000363\t3\n+FBgn0000370\t6358\n+FBgn0000376\t808\n+FBgn0000377\t597\n+FBgn0000382\t426\n+FBgn0000384\t395\n+FBgn0000392\t842\n+FBgn0000394\t316\n+FBgn0000395\t267\n+FBgn0000404\t1467\n+FBgn0000405\t1809\n+FBgn0000406\t57\n+FBgn0000409\t2620\n+FBgn0000411\t0\n+FBgn0000412\t1816\n+FBgn0000413\t1650\n+FBgn0000414\t1231\n+FBgn0000416\t20885\n+FBgn0000422\t0\n+FBgn0000426\t413\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t471\n+FBgn0000448\t0\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t1723\n+FBgn0000455\t356\n+FBgn0000459\t2\n+FBgn0000463\t0\n+FBgn0000464\t934\n+FBgn0000472\t1337\n+FBgn0000473\t4\n+FBgn0000477\t0\n+FBgn0000479\t541\n+FBgn0000482\t637\n+FBgn0000489\t60\n+FBgn0000490\t162\n+FBgn0000492\t1\n+FBgn0000497\t0\n+FBgn0000499\t626\n+FBgn0000500\t7\n+FBgn0000504\t4\n+FBgn0000520\t392\n+FBgn0000524\t702\n+FBgn0000527\t71\n+FBgn0000529\t0\n+FBgn0000533\t4\n+FBgn0000535\t81\n+FBgn0000536\t528\n+FBgn0000541\t2699\n+FBgn0000542\t100\n+FBgn0000543\t506\n+FBgn0000546\t583\n+FBgn0000547\t231\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t116127\n+FBgn0000557\t29\n+FBgn0000559\t69701\n+FBgn0000560\t0\n+FBgn0000562\t891\n+FBgn0000564\t0\n+FBgn0000565\t517\n+FBgn0000566\t598\n+FBgn0000567\t85\n+FBgn0000568\t2091\n+FBgn0000575\t780\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t2813\n+FBgn0000579\t6646\n+FBgn0000581\t2111\n+FBgn0000588\t248\n+FBgn0000591\t0\n+FBgn0000592\t0\n+FBgn0000594\t10\n+FBgn0000606\t1\n+FBgn0000611\t731\n+FBgn0000615\t255\n+FBgn0000617\t500\n+FBgn0000618\t97\n+FBgn0000625\t0\n+FBgn0000629\t599\n+FBgn0000630\t4\n+FBgn0000633\t17\n+FBgn0000634\t237\n+FBgn0000635\t114\n+FBgn0000636\t18\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t0\n+FBgn0000658\t3\n+FBgn0000659\t0\n+FBgn0000662\t693\n+FBgn0000667\t905\n+FBgn0000709\t1348\n+FBgn0000711\t588\n+FBgn0000715\t0\n+FBgn0000719\t1157\n+FBgn0000721\t546\n+FBgn0000723\t1180\n+FBgn0000808\t66\n+FBgn0000810\t155\n+FBgn0000826\t84\n+FBgn0000927\t29\n+FBgn0000928\t493\n+FBgn0000964\t0\n+FBgn0000986\t1544\n+FBgn0000996\t626\n+FBgn0001075\t27\n+FBgn0001077\t0\n+FBgn0'..b'\n+FBgn0030349\t918\n+FBgn0030350\t458\n+FBgn0030351\t81\n+FBgn0030352\t190\n+FBgn0030354\t1148\n+FBgn0030356\t0\n+FBgn0030357\t45\n+FBgn0030358\t117\n+FBgn0030359\t2\n+FBgn0030360\t20\n+FBgn0030361\t75\n+FBgn0030362\t3681\n+FBgn0030364\t343\n+FBgn0030365\t483\n+FBgn0030366\t2409\n+FBgn0030367\t47\n+FBgn0030369\t31\n+FBgn0030370\t0\n+FBgn0030373\t194\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t35\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t1\n+FBgn0030391\t189\n+FBgn0030394\t0\n+FBgn0030395\t0\n+FBgn0030396\t23\n+FBgn0030398\t0\n+FBgn0030399\t5\n+FBgn0030400\t827\n+FBgn0030403\t609\n+FBgn0030406\t110\n+FBgn0030407\t25\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t70\n+FBgn0030411\t66\n+FBgn0030412\t627\n+FBgn0030417\t44\n+FBgn0030418\t182\n+FBgn0030420\t477\n+FBgn0030421\t81\n+FBgn0030425\t2\n+FBgn0030429\t5\n+FBgn0030431\t271\n+FBgn0030432\t16\n+FBgn0030433\t339\n+FBgn0030434\t512\n+FBgn0030435\t459\n+FBgn0030437\t0\n+FBgn0030438\t3\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t387\n+FBgn0030448\t333\n+FBgn0030449\t0\n+FBgn0030451\t580\n+FBgn0030452\t464\n+FBgn0030455\t0\n+FBgn0030456\t513\n+FBgn0030457\t323\n+FBgn0030459\t4\n+FBgn0030460\t260\n+FBgn0030462\t0\n+FBgn0030465\t356\n+FBgn0030466\t2032\n+FBgn0030467\t547\n+FBgn0030468\t1021\n+FBgn0030469\t1509\n+FBgn0030474\t552\n+FBgn0030477\t1\n+FBgn0030478\t871\n+FBgn0030479\t108\n+FBgn0030480\t116\n+FBgn0030481\t308\n+FBgn0030482\t2385\n+FBgn0030483\t0\n+FBgn0030484\t777\n+FBgn0030485\t242\n+FBgn0030486\t1389\n+FBgn0030491\t4\n+FBgn0030492\t0\n+FBgn0030493\t1\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t496\n+FBgn0030500\t404\n+FBgn0030501\t571\n+FBgn0030502\t1309\n+FBgn0030503\t107\n+FBgn0030504\t1894\n+FBgn0030505\t983\n+FBgn0030506\t248\n+FBgn0030507\t183\n+FBgn0030508\t6\n+FBgn0030509\t1\n+FBgn0030510\t297\n+FBgn0030511\t119\n+FBgn0030512\t776\n+FBgn0030514\t927\n+FBgn0030518\t148\n+FBgn0030519\t595\n+FBgn0030520\t3149\n+FBgn0030521\t3016\n+FBgn0030522\t179\n+FBgn0030524\t2\n+FBgn0030525\t0\n+FBgn0030528\t62\n+FBgn0030529\t4060\n+FBgn0030530\t1204\n+FBgn0030532\t1224\n+FBgn0030536\t0\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t216\n+FBgn0030551\t2\n+FBgn0030552\t311\n+FBgn0030554\t163\n+FBgn0030555\t136\n+FBgn0030556\t903\n+FBgn0030558\t0\n+FBgn0030559\t4\n+FBgn0030562\t22\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t0\n+FBgn0030570\t0\n+FBgn0030571\t164\n+FBgn0030572\t201\n+FBgn0030573\t16\n+FBgn0030574\t3\n+FBgn0030575\t42\n+FBgn0030576\t143\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t310\n+FBgn0030582\t610\n+FBgn0030583\t31\n+FBgn0030584\t164\n+FBgn0030586\t2\n+FBgn0030587\t3\n+FBgn0030588\t119\n+FBgn0030589\t1\n+FBgn0030590\t28\n+FBgn0030591\t1\n+FBgn0030592\t12\n+FBgn0030593\t2\n+FBgn0030594\t5\n+FBgn0030595\t0\n+FBgn0030596\t10\n+FBgn0030597\t4\n+FBgn0030598\t59\n+FBgn0030599\t1\n+FBgn0030600\t1649\n+FBgn0030603\t429\n+FBgn0030605\t388\n+FBgn0030606\t359\n+FBgn0030607\t12\n+FBgn0030608\t0\n+FBgn0030610\t163\n+FBgn0030611\t77\n+FBgn0030612\t201\n+FBgn0030613\t6\n+FBgn0030614\t2\n+FBgn0030615\t27\n+FBgn0030616\t14496\n+FBgn0030617\t1\n+FBgn0030618\t1\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t177\n+FBgn0030626\t250\n+FBgn0030627\t618\n+FBgn0030628\t300\n+FBgn0030629\t117\n+FBgn0030630\t337\n+FBgn0030631\t747\n+FBgn0030634\t0\n+FBgn0030636\t7\n+FBgn0030638\t663\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t17\n+FBgn0030643\t2\n+FBgn0030645\t64\n+FBgn0030646\t145\n+FBgn0030647\t6\n+FBgn0030648\t235\n+FBgn0030653\t156\n+FBgn0030654\t55\n+FBgn0030655\t148\n+FBgn0030657\t38\n+FBgn0030658\t710\n+FBgn0030659\t288\n+FBgn0030660\t114\n+FBgn0030661\t10\n+FBgn0030662\t570\n+FBgn0030663\t4\n+FBgn0030664\t5\n+FBgn0030665\t1\n+FBgn0030666\t1\n+FBgn0030667\t68\n+FBgn0030668\t139\n+FBgn0030669\t108\n+FBgn0030670\t323\n+FBgn0030671\t177\n+FBgn0030672\t3338\n+FBgn0030673\t44\n+FBgn0030674\t6438\n+FBgn0030675\t48\n+FBgn0030676\t1\n+FBgn0030678\t144\n+FBgn0030679\t268\n+FBgn0030680\t326\n+FBgn0030683\t171\n+FBgn0030684\t2\n+FBgn0030685\t1056\n+FBgn0030686\t269\n+FBgn0030687\t538\n+FBgn0030688\t0\n+FBgn0030691\t20\n+FBgn0030692\t499\n+FBgn0030693\t194\n+FBgn0030694\t111\n+no_feature\t252750\n+ambiguous\t83194\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t11922916\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461181_treat_paired.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461181_treat_paired.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\ttreat3\n+FBgn0000003\t0\n+FBgn0000008\t59\n+FBgn0000014\t2\n+FBgn0000015\t0\n+FBgn0000017\t3169\n+FBgn0000018\t271\n+FBgn0000022\t0\n+FBgn0000024\t1\n+FBgn0000028\t1\n+FBgn0000032\t695\n+FBgn0000036\t0\n+FBgn0000037\t8\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t80672\n+FBgn0000043\t33078\n+FBgn0000044\t18\n+FBgn0000045\t20\n+FBgn0000046\t18\n+FBgn0000047\t10\n+FBgn0000052\t1767\n+FBgn0000053\t1978\n+FBgn0000054\t571\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t611\n+FBgn0000061\t0\n+FBgn0000063\t316\n+FBgn0000064\t7313\n+FBgn0000071\t581\n+FBgn0000075\t1\n+FBgn0000077\t184\n+FBgn0000078\t16\n+FBgn0000079\t93\n+FBgn0000083\t4685\n+FBgn0000084\t1491\n+FBgn0000092\t8\n+FBgn0000094\t7\n+FBgn0000097\t2231\n+FBgn0000099\t0\n+FBgn0000100\t20091\n+FBgn0000108\t38\n+FBgn0000109\t89\n+FBgn0000114\t4\n+FBgn0000115\t513\n+FBgn0000116\t842\n+FBgn0000117\t9795\n+FBgn0000119\t497\n+FBgn0000120\t0\n+FBgn0000121\t5\n+FBgn0000137\t0\n+FBgn0000139\t455\n+FBgn0000140\t623\n+FBgn0000142\t1456\n+FBgn0000146\t1366\n+FBgn0000147\t361\n+FBgn0000150\t7686\n+FBgn0000152\t457\n+FBgn0000153\t8\n+FBgn0000157\t0\n+FBgn0000158\t3\n+FBgn0000163\t652\n+FBgn0000166\t0\n+FBgn0000171\t5353\n+FBgn0000173\t1277\n+FBgn0000179\t1\n+FBgn0000180\t19\n+FBgn0000181\t9968\n+FBgn0000182\t2\n+FBgn0000183\t2052\n+FBgn0000206\t0\n+FBgn0000210\t1151\n+FBgn0000212\t2925\n+FBgn0000216\t0\n+FBgn0000221\t157\n+FBgn0000227\t0\n+FBgn0000228\t577\n+FBgn0000229\t544\n+FBgn0000233\t5\n+FBgn0000239\t1762\n+FBgn0000241\t2\n+FBgn0000242\t112\n+FBgn0000244\t332\n+FBgn0000246\t87\n+FBgn0000247\t1944\n+FBgn0000250\t1926\n+FBgn0000251\t0\n+FBgn0000253\t7954\n+FBgn0000256\t1395\n+FBgn0000257\t725\n+FBgn0000258\t614\n+FBgn0000259\t1354\n+FBgn0000261\t1530\n+FBgn0000273\t1458\n+FBgn0000274\t0\n+FBgn0000276\t43\n+FBgn0000277\t16\n+FBgn0000278\t29\n+FBgn0000279\t36\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2647\n+FBgn0000286\t326\n+FBgn0000287\t1\n+FBgn0000289\t2526\n+FBgn0000299\t50107\n+FBgn0000303\t2\n+FBgn0000307\t1220\n+FBgn0000308\t13203\n+FBgn0000313\t43\n+FBgn0000316\t0\n+FBgn0000317\t994\n+FBgn0000318\t972\n+FBgn0000319\t11180\n+FBgn0000320\t0\n+FBgn0000326\t205\n+FBgn0000330\t185\n+FBgn0000337\t11\n+FBgn0000338\t1443\n+FBgn0000339\t395\n+FBgn0000346\t73\n+FBgn0000351\t34\n+FBgn0000352\t646\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t2\n+FBgn0000370\t8147\n+FBgn0000376\t1033\n+FBgn0000377\t788\n+FBgn0000382\t507\n+FBgn0000384\t483\n+FBgn0000392\t1048\n+FBgn0000394\t453\n+FBgn0000395\t303\n+FBgn0000404\t1959\n+FBgn0000405\t2190\n+FBgn0000406\t90\n+FBgn0000409\t3297\n+FBgn0000411\t0\n+FBgn0000412\t2165\n+FBgn0000413\t2105\n+FBgn0000414\t1570\n+FBgn0000416\t27351\n+FBgn0000422\t9\n+FBgn0000426\t653\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t4\n+FBgn0000447\t600\n+FBgn0000448\t2\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t2332\n+FBgn0000455\t378\n+FBgn0000459\t2\n+FBgn0000463\t2\n+FBgn0000464\t1060\n+FBgn0000472\t1811\n+FBgn0000473\t16\n+FBgn0000477\t2\n+FBgn0000479\t582\n+FBgn0000482\t850\n+FBgn0000489\t78\n+FBgn0000490\t188\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t840\n+FBgn0000500\t10\n+FBgn0000504\t0\n+FBgn0000520\t518\n+FBgn0000524\t753\n+FBgn0000527\t57\n+FBgn0000529\t1\n+FBgn0000533\t7\n+FBgn0000535\t68\n+FBgn0000536\t632\n+FBgn0000541\t2907\n+FBgn0000542\t158\n+FBgn0000543\t723\n+FBgn0000546\t618\n+FBgn0000547\t356\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t157119\n+FBgn0000557\t36\n+FBgn0000559\t92318\n+FBgn0000560\t1\n+FBgn0000562\t1081\n+FBgn0000564\t0\n+FBgn0000565\t782\n+FBgn0000566\t648\n+FBgn0000567\t94\n+FBgn0000568\t2515\n+FBgn0000575\t1051\n+FBgn0000576\t0\n+FBgn0000577\t2\n+FBgn0000578\t3569\n+FBgn0000579\t8823\n+FBgn0000581\t2435\n+FBgn0000588\t214\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t6\n+FBgn0000606\t0\n+FBgn0000611\t872\n+FBgn0000615\t249\n+FBgn0000617\t666\n+FBgn0000618\t145\n+FBgn0000625\t4\n+FBgn0000629\t833\n+FBgn0000630\t10\n+FBgn0000633\t27\n+FBgn0000634\t273\n+FBgn0000635\t148\n+FBgn0000636\t24\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t1\n+FBgn0000659\t1\n+FBgn0000662\t881\n+FBgn0000667\t1271\n+FBgn0000709\t1718\n+FBgn0000711\t753\n+FBgn0000715\t0\n+FBgn0000719\t1650\n+FBgn0000721\t683\n+FBgn0000723\t1651\n+FBgn0000808\t107\n+FBgn0000810\t172\n+FBgn0000826\t114\n+FBgn0000927\t22\n+FBgn0000928\t624\n+FBgn0000964\t0\n+FBgn0000986\t1872\n+FBgn0000996\t845\n+FBgn0'..b'9\t1156\n+FBgn0030350\t644\n+FBgn0030351\t87\n+FBgn0030352\t187\n+FBgn0030354\t1553\n+FBgn0030356\t0\n+FBgn0030357\t39\n+FBgn0030358\t156\n+FBgn0030359\t8\n+FBgn0030360\t12\n+FBgn0030361\t147\n+FBgn0030362\t4615\n+FBgn0030364\t499\n+FBgn0030365\t743\n+FBgn0030366\t3118\n+FBgn0030367\t58\n+FBgn0030369\t53\n+FBgn0030370\t0\n+FBgn0030373\t247\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t38\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t1\n+FBgn0030391\t343\n+FBgn0030394\t2\n+FBgn0030395\t0\n+FBgn0030396\t35\n+FBgn0030398\t1\n+FBgn0030399\t5\n+FBgn0030400\t873\n+FBgn0030403\t823\n+FBgn0030406\t122\n+FBgn0030407\t21\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t96\n+FBgn0030411\t85\n+FBgn0030412\t789\n+FBgn0030417\t48\n+FBgn0030418\t258\n+FBgn0030420\t661\n+FBgn0030421\t94\n+FBgn0030425\t1\n+FBgn0030429\t0\n+FBgn0030431\t388\n+FBgn0030432\t24\n+FBgn0030433\t438\n+FBgn0030434\t647\n+FBgn0030435\t566\n+FBgn0030437\t0\n+FBgn0030438\t7\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t1\n+FBgn0030447\t489\n+FBgn0030448\t475\n+FBgn0030449\t0\n+FBgn0030451\t825\n+FBgn0030452\t565\n+FBgn0030455\t5\n+FBgn0030456\t631\n+FBgn0030457\t435\n+FBgn0030459\t18\n+FBgn0030460\t372\n+FBgn0030462\t0\n+FBgn0030465\t488\n+FBgn0030466\t2459\n+FBgn0030467\t704\n+FBgn0030468\t1385\n+FBgn0030469\t1944\n+FBgn0030474\t788\n+FBgn0030477\t2\n+FBgn0030478\t1024\n+FBgn0030479\t155\n+FBgn0030480\t153\n+FBgn0030481\t371\n+FBgn0030482\t3023\n+FBgn0030483\t12\n+FBgn0030484\t969\n+FBgn0030485\t289\n+FBgn0030486\t1829\n+FBgn0030491\t4\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t718\n+FBgn0030500\t528\n+FBgn0030501\t862\n+FBgn0030502\t1733\n+FBgn0030503\t109\n+FBgn0030504\t2053\n+FBgn0030505\t1151\n+FBgn0030506\t383\n+FBgn0030507\t251\n+FBgn0030508\t8\n+FBgn0030509\t0\n+FBgn0030510\t410\n+FBgn0030511\t164\n+FBgn0030512\t969\n+FBgn0030514\t1259\n+FBgn0030518\t233\n+FBgn0030519\t950\n+FBgn0030520\t4224\n+FBgn0030521\t4308\n+FBgn0030522\t233\n+FBgn0030524\t2\n+FBgn0030525\t2\n+FBgn0030528\t118\n+FBgn0030529\t5638\n+FBgn0030530\t1647\n+FBgn0030532\t1628\n+FBgn0030536\t2\n+FBgn0030537\t0\n+FBgn0030538\t1\n+FBgn0030539\t1\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t327\n+FBgn0030551\t1\n+FBgn0030552\t486\n+FBgn0030554\t209\n+FBgn0030555\t192\n+FBgn0030556\t1175\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t29\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t3\n+FBgn0030570\t0\n+FBgn0030571\t205\n+FBgn0030572\t249\n+FBgn0030573\t29\n+FBgn0030574\t19\n+FBgn0030575\t34\n+FBgn0030576\t190\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t414\n+FBgn0030582\t783\n+FBgn0030583\t34\n+FBgn0030584\t276\n+FBgn0030586\t1\n+FBgn0030587\t7\n+FBgn0030588\t183\n+FBgn0030589\t1\n+FBgn0030590\t20\n+FBgn0030591\t2\n+FBgn0030592\t1\n+FBgn0030593\t7\n+FBgn0030594\t6\n+FBgn0030595\t2\n+FBgn0030596\t13\n+FBgn0030597\t4\n+FBgn0030598\t31\n+FBgn0030599\t2\n+FBgn0030600\t1996\n+FBgn0030603\t538\n+FBgn0030605\t522\n+FBgn0030606\t483\n+FBgn0030607\t34\n+FBgn0030608\t0\n+FBgn0030610\t225\n+FBgn0030611\t110\n+FBgn0030612\t255\n+FBgn0030613\t4\n+FBgn0030614\t0\n+FBgn0030615\t40\n+FBgn0030616\t20187\n+FBgn0030617\t2\n+FBgn0030618\t0\n+FBgn0030619\t1\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t166\n+FBgn0030626\t322\n+FBgn0030627\t833\n+FBgn0030628\t444\n+FBgn0030629\t158\n+FBgn0030630\t528\n+FBgn0030631\t987\n+FBgn0030634\t0\n+FBgn0030636\t9\n+FBgn0030638\t915\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t17\n+FBgn0030643\t4\n+FBgn0030645\t64\n+FBgn0030646\t214\n+FBgn0030647\t9\n+FBgn0030648\t281\n+FBgn0030653\t187\n+FBgn0030654\t73\n+FBgn0030655\t216\n+FBgn0030657\t80\n+FBgn0030658\t854\n+FBgn0030659\t390\n+FBgn0030660\t118\n+FBgn0030661\t30\n+FBgn0030662\t781\n+FBgn0030663\t3\n+FBgn0030664\t11\n+FBgn0030665\t2\n+FBgn0030666\t4\n+FBgn0030667\t72\n+FBgn0030668\t178\n+FBgn0030669\t148\n+FBgn0030670\t433\n+FBgn0030671\t205\n+FBgn0030672\t4409\n+FBgn0030673\t66\n+FBgn0030674\t7447\n+FBgn0030675\t76\n+FBgn0030676\t9\n+FBgn0030678\t188\n+FBgn0030679\t371\n+FBgn0030680\t445\n+FBgn0030683\t194\n+FBgn0030684\t0\n+FBgn0030685\t1408\n+FBgn0030686\t334\n+FBgn0030687\t676\n+FBgn0030688\t2\n+FBgn0030691\t13\n+FBgn0030692\t625\n+FBgn0030693\t236\n+FBgn0030694\t212\n+no_feature\t300140\n+ambiguous\t107409\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t12749496\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461181_treat_paired.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461181_treat_paired.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t59\n+FBgn0000014\t2\n+FBgn0000015\t0\n+FBgn0000017\t3169\n+FBgn0000018\t271\n+FBgn0000022\t0\n+FBgn0000024\t1\n+FBgn0000028\t1\n+FBgn0000032\t695\n+FBgn0000036\t0\n+FBgn0000037\t8\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t80672\n+FBgn0000043\t33078\n+FBgn0000044\t18\n+FBgn0000045\t20\n+FBgn0000046\t18\n+FBgn0000047\t10\n+FBgn0000052\t1767\n+FBgn0000053\t1978\n+FBgn0000054\t571\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t611\n+FBgn0000061\t0\n+FBgn0000063\t316\n+FBgn0000064\t7313\n+FBgn0000071\t581\n+FBgn0000075\t1\n+FBgn0000077\t184\n+FBgn0000078\t16\n+FBgn0000079\t93\n+FBgn0000083\t4685\n+FBgn0000084\t1491\n+FBgn0000092\t8\n+FBgn0000094\t7\n+FBgn0000097\t2231\n+FBgn0000099\t0\n+FBgn0000100\t20091\n+FBgn0000108\t38\n+FBgn0000109\t89\n+FBgn0000114\t4\n+FBgn0000115\t513\n+FBgn0000116\t842\n+FBgn0000117\t9795\n+FBgn0000119\t497\n+FBgn0000120\t0\n+FBgn0000121\t5\n+FBgn0000137\t0\n+FBgn0000139\t455\n+FBgn0000140\t623\n+FBgn0000142\t1456\n+FBgn0000146\t1366\n+FBgn0000147\t361\n+FBgn0000150\t7686\n+FBgn0000152\t457\n+FBgn0000153\t8\n+FBgn0000157\t0\n+FBgn0000158\t3\n+FBgn0000163\t652\n+FBgn0000166\t0\n+FBgn0000171\t5353\n+FBgn0000173\t1277\n+FBgn0000179\t1\n+FBgn0000180\t19\n+FBgn0000181\t9968\n+FBgn0000182\t2\n+FBgn0000183\t2052\n+FBgn0000206\t0\n+FBgn0000210\t1151\n+FBgn0000212\t2925\n+FBgn0000216\t0\n+FBgn0000221\t157\n+FBgn0000227\t0\n+FBgn0000228\t577\n+FBgn0000229\t544\n+FBgn0000233\t5\n+FBgn0000239\t1762\n+FBgn0000241\t2\n+FBgn0000242\t112\n+FBgn0000244\t332\n+FBgn0000246\t87\n+FBgn0000247\t1944\n+FBgn0000250\t1926\n+FBgn0000251\t0\n+FBgn0000253\t7954\n+FBgn0000256\t1395\n+FBgn0000257\t725\n+FBgn0000258\t614\n+FBgn0000259\t1354\n+FBgn0000261\t1530\n+FBgn0000273\t1458\n+FBgn0000274\t0\n+FBgn0000276\t43\n+FBgn0000277\t16\n+FBgn0000278\t29\n+FBgn0000279\t36\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t2647\n+FBgn0000286\t326\n+FBgn0000287\t1\n+FBgn0000289\t2526\n+FBgn0000299\t50107\n+FBgn0000303\t2\n+FBgn0000307\t1220\n+FBgn0000308\t13203\n+FBgn0000313\t43\n+FBgn0000316\t0\n+FBgn0000317\t994\n+FBgn0000318\t972\n+FBgn0000319\t11180\n+FBgn0000320\t0\n+FBgn0000326\t205\n+FBgn0000330\t185\n+FBgn0000337\t11\n+FBgn0000338\t1443\n+FBgn0000339\t395\n+FBgn0000346\t73\n+FBgn0000351\t34\n+FBgn0000352\t646\n+FBgn0000355\t0\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t2\n+FBgn0000370\t8147\n+FBgn0000376\t1033\n+FBgn0000377\t788\n+FBgn0000382\t507\n+FBgn0000384\t483\n+FBgn0000392\t1048\n+FBgn0000394\t453\n+FBgn0000395\t303\n+FBgn0000404\t1959\n+FBgn0000405\t2190\n+FBgn0000406\t90\n+FBgn0000409\t3297\n+FBgn0000411\t0\n+FBgn0000412\t2165\n+FBgn0000413\t2105\n+FBgn0000414\t1570\n+FBgn0000416\t27351\n+FBgn0000422\t9\n+FBgn0000426\t653\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t4\n+FBgn0000447\t600\n+FBgn0000448\t2\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t2332\n+FBgn0000455\t378\n+FBgn0000459\t2\n+FBgn0000463\t2\n+FBgn0000464\t1060\n+FBgn0000472\t1811\n+FBgn0000473\t16\n+FBgn0000477\t2\n+FBgn0000479\t582\n+FBgn0000482\t850\n+FBgn0000489\t78\n+FBgn0000490\t188\n+FBgn0000492\t0\n+FBgn0000497\t0\n+FBgn0000499\t840\n+FBgn0000500\t10\n+FBgn0000504\t0\n+FBgn0000520\t518\n+FBgn0000524\t753\n+FBgn0000527\t57\n+FBgn0000529\t1\n+FBgn0000533\t7\n+FBgn0000535\t68\n+FBgn0000536\t632\n+FBgn0000541\t2907\n+FBgn0000542\t158\n+FBgn0000543\t723\n+FBgn0000546\t618\n+FBgn0000547\t356\n+FBgn0000551\t1\n+FBgn0000552\t0\n+FBgn0000556\t157119\n+FBgn0000557\t36\n+FBgn0000559\t92318\n+FBgn0000560\t1\n+FBgn0000562\t1081\n+FBgn0000564\t0\n+FBgn0000565\t782\n+FBgn0000566\t648\n+FBgn0000567\t94\n+FBgn0000568\t2515\n+FBgn0000575\t1051\n+FBgn0000576\t0\n+FBgn0000577\t2\n+FBgn0000578\t3569\n+FBgn0000579\t8823\n+FBgn0000581\t2435\n+FBgn0000588\t214\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t6\n+FBgn0000606\t0\n+FBgn0000611\t872\n+FBgn0000615\t249\n+FBgn0000617\t666\n+FBgn0000618\t145\n+FBgn0000625\t4\n+FBgn0000629\t833\n+FBgn0000630\t10\n+FBgn0000633\t27\n+FBgn0000634\t273\n+FBgn0000635\t148\n+FBgn0000636\t24\n+FBgn0000639\t0\n+FBgn0000640\t0\n+FBgn0000644\t2\n+FBgn0000658\t1\n+FBgn0000659\t1\n+FBgn0000662\t881\n+FBgn0000667\t1271\n+FBgn0000709\t1718\n+FBgn0000711\t753\n+FBgn0000715\t0\n+FBgn0000719\t1650\n+FBgn0000721\t683\n+FBgn0000723\t1651\n+FBgn0000808\t107\n+FBgn0000810\t172\n+FBgn0000826\t114\n+FBgn0000927\t22\n+FBgn0000928\t624\n+FBgn0000964\t0\n+FBgn0000986\t1872\n+FBgn0000996\t845\n+FBgn0001075\t13\n+FBgn'..b'9\t1156\n+FBgn0030350\t644\n+FBgn0030351\t87\n+FBgn0030352\t187\n+FBgn0030354\t1553\n+FBgn0030356\t0\n+FBgn0030357\t39\n+FBgn0030358\t156\n+FBgn0030359\t8\n+FBgn0030360\t12\n+FBgn0030361\t147\n+FBgn0030362\t4615\n+FBgn0030364\t499\n+FBgn0030365\t743\n+FBgn0030366\t3118\n+FBgn0030367\t58\n+FBgn0030369\t53\n+FBgn0030370\t0\n+FBgn0030373\t247\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t38\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t1\n+FBgn0030391\t343\n+FBgn0030394\t2\n+FBgn0030395\t0\n+FBgn0030396\t35\n+FBgn0030398\t1\n+FBgn0030399\t5\n+FBgn0030400\t873\n+FBgn0030403\t823\n+FBgn0030406\t122\n+FBgn0030407\t21\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t96\n+FBgn0030411\t85\n+FBgn0030412\t789\n+FBgn0030417\t48\n+FBgn0030418\t258\n+FBgn0030420\t661\n+FBgn0030421\t94\n+FBgn0030425\t1\n+FBgn0030429\t0\n+FBgn0030431\t388\n+FBgn0030432\t24\n+FBgn0030433\t438\n+FBgn0030434\t647\n+FBgn0030435\t566\n+FBgn0030437\t0\n+FBgn0030438\t7\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t1\n+FBgn0030447\t489\n+FBgn0030448\t475\n+FBgn0030449\t0\n+FBgn0030451\t825\n+FBgn0030452\t565\n+FBgn0030455\t5\n+FBgn0030456\t631\n+FBgn0030457\t435\n+FBgn0030459\t18\n+FBgn0030460\t372\n+FBgn0030462\t0\n+FBgn0030465\t488\n+FBgn0030466\t2459\n+FBgn0030467\t704\n+FBgn0030468\t1385\n+FBgn0030469\t1944\n+FBgn0030474\t788\n+FBgn0030477\t2\n+FBgn0030478\t1024\n+FBgn0030479\t155\n+FBgn0030480\t153\n+FBgn0030481\t371\n+FBgn0030482\t3023\n+FBgn0030483\t12\n+FBgn0030484\t969\n+FBgn0030485\t289\n+FBgn0030486\t1829\n+FBgn0030491\t4\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t718\n+FBgn0030500\t528\n+FBgn0030501\t862\n+FBgn0030502\t1733\n+FBgn0030503\t109\n+FBgn0030504\t2053\n+FBgn0030505\t1151\n+FBgn0030506\t383\n+FBgn0030507\t251\n+FBgn0030508\t8\n+FBgn0030509\t0\n+FBgn0030510\t410\n+FBgn0030511\t164\n+FBgn0030512\t969\n+FBgn0030514\t1259\n+FBgn0030518\t233\n+FBgn0030519\t950\n+FBgn0030520\t4224\n+FBgn0030521\t4308\n+FBgn0030522\t233\n+FBgn0030524\t2\n+FBgn0030525\t2\n+FBgn0030528\t118\n+FBgn0030529\t5638\n+FBgn0030530\t1647\n+FBgn0030532\t1628\n+FBgn0030536\t2\n+FBgn0030537\t0\n+FBgn0030538\t1\n+FBgn0030539\t1\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t327\n+FBgn0030551\t1\n+FBgn0030552\t486\n+FBgn0030554\t209\n+FBgn0030555\t192\n+FBgn0030556\t1175\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t29\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t3\n+FBgn0030570\t0\n+FBgn0030571\t205\n+FBgn0030572\t249\n+FBgn0030573\t29\n+FBgn0030574\t19\n+FBgn0030575\t34\n+FBgn0030576\t190\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t414\n+FBgn0030582\t783\n+FBgn0030583\t34\n+FBgn0030584\t276\n+FBgn0030586\t1\n+FBgn0030587\t7\n+FBgn0030588\t183\n+FBgn0030589\t1\n+FBgn0030590\t20\n+FBgn0030591\t2\n+FBgn0030592\t1\n+FBgn0030593\t7\n+FBgn0030594\t6\n+FBgn0030595\t2\n+FBgn0030596\t13\n+FBgn0030597\t4\n+FBgn0030598\t31\n+FBgn0030599\t2\n+FBgn0030600\t1996\n+FBgn0030603\t538\n+FBgn0030605\t522\n+FBgn0030606\t483\n+FBgn0030607\t34\n+FBgn0030608\t0\n+FBgn0030610\t225\n+FBgn0030611\t110\n+FBgn0030612\t255\n+FBgn0030613\t4\n+FBgn0030614\t0\n+FBgn0030615\t40\n+FBgn0030616\t20187\n+FBgn0030617\t2\n+FBgn0030618\t0\n+FBgn0030619\t1\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t166\n+FBgn0030626\t322\n+FBgn0030627\t833\n+FBgn0030628\t444\n+FBgn0030629\t158\n+FBgn0030630\t528\n+FBgn0030631\t987\n+FBgn0030634\t0\n+FBgn0030636\t9\n+FBgn0030638\t915\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t17\n+FBgn0030643\t4\n+FBgn0030645\t64\n+FBgn0030646\t214\n+FBgn0030647\t9\n+FBgn0030648\t281\n+FBgn0030653\t187\n+FBgn0030654\t73\n+FBgn0030655\t216\n+FBgn0030657\t80\n+FBgn0030658\t854\n+FBgn0030659\t390\n+FBgn0030660\t118\n+FBgn0030661\t30\n+FBgn0030662\t781\n+FBgn0030663\t3\n+FBgn0030664\t11\n+FBgn0030665\t2\n+FBgn0030666\t4\n+FBgn0030667\t72\n+FBgn0030668\t178\n+FBgn0030669\t148\n+FBgn0030670\t433\n+FBgn0030671\t205\n+FBgn0030672\t4409\n+FBgn0030673\t66\n+FBgn0030674\t7447\n+FBgn0030675\t76\n+FBgn0030676\t9\n+FBgn0030678\t188\n+FBgn0030679\t371\n+FBgn0030680\t445\n+FBgn0030683\t194\n+FBgn0030684\t0\n+FBgn0030685\t1408\n+FBgn0030686\t334\n+FBgn0030687\t676\n+FBgn0030688\t2\n+FBgn0030691\t13\n+FBgn0030692\t625\n+FBgn0030693\t236\n+FBgn0030694\t212\n+no_feature\t300140\n+ambiguous\t107409\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t12749496\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461182_untreat_single.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461182_untreat_single.counts Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4005 @@\n+GeneID\tuntreat4\n+FBgn0000003\t0\n+FBgn0000008\t29\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t1213\n+FBgn0000018\t114\n+FBgn0000022\t0\n+FBgn0000024\t3\n+FBgn0000028\t0\n+FBgn0000032\t399\n+FBgn0000036\t0\n+FBgn0000037\t4\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t29229\n+FBgn0000043\t8594\n+FBgn0000044\t6\n+FBgn0000045\t0\n+FBgn0000046\t0\n+FBgn0000047\t1\n+FBgn0000052\t723\n+FBgn0000053\t510\n+FBgn0000054\t220\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t215\n+FBgn0000061\t0\n+FBgn0000063\t118\n+FBgn0000064\t1967\n+FBgn0000071\t19\n+FBgn0000075\t0\n+FBgn0000077\t64\n+FBgn0000078\t5\n+FBgn0000079\t48\n+FBgn0000083\t1428\n+FBgn0000084\t499\n+FBgn0000092\t2\n+FBgn0000094\t1\n+FBgn0000097\t752\n+FBgn0000099\t1\n+FBgn0000100\t6726\n+FBgn0000108\t2\n+FBgn0000109\t57\n+FBgn0000114\t0\n+FBgn0000115\t169\n+FBgn0000116\t91\n+FBgn0000117\t2741\n+FBgn0000119\t202\n+FBgn0000120\t0\n+FBgn0000121\t3\n+FBgn0000137\t0\n+FBgn0000139\t234\n+FBgn0000140\t314\n+FBgn0000142\t567\n+FBgn0000146\t411\n+FBgn0000147\t110\n+FBgn0000150\t1983\n+FBgn0000152\t167\n+FBgn0000153\t8\n+FBgn0000157\t1\n+FBgn0000158\t2\n+FBgn0000163\t220\n+FBgn0000166\t0\n+FBgn0000171\t1432\n+FBgn0000173\t452\n+FBgn0000179\t0\n+FBgn0000180\t0\n+FBgn0000181\t3326\n+FBgn0000182\t1\n+FBgn0000183\t853\n+FBgn0000206\t0\n+FBgn0000210\t371\n+FBgn0000212\t918\n+FBgn0000216\t0\n+FBgn0000221\t62\n+FBgn0000227\t0\n+FBgn0000228\t218\n+FBgn0000229\t332\n+FBgn0000233\t0\n+FBgn0000239\t782\n+FBgn0000241\t1\n+FBgn0000242\t34\n+FBgn0000244\t179\n+FBgn0000246\t50\n+FBgn0000247\t825\n+FBgn0000250\t609\n+FBgn0000251\t0\n+FBgn0000253\t3365\n+FBgn0000256\t512\n+FBgn0000257\t186\n+FBgn0000258\t383\n+FBgn0000259\t563\n+FBgn0000261\t499\n+FBgn0000273\t487\n+FBgn0000274\t0\n+FBgn0000276\t46\n+FBgn0000277\t12\n+FBgn0000278\t21\n+FBgn0000279\t27\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t1062\n+FBgn0000286\t144\n+FBgn0000287\t0\n+FBgn0000289\t1101\n+FBgn0000299\t9089\n+FBgn0000303\t2\n+FBgn0000307\t467\n+FBgn0000308\t4803\n+FBgn0000313\t19\n+FBgn0000316\t0\n+FBgn0000317\t514\n+FBgn0000318\t251\n+FBgn0000319\t4787\n+FBgn0000320\t0\n+FBgn0000326\t75\n+FBgn0000330\t70\n+FBgn0000337\t4\n+FBgn0000338\t335\n+FBgn0000339\t242\n+FBgn0000346\t31\n+FBgn0000351\t6\n+FBgn0000352\t237\n+FBgn0000355\t1\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t1\n+FBgn0000370\t3832\n+FBgn0000376\t289\n+FBgn0000377\t208\n+FBgn0000382\t173\n+FBgn0000384\t247\n+FBgn0000392\t222\n+FBgn0000394\t209\n+FBgn0000395\t106\n+FBgn0000404\t812\n+FBgn0000405\t649\n+FBgn0000406\t61\n+FBgn0000409\t1298\n+FBgn0000411\t0\n+FBgn0000412\t590\n+FBgn0000413\t563\n+FBgn0000414\t916\n+FBgn0000416\t13542\n+FBgn0000422\t1\n+FBgn0000426\t167\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t132\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t756\n+FBgn0000455\t142\n+FBgn0000459\t0\n+FBgn0000463\t1\n+FBgn0000464\t438\n+FBgn0000472\t509\n+FBgn0000473\t2\n+FBgn0000477\t0\n+FBgn0000479\t244\n+FBgn0000482\t279\n+FBgn0000489\t31\n+FBgn0000490\t26\n+FBgn0000492\t0\n+FBgn0000497\t2\n+FBgn0000499\t251\n+FBgn0000500\t1\n+FBgn0000504\t0\n+FBgn0000520\t122\n+FBgn0000524\t238\n+FBgn0000527\t46\n+FBgn0000529\t0\n+FBgn0000533\t0\n+FBgn0000535\t26\n+FBgn0000536\t298\n+FBgn0000541\t1634\n+FBgn0000542\t21\n+FBgn0000543\t162\n+FBgn0000546\t256\n+FBgn0000547\t56\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t60017\n+FBgn0000557\t8\n+FBgn0000559\t31536\n+FBgn0000560\t0\n+FBgn0000562\t426\n+FBgn0000564\t0\n+FBgn0000565\t89\n+FBgn0000566\t244\n+FBgn0000567\t84\n+FBgn0000568\t600\n+FBgn0000575\t330\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t1453\n+FBgn0000579\t1744\n+FBgn0000581\t954\n+FBgn0000588\t111\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t5\n+FBgn0000606\t0\n+FBgn0000611\t483\n+FBgn0000615\t130\n+FBgn0000617\t202\n+FBgn0000618\t34\n+FBgn0000625\t0\n+FBgn0000629\t308\n+FBgn0000630\t1\n+FBgn0000633\t3\n+FBgn0000634\t109\n+FBgn0000635\t16\n+FBgn0000636\t12\n+FBgn0000639\t1\n+FBgn0000640\t0\n+FBgn0000644\t1\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t362\n+FBgn0000667\t424\n+FBgn0000709\t608\n+FBgn0000711\t347\n+FBgn0000715\t0\n+FBgn0000719\t605\n+FBgn0000721\t246\n+FBgn0000723\t501\n+FBgn0000808\t24\n+FBgn0000810\t80\n+FBgn0000826\t27\n+FBgn0000927\t7\n+FBgn0000928\t178\n+FBgn0000964\t0\n+FBgn0000986\t777\n+FBgn0000996\t335\n+FBgn0001075\t6\n+FBgn0001077\t0\n+FBgn0001078\t227\n+FBgn0001079\t118\n+FBgn0001083\t53'..b'0030345\t64\n+FBgn0030346\t41\n+FBgn0030347\t69\n+FBgn0030348\t1\n+FBgn0030349\t691\n+FBgn0030350\t214\n+FBgn0030351\t43\n+FBgn0030352\t83\n+FBgn0030354\t550\n+FBgn0030356\t0\n+FBgn0030357\t31\n+FBgn0030358\t54\n+FBgn0030359\t2\n+FBgn0030360\t6\n+FBgn0030361\t27\n+FBgn0030362\t1789\n+FBgn0030364\t136\n+FBgn0030365\t189\n+FBgn0030366\t1230\n+FBgn0030367\t21\n+FBgn0030369\t20\n+FBgn0030370\t0\n+FBgn0030373\t70\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t0\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t101\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t10\n+FBgn0030398\t0\n+FBgn0030399\t1\n+FBgn0030400\t301\n+FBgn0030403\t294\n+FBgn0030406\t41\n+FBgn0030407\t16\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t27\n+FBgn0030411\t26\n+FBgn0030412\t412\n+FBgn0030417\t9\n+FBgn0030418\t97\n+FBgn0030420\t343\n+FBgn0030421\t93\n+FBgn0030425\t2\n+FBgn0030429\t1\n+FBgn0030431\t174\n+FBgn0030432\t9\n+FBgn0030433\t136\n+FBgn0030434\t224\n+FBgn0030435\t240\n+FBgn0030437\t0\n+FBgn0030438\t1\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t157\n+FBgn0030448\t111\n+FBgn0030449\t0\n+FBgn0030451\t298\n+FBgn0030452\t341\n+FBgn0030455\t1\n+FBgn0030456\t227\n+FBgn0030457\t169\n+FBgn0030459\t1\n+FBgn0030460\t127\n+FBgn0030462\t0\n+FBgn0030465\t165\n+FBgn0030466\t705\n+FBgn0030467\t237\n+FBgn0030468\t452\n+FBgn0030469\t357\n+FBgn0030474\t239\n+FBgn0030477\t0\n+FBgn0030478\t427\n+FBgn0030479\t50\n+FBgn0030480\t72\n+FBgn0030481\t123\n+FBgn0030482\t1315\n+FBgn0030483\t0\n+FBgn0030484\t275\n+FBgn0030485\t70\n+FBgn0030486\t534\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t186\n+FBgn0030500\t158\n+FBgn0030501\t299\n+FBgn0030502\t735\n+FBgn0030503\t33\n+FBgn0030504\t894\n+FBgn0030505\t397\n+FBgn0030506\t108\n+FBgn0030507\t141\n+FBgn0030508\t0\n+FBgn0030509\t0\n+FBgn0030510\t93\n+FBgn0030511\t57\n+FBgn0030512\t369\n+FBgn0030514\t452\n+FBgn0030518\t101\n+FBgn0030519\t355\n+FBgn0030520\t1140\n+FBgn0030521\t1299\n+FBgn0030522\t83\n+FBgn0030524\t5\n+FBgn0030525\t1\n+FBgn0030528\t40\n+FBgn0030529\t2773\n+FBgn0030530\t450\n+FBgn0030532\t444\n+FBgn0030536\t1\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t100\n+FBgn0030551\t1\n+FBgn0030552\t131\n+FBgn0030554\t95\n+FBgn0030555\t59\n+FBgn0030556\t395\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t16\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t0\n+FBgn0030570\t0\n+FBgn0030571\t59\n+FBgn0030572\t87\n+FBgn0030573\t10\n+FBgn0030574\t1\n+FBgn0030575\t14\n+FBgn0030576\t91\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t133\n+FBgn0030582\t329\n+FBgn0030583\t12\n+FBgn0030584\t92\n+FBgn0030586\t0\n+FBgn0030587\t0\n+FBgn0030588\t54\n+FBgn0030589\t0\n+FBgn0030590\t4\n+FBgn0030591\t1\n+FBgn0030592\t1\n+FBgn0030593\t4\n+FBgn0030594\t2\n+FBgn0030595\t1\n+FBgn0030596\t1\n+FBgn0030597\t1\n+FBgn0030598\t5\n+FBgn0030599\t6\n+FBgn0030600\t619\n+FBgn0030603\t230\n+FBgn0030605\t170\n+FBgn0030606\t180\n+FBgn0030607\t0\n+FBgn0030608\t0\n+FBgn0030610\t74\n+FBgn0030611\t45\n+FBgn0030612\t161\n+FBgn0030613\t0\n+FBgn0030614\t0\n+FBgn0030615\t19\n+FBgn0030616\t6362\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t85\n+FBgn0030626\t118\n+FBgn0030627\t268\n+FBgn0030628\t175\n+FBgn0030629\t41\n+FBgn0030630\t145\n+FBgn0030631\t349\n+FBgn0030634\t2\n+FBgn0030636\t1\n+FBgn0030638\t277\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t4\n+FBgn0030643\t3\n+FBgn0030645\t29\n+FBgn0030646\t75\n+FBgn0030647\t5\n+FBgn0030648\t88\n+FBgn0030653\t28\n+FBgn0030654\t39\n+FBgn0030655\t91\n+FBgn0030657\t30\n+FBgn0030658\t336\n+FBgn0030659\t123\n+FBgn0030660\t61\n+FBgn0030661\t5\n+FBgn0030662\t108\n+FBgn0030663\t0\n+FBgn0030664\t2\n+FBgn0030665\t2\n+FBgn0030666\t5\n+FBgn0030667\t27\n+FBgn0030668\t79\n+FBgn0030669\t75\n+FBgn0030670\t247\n+FBgn0030671\t78\n+FBgn0030672\t2028\n+FBgn0030673\t31\n+FBgn0030674\t2711\n+FBgn0030675\t21\n+FBgn0030676\t0\n+FBgn0030678\t76\n+FBgn0030679\t110\n+FBgn0030680\t153\n+FBgn0030683\t102\n+FBgn0030684\t3\n+FBgn0030685\t753\n+FBgn0030686\t138\n+FBgn0030687\t255\n+FBgn0030688\t1\n+FBgn0030691\t9\n+FBgn0030692\t241\n+FBgn0030693\t126\n+FBgn0030694\t55\n+no_feature\t165407\n+ambiguous\t48373\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t6896814\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/GSM461182_untreat_single.counts.noheader --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSM461182_untreat_single.counts.noheader Wed Sep 05 15:54:16 2018 -0400 |
| b |
| b'@@ -0,0 +1,4004 @@\n+FBgn0000003\t0\n+FBgn0000008\t29\n+FBgn0000014\t0\n+FBgn0000015\t0\n+FBgn0000017\t1213\n+FBgn0000018\t114\n+FBgn0000022\t0\n+FBgn0000024\t3\n+FBgn0000028\t0\n+FBgn0000032\t399\n+FBgn0000036\t0\n+FBgn0000037\t4\n+FBgn0000038\t0\n+FBgn0000039\t0\n+FBgn0000042\t29229\n+FBgn0000043\t8594\n+FBgn0000044\t6\n+FBgn0000045\t0\n+FBgn0000046\t0\n+FBgn0000047\t1\n+FBgn0000052\t723\n+FBgn0000053\t510\n+FBgn0000054\t220\n+FBgn0000055\t0\n+FBgn0000056\t0\n+FBgn0000057\t215\n+FBgn0000061\t0\n+FBgn0000063\t118\n+FBgn0000064\t1967\n+FBgn0000071\t19\n+FBgn0000075\t0\n+FBgn0000077\t64\n+FBgn0000078\t5\n+FBgn0000079\t48\n+FBgn0000083\t1428\n+FBgn0000084\t499\n+FBgn0000092\t2\n+FBgn0000094\t1\n+FBgn0000097\t752\n+FBgn0000099\t1\n+FBgn0000100\t6726\n+FBgn0000108\t2\n+FBgn0000109\t57\n+FBgn0000114\t0\n+FBgn0000115\t169\n+FBgn0000116\t91\n+FBgn0000117\t2741\n+FBgn0000119\t202\n+FBgn0000120\t0\n+FBgn0000121\t3\n+FBgn0000137\t0\n+FBgn0000139\t234\n+FBgn0000140\t314\n+FBgn0000142\t567\n+FBgn0000146\t411\n+FBgn0000147\t110\n+FBgn0000150\t1983\n+FBgn0000152\t167\n+FBgn0000153\t8\n+FBgn0000157\t1\n+FBgn0000158\t2\n+FBgn0000163\t220\n+FBgn0000166\t0\n+FBgn0000171\t1432\n+FBgn0000173\t452\n+FBgn0000179\t0\n+FBgn0000180\t0\n+FBgn0000181\t3326\n+FBgn0000182\t1\n+FBgn0000183\t853\n+FBgn0000206\t0\n+FBgn0000210\t371\n+FBgn0000212\t918\n+FBgn0000216\t0\n+FBgn0000221\t62\n+FBgn0000227\t0\n+FBgn0000228\t218\n+FBgn0000229\t332\n+FBgn0000233\t0\n+FBgn0000239\t782\n+FBgn0000241\t1\n+FBgn0000242\t34\n+FBgn0000244\t179\n+FBgn0000246\t50\n+FBgn0000247\t825\n+FBgn0000250\t609\n+FBgn0000251\t0\n+FBgn0000253\t3365\n+FBgn0000256\t512\n+FBgn0000257\t186\n+FBgn0000258\t383\n+FBgn0000259\t563\n+FBgn0000261\t499\n+FBgn0000273\t487\n+FBgn0000274\t0\n+FBgn0000276\t46\n+FBgn0000277\t12\n+FBgn0000278\t21\n+FBgn0000279\t27\n+FBgn0000280\t0\n+FBgn0000281\t0\n+FBgn0000283\t1062\n+FBgn0000286\t144\n+FBgn0000287\t0\n+FBgn0000289\t1101\n+FBgn0000299\t9089\n+FBgn0000303\t2\n+FBgn0000307\t467\n+FBgn0000308\t4803\n+FBgn0000313\t19\n+FBgn0000316\t0\n+FBgn0000317\t514\n+FBgn0000318\t251\n+FBgn0000319\t4787\n+FBgn0000320\t0\n+FBgn0000326\t75\n+FBgn0000330\t70\n+FBgn0000337\t4\n+FBgn0000338\t335\n+FBgn0000339\t242\n+FBgn0000346\t31\n+FBgn0000351\t6\n+FBgn0000352\t237\n+FBgn0000355\t1\n+FBgn0000356\t0\n+FBgn0000357\t1\n+FBgn0000358\t0\n+FBgn0000359\t0\n+FBgn0000360\t0\n+FBgn0000363\t1\n+FBgn0000370\t3832\n+FBgn0000376\t289\n+FBgn0000377\t208\n+FBgn0000382\t173\n+FBgn0000384\t247\n+FBgn0000392\t222\n+FBgn0000394\t209\n+FBgn0000395\t106\n+FBgn0000404\t812\n+FBgn0000405\t649\n+FBgn0000406\t61\n+FBgn0000409\t1298\n+FBgn0000411\t0\n+FBgn0000412\t590\n+FBgn0000413\t563\n+FBgn0000414\t916\n+FBgn0000416\t13542\n+FBgn0000422\t1\n+FBgn0000426\t167\n+FBgn0000427\t0\n+FBgn0000439\t0\n+FBgn0000442\t0\n+FBgn0000447\t132\n+FBgn0000448\t1\n+FBgn0000449\t0\n+FBgn0000451\t0\n+FBgn0000454\t756\n+FBgn0000455\t142\n+FBgn0000459\t0\n+FBgn0000463\t1\n+FBgn0000464\t438\n+FBgn0000472\t509\n+FBgn0000473\t2\n+FBgn0000477\t0\n+FBgn0000479\t244\n+FBgn0000482\t279\n+FBgn0000489\t31\n+FBgn0000490\t26\n+FBgn0000492\t0\n+FBgn0000497\t2\n+FBgn0000499\t251\n+FBgn0000500\t1\n+FBgn0000504\t0\n+FBgn0000520\t122\n+FBgn0000524\t238\n+FBgn0000527\t46\n+FBgn0000529\t0\n+FBgn0000533\t0\n+FBgn0000535\t26\n+FBgn0000536\t298\n+FBgn0000541\t1634\n+FBgn0000542\t21\n+FBgn0000543\t162\n+FBgn0000546\t256\n+FBgn0000547\t56\n+FBgn0000551\t0\n+FBgn0000552\t0\n+FBgn0000556\t60017\n+FBgn0000557\t8\n+FBgn0000559\t31536\n+FBgn0000560\t0\n+FBgn0000562\t426\n+FBgn0000564\t0\n+FBgn0000565\t89\n+FBgn0000566\t244\n+FBgn0000567\t84\n+FBgn0000568\t600\n+FBgn0000575\t330\n+FBgn0000576\t0\n+FBgn0000577\t0\n+FBgn0000578\t1453\n+FBgn0000579\t1744\n+FBgn0000581\t954\n+FBgn0000588\t111\n+FBgn0000591\t0\n+FBgn0000592\t1\n+FBgn0000594\t5\n+FBgn0000606\t0\n+FBgn0000611\t483\n+FBgn0000615\t130\n+FBgn0000617\t202\n+FBgn0000618\t34\n+FBgn0000625\t0\n+FBgn0000629\t308\n+FBgn0000630\t1\n+FBgn0000633\t3\n+FBgn0000634\t109\n+FBgn0000635\t16\n+FBgn0000636\t12\n+FBgn0000639\t1\n+FBgn0000640\t0\n+FBgn0000644\t1\n+FBgn0000658\t0\n+FBgn0000659\t0\n+FBgn0000662\t362\n+FBgn0000667\t424\n+FBgn0000709\t608\n+FBgn0000711\t347\n+FBgn0000715\t0\n+FBgn0000719\t605\n+FBgn0000721\t246\n+FBgn0000723\t501\n+FBgn0000808\t24\n+FBgn0000810\t80\n+FBgn0000826\t27\n+FBgn0000927\t7\n+FBgn0000928\t178\n+FBgn0000964\t0\n+FBgn0000986\t777\n+FBgn0000996\t335\n+FBgn0001075\t6\n+FBgn0001077\t0\n+FBgn0001078\t227\n+FBgn0001079\t118\n+FBgn0001083\t53\n+FBgn0001084\t17\n'..b'0030345\t64\n+FBgn0030346\t41\n+FBgn0030347\t69\n+FBgn0030348\t1\n+FBgn0030349\t691\n+FBgn0030350\t214\n+FBgn0030351\t43\n+FBgn0030352\t83\n+FBgn0030354\t550\n+FBgn0030356\t0\n+FBgn0030357\t31\n+FBgn0030358\t54\n+FBgn0030359\t2\n+FBgn0030360\t6\n+FBgn0030361\t27\n+FBgn0030362\t1789\n+FBgn0030364\t136\n+FBgn0030365\t189\n+FBgn0030366\t1230\n+FBgn0030367\t21\n+FBgn0030369\t20\n+FBgn0030370\t0\n+FBgn0030373\t70\n+FBgn0030374\t0\n+FBgn0030375\t0\n+FBgn0030376\t0\n+FBgn0030377\t0\n+FBgn0030384\t0\n+FBgn0030385\t0\n+FBgn0030386\t0\n+FBgn0030389\t0\n+FBgn0030390\t0\n+FBgn0030391\t101\n+FBgn0030394\t3\n+FBgn0030395\t0\n+FBgn0030396\t10\n+FBgn0030398\t0\n+FBgn0030399\t1\n+FBgn0030400\t301\n+FBgn0030403\t294\n+FBgn0030406\t41\n+FBgn0030407\t16\n+FBgn0030408\t0\n+FBgn0030409\t0\n+FBgn0030410\t27\n+FBgn0030411\t26\n+FBgn0030412\t412\n+FBgn0030417\t9\n+FBgn0030418\t97\n+FBgn0030420\t343\n+FBgn0030421\t93\n+FBgn0030425\t2\n+FBgn0030429\t1\n+FBgn0030431\t174\n+FBgn0030432\t9\n+FBgn0030433\t136\n+FBgn0030434\t224\n+FBgn0030435\t240\n+FBgn0030437\t0\n+FBgn0030438\t1\n+FBgn0030439\t0\n+FBgn0030440\t0\n+FBgn0030441\t0\n+FBgn0030443\t0\n+FBgn0030447\t157\n+FBgn0030448\t111\n+FBgn0030449\t0\n+FBgn0030451\t298\n+FBgn0030452\t341\n+FBgn0030455\t1\n+FBgn0030456\t227\n+FBgn0030457\t169\n+FBgn0030459\t1\n+FBgn0030460\t127\n+FBgn0030462\t0\n+FBgn0030465\t165\n+FBgn0030466\t705\n+FBgn0030467\t237\n+FBgn0030468\t452\n+FBgn0030469\t357\n+FBgn0030474\t239\n+FBgn0030477\t0\n+FBgn0030478\t427\n+FBgn0030479\t50\n+FBgn0030480\t72\n+FBgn0030481\t123\n+FBgn0030482\t1315\n+FBgn0030483\t0\n+FBgn0030484\t275\n+FBgn0030485\t70\n+FBgn0030486\t534\n+FBgn0030491\t0\n+FBgn0030492\t0\n+FBgn0030493\t0\n+FBgn0030494\t0\n+FBgn0030495\t0\n+FBgn0030499\t186\n+FBgn0030500\t158\n+FBgn0030501\t299\n+FBgn0030502\t735\n+FBgn0030503\t33\n+FBgn0030504\t894\n+FBgn0030505\t397\n+FBgn0030506\t108\n+FBgn0030507\t141\n+FBgn0030508\t0\n+FBgn0030509\t0\n+FBgn0030510\t93\n+FBgn0030511\t57\n+FBgn0030512\t369\n+FBgn0030514\t452\n+FBgn0030518\t101\n+FBgn0030519\t355\n+FBgn0030520\t1140\n+FBgn0030521\t1299\n+FBgn0030522\t83\n+FBgn0030524\t5\n+FBgn0030525\t1\n+FBgn0030528\t40\n+FBgn0030529\t2773\n+FBgn0030530\t450\n+FBgn0030532\t444\n+FBgn0030536\t1\n+FBgn0030537\t0\n+FBgn0030538\t0\n+FBgn0030539\t0\n+FBgn0030540\t0\n+FBgn0030541\t0\n+FBgn0030542\t0\n+FBgn0030543\t0\n+FBgn0030544\t0\n+FBgn0030545\t100\n+FBgn0030551\t1\n+FBgn0030552\t131\n+FBgn0030554\t95\n+FBgn0030555\t59\n+FBgn0030556\t395\n+FBgn0030558\t0\n+FBgn0030559\t1\n+FBgn0030562\t16\n+FBgn0030563\t0\n+FBgn0030566\t0\n+FBgn0030569\t0\n+FBgn0030570\t0\n+FBgn0030571\t59\n+FBgn0030572\t87\n+FBgn0030573\t10\n+FBgn0030574\t1\n+FBgn0030575\t14\n+FBgn0030576\t91\n+FBgn0030577\t0\n+FBgn0030578\t0\n+FBgn0030581\t133\n+FBgn0030582\t329\n+FBgn0030583\t12\n+FBgn0030584\t92\n+FBgn0030586\t0\n+FBgn0030587\t0\n+FBgn0030588\t54\n+FBgn0030589\t0\n+FBgn0030590\t4\n+FBgn0030591\t1\n+FBgn0030592\t1\n+FBgn0030593\t4\n+FBgn0030594\t2\n+FBgn0030595\t1\n+FBgn0030596\t1\n+FBgn0030597\t1\n+FBgn0030598\t5\n+FBgn0030599\t6\n+FBgn0030600\t619\n+FBgn0030603\t230\n+FBgn0030605\t170\n+FBgn0030606\t180\n+FBgn0030607\t0\n+FBgn0030608\t0\n+FBgn0030610\t74\n+FBgn0030611\t45\n+FBgn0030612\t161\n+FBgn0030613\t0\n+FBgn0030614\t0\n+FBgn0030615\t19\n+FBgn0030616\t6362\n+FBgn0030617\t0\n+FBgn0030618\t0\n+FBgn0030619\t0\n+FBgn0030620\t0\n+FBgn0030621\t0\n+FBgn0030622\t0\n+FBgn0030623\t0\n+FBgn0030624\t0\n+FBgn0030625\t85\n+FBgn0030626\t118\n+FBgn0030627\t268\n+FBgn0030628\t175\n+FBgn0030629\t41\n+FBgn0030630\t145\n+FBgn0030631\t349\n+FBgn0030634\t2\n+FBgn0030636\t1\n+FBgn0030638\t277\n+FBgn0030640\t0\n+FBgn0030641\t4\n+FBgn0030642\t4\n+FBgn0030643\t3\n+FBgn0030645\t29\n+FBgn0030646\t75\n+FBgn0030647\t5\n+FBgn0030648\t88\n+FBgn0030653\t28\n+FBgn0030654\t39\n+FBgn0030655\t91\n+FBgn0030657\t30\n+FBgn0030658\t336\n+FBgn0030659\t123\n+FBgn0030660\t61\n+FBgn0030661\t5\n+FBgn0030662\t108\n+FBgn0030663\t0\n+FBgn0030664\t2\n+FBgn0030665\t2\n+FBgn0030666\t5\n+FBgn0030667\t27\n+FBgn0030668\t79\n+FBgn0030669\t75\n+FBgn0030670\t247\n+FBgn0030671\t78\n+FBgn0030672\t2028\n+FBgn0030673\t31\n+FBgn0030674\t2711\n+FBgn0030675\t21\n+FBgn0030676\t0\n+FBgn0030678\t76\n+FBgn0030679\t110\n+FBgn0030680\t153\n+FBgn0030683\t102\n+FBgn0030684\t3\n+FBgn0030685\t753\n+FBgn0030686\t138\n+FBgn0030687\t255\n+FBgn0030688\t1\n+FBgn0030691\t9\n+FBgn0030692\t241\n+FBgn0030693\t126\n+FBgn0030694\t55\n+no_feature\t165407\n+ambiguous\t48373\n+too_low_aQual\t0\n+not_aligned\t0\n+alignment_not_unique\t6896814\n' |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/ruvseq_diag.pdf |
| b |
| Binary file test-data/ruvseq_diag.pdf has changed |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/ruvseq_diag_sailfish.pdf |
| b |
| Binary file test-data/ruvseq_diag_sailfish.pdf has changed |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf1.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1759.2 0 0 +NM_014212 2035 1837.2 0 0 +NM_173860 847 649.348 0 0 +NM_017410 2395 2555.05 0.0173509 1 +NM_014620 2305 2261.56 0.114436 5.83783 +NM_153633 1665 1561.63 3.55316 125.162 +NM_018953 1610 1412.2 0 0 +NR_003084 1644 1446.2 0 0 +NM_004503 1680 1482.2 0 0 +NM_153693 2077 1879.2 0 0 +NM_022658 2286 2088.2 0 0 +NM_006897 1539 1341.2 0 0 +NM_001168316 2281 2071 0.085625 4 +NM_174914 2383 2153.11 0 0 +NR_031764 1851 1659.15 0 0 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf2.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1764.64 0 0 +NM_014212 2035 2171.69 0.0161522 1 +NM_173860 847 655.215 0 0 +NM_017410 2395 2567.91 0.01366 1 +NM_014620 2305 2235.74 0 0 +NM_153633 1665 1576.16 1.7359 78 +NM_018953 1610 1726.1 1.31761e-06 6.48367e-05 +NR_003084 1644 1704.36 0.0411608 1.99994 +NM_004503 1680 1679.47 0.10443 5 +NM_153693 2077 2069.83 0 0 +NM_022658 2286 2093.64 0 0 +NM_006897 1539 1557.46 0.0675669 3 +NM_001168316 2281 2088.64 0 0 +NM_174914 2383 2190.64 0 0 +NR_031764 1851 1658.64 0 0 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf3.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf3.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1760.44 0 0 +NM_014212 2035 2127.85 0.0280759 2 +NM_173860 847 650.573 0 0 +NM_017410 2395 2198.44 0 0 +NM_014620 2305 2223.92 0.0661957 4.92838 +NM_153633 1665 1536.71 2.08127 107.072 +NM_018953 1610 1685.74 1.23894e-08 6.99193e-07 +NR_003084 1644 1658.72 0.0720329 4 +NM_004503 1680 1638.79 0.0546819 3 +NM_153693 2077 2026.99 0 0 +NM_022658 2286 2089.44 0 0 +NM_006897 1539 1342.44 0 0 +NM_001168316 2281 2047.58 0 0 +NM_174914 2383 2143.36 0 0 +NR_031764 1851 1659.97 0.0359895 2 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf4.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf4.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1738.38 0 0 +NM_014212 2035 1816.38 0 0 +NM_173860 847 628.444 0 0 +NM_017410 2395 2176.38 0 0 +NM_014620 2305 2086.38 0 0 +NM_153633 1665 1510.43 2.31417 89.0334 +NM_018953 1610 1391.38 0 0 +NR_003084 1644 1425.38 0 0 +NM_004503 1680 1612.63 0.0730348 3 +NM_153693 2077 1998.27 0 0 +NM_022658 2286 2067.38 0 0 +NM_006897 1539 1320.38 0 0 +NM_001168316 2281 2033.58 0 0 +NM_174914 2383 2129.01 0 0 +NR_031764 1851 1639.11 0.071855 3 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf5.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf5.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1781.23 0 0 +NM_014212 2035 1859.23 0 0 +NM_173860 847 671.305 0 0 +NM_017410 2395 2219.23 0 0 +NM_014620 2305 2195.37 0 0 +NM_153633 1665 1545.8 3.39643 119.002 +NM_018953 1610 1715.91 0.128558 5 +NR_003084 1644 1468.23 0 0 +NM_004503 1680 1654.16 0.0800141 3 +NM_153693 2077 2034.63 0 0 +NM_022658 2286 2148.18 0.0205378 1 +NM_006897 1539 1363.23 0 0 +NM_001168316 2281 2061.52 0 0 +NM_174914 2383 2156.64 0 0 +NR_031764 1851 1671.47 0.0527904 2 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/sailfish/sailfish_quant.sf6.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sailfish/sailfish_quant.sf6.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_017409 1957 1747.9 0 0 +NM_014212 2035 1825.9 0 0 +NM_173860 847 638.159 0 0 +NM_017410 2395 2562.99 0.0171188 1 +NM_014620 2305 2272.12 0.152979 7.92213 +NM_153633 1665 1572.52 3.54659 127.112 +NM_018953 1610 1731.28 0.0760279 3 +NR_003084 1644 1434.9 0 0 +NM_004503 1680 1673.79 0.104853 4 +NM_153693 2077 2057.73 0 0 +NM_022658 2286 2185.1 0.0200793 1 +NM_006897 1539 1329.9 0 0 +NM_001168316 2281 2047.55 0 0 +NM_174914 2383 2143.62 0 0 +NR_031764 1851 1663.05 0.0263825 1 |
| b |
| diff -r 000000000000 -r 61dffb20b6f9 test-data/tx2gene.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tx2gene.tab Wed Sep 05 15:54:16 2018 -0400 |
| b |
| @@ -0,0 +1,16 @@ +TXNAME GENEID +NM_001168316 DDX11L1 +NM_174914 DDX11L1 +NR_031764 DDX11L1 +NM_004503 WASH7P +NM_006897 WASH7P +NM_014212 WASH7P +NM_014620 WASH7P +NM_017409 WASH7P +NM_017410 WASH7P +NM_018953 MIR6859-2 +NM_022658 MIR6859-1 +NM_153633 WASH7P +NM_153693 WASH7P +NM_173860 WASH7P +NR_003084 WASH7P |