Commit 181f3be8 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding histrograms as tsv files

parent 3cc48dad
......@@ -104,7 +104,21 @@ object BamStats extends ToolCommand {
val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.map(_._2))
stats.flagstat.writeAsTsv(new File(outputDir, "flagstats.tsv"))
stats.insertSizeHistogram
stats.insertSizeHistogram.writeHistogramToTsv(new File(outputDir, "insertsize.histogram.tsv"))
stats.insertSizeHistogram.writeAggregateToTsv(new File(outputDir, "insertsize.stats.tsv"))
stats.mappingQualityHistogram.writeHistogramToTsv(new File(outputDir, "mappingQuality.histogram.tsv"))
stats.mappingQualityHistogram.writeAggregateToTsv(new File(outputDir, "mappingQualityHistogram.stats.tsv"))
stats.clippingHistogram.writeHistogramToTsv(new File(outputDir, "clipping.histogram.tsv"))
stats.clippingHistogram.writeAggregateToTsv(new File(outputDir, "clipping.stats.tsv"))
stats.leftClippingHistogram.writeHistogramToTsv(new File(outputDir, "left_clipping.histogram.tsv"))
stats.leftClippingHistogram.writeAggregateToTsv(new File(outputDir, "left_clipping.stats.tsv"))
stats.rightClippingHistogram.writeHistogramToTsv(new File(outputDir, "right_clipping.histogram.tsv"))
stats.rightClippingHistogram.writeAggregateToTsv(new File(outputDir, "right_clipping.stats.tsv"))
stats._3_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "3prime_clipping.histogram.tsv"))
stats._3_ClippingHistogram.writeAggregateToTsv(new File(outputDir, "3prime_clipping.stats.tsv"))
stats._5_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "5prime_clipping.histogram.tsv"))
stats._5_ClippingHistogram.writeAggregateToTsv(new File(outputDir, "5prime_clipping.stats.tsv"))
val statsWriter = new PrintWriter(new File(outputDir, "bamstats.json"))
val totalStats = stats.toSummaryMap
......
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