Commit a2d728c3 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed bamstats for single end

parent 733260e8
......@@ -166,7 +166,7 @@ object BamStats extends ToolCommand {
if (!samRecord.getReadUnmappedFlag) { // Mapped read
totalStats.mappingQualityHistogram.add(samRecord.getMappingQuality)
}
if (samRecord.getProperPairFlag && samRecord.getFirstOfPairFlag && !samRecord.getSecondOfPairFlag)
if (samRecord.getReadPairedFlag && samRecord.getProperPairFlag && samRecord.getFirstOfPairFlag && !samRecord.getSecondOfPairFlag)
totalStats.insertSizeHistogram.add(samRecord.getInferredInsertSize.abs)
val leftClipping = samRecord.getAlignmentStart - samRecord.getUnclippedStart
......
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