Commit af39664b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switched to ToolCommand args parsing

parent b443f31f
......@@ -110,7 +110,8 @@ object BiopetFlagstat extends ToolCommand {
flagstatCollector.addFunction("Mate in same strand", record => record.getReadPairedFlag && record.getReadNegativeStrandFlag && record.getMateNegativeStrandFlag &&
record.getReferenceIndex == record.getMateReferenceIndex)
flagstatCollector.addFunction("Mate on other chr", record => record.getReadPairedFlag && record.getReferenceIndex != record.getMateReferenceIndex)
logger.info("Start reading file: " + commandArgs.inputFile)
for (record <- iterSam) {
if (flagstatCollector.readsCount % 1e6 == 0 && flagstatCollector.readsCount > 0)
logger.info("Reads prosessed: " + flagstatCollector.readsCount)
......
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