From e991307eb56670172969b17c49f861a06c5dbef0 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 15 Aug 2013 11:54:49 -0400 Subject: [PATCH] Including SplitByRG in the FullProcessingPipeline Why wasn't it there before, you ask ---------------------------------- Before I was running it separately (by hand), but now it's integrated in the FullProcessingPipeline. Integration was a pain because of Queue's limitation of only allowing 1 @Output file. This forced me to write the ugliest piece of code of my life, but it's working and it's processing the YRI from scratch using that right now. So I'm happy... somewhat. Other changes to the pipeline ----------------------------- * Add --filter_bases_not_stored to the IndelRealigner step -- sometimes BAM files have reads with no bases stored in the unmapped section (no idea why) but this disrupts the pipeline. * Change adaptor marking parameter to "dual indexed" instead of "pair-ended" -- for PCR Free data. --- .../src/org/broadinstitute/sting/queue/util/QScriptUtils.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala index 0b6fc44d9..7b0e5d1be 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala @@ -73,7 +73,7 @@ object QScriptUtils { /** * Check if there are multiple samples in a BAM file */ - def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = { + def hasMultipleSamples(readGroups: Seq[SAMReadGroupRecord]): Boolean = { var sample: String = "" for (r <- readGroups) { if (sample.isEmpty)