From 431392330e45139536ec288d62653f951e156698 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 27 Aug 2010 16:42:49 +0000 Subject: [PATCH] Re-enable the max records in ram argument, which I accidentally removed git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4145 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 7479ac988..08db26acb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -80,6 +80,10 @@ public class IndelRealigner extends ReadWalker { @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs for constructing the alternate references.") protected boolean USE_KNOWN_INDELS_ONLY = false; + @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+ + "If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false) + protected int MAX_RECORDS_IN_RAM = 500000; + // ADVANCED OPTIONS FOLLOW @Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false) @@ -236,6 +240,7 @@ public class IndelRealigner extends ReadWalker { writer.writeHeader(header); writer.setPresorted(false); + writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM); } private void emit(final SAMRecord read) {