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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
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ebanks 2010-08-27 16:42:49 +00:00
parent 7908237b90
commit 431392330e
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -80,6 +80,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@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<Integer, Integer> {
writer.writeHeader(header);
writer.setPresorted(false);
writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
}
private void emit(final SAMRecord read) {