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gatk-3.8
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Fix PrintReads out of space issue 

Problem:
--------
Print Reads was running out of disk space when using the -BQSR option even for small bam files

Solution:
---------
Configure setupWriter to expect pre sorted reads
This commit is contained in:
Mauricio Carneiro 2013-04-09 08:19:52 -04:00
parent ae0612b6e8
commit 3960733c88
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
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@ -190,7 +190,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
final boolean preSorted = true;
if (getToolkit() != null && getToolkit().getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) {
Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, this, PROGRAM_RECORD_NAME);
Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), preSorted, this, PROGRAM_RECORD_NAME);
}
}