From 3960733c88bf1965a3b1a20eba630588e84ea318 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 9 Apr 2013 08:19:52 -0400 Subject: [PATCH] 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 --- .../broadinstitute/sting/gatk/walkers/readutils/PrintReads.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java index add567b36..a28523369 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java @@ -190,7 +190,7 @@ public class PrintReads extends ReadWalker 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); } }