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); } }