From 73fc7f6ab1214f68cab4c7231421a6c4fb94090b Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 8 Jul 2013 10:33:36 -0400 Subject: [PATCH] Reduce Reads output should never be expected to be sorted (hence the need to sort on disk) but for some reason it was with -nwayout mode. --- .../gatk/walkers/compression/reducereads/ReduceReads.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index e636f8f17..31fe7e380 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -320,18 +320,17 @@ public class ReduceReads extends ReadWalker, Redu if (toolkit.getIntervals() != null) intervalList.addAll(toolkit.getIntervals()); - final boolean preSorted = true; final boolean indexOnTheFly = true; final SAMFileHeader.SortOrder sortOrder = SAMFileHeader.SortOrder.coordinate; if (nwayout) { SAMProgramRecord programRecord = NO_PG_TAG ? null : Utils.createProgramRecord(toolkit, this, PROGRAM_RECORD_NAME); - writerToUse = new BySampleSAMFileWriter(toolkit, PROGRAM_FILENAME_EXTENSION, sortOrder, preSorted, indexOnTheFly, NO_PG_TAG, programRecord, true); + writerToUse = new BySampleSAMFileWriter(toolkit, PROGRAM_FILENAME_EXTENSION, sortOrder, false, indexOnTheFly, NO_PG_TAG, programRecord, true); } else { writerToUse = out; out.setPresorted(false); if (!NO_PG_TAG) { - Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), !preSorted, this, PROGRAM_RECORD_NAME); + Utils.setupWriter(out, toolkit, toolkit.getSAMFileHeader(), false, this, PROGRAM_RECORD_NAME); } } }