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Merge pull request #323 from broadinstitute/eb_fix_sorting_in_reduce_reads 

Reduce Reads output should never be expected to be sorted (hence the nee...
This commit is contained in:
Eric Banks 2013-07-08 10:15:28 -07:00
parent c5a2a8f39f 73fc7f6ab1
commit 4fe26ea2cf
1 changed files with 2 additions and 3 deletions
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5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -320,18 +320,17 @@ public class ReduceReads extends ReadWalker<ObjectArrayList<GATKSAMRecord>, 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);
}
}
}