diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 3142e9438..a855e3658 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -402,9 +402,10 @@ public class IndelRealigner extends ReadWalker { } private void emitReadLists() { - // pre-merge lists with priority queue for constrained SAMFileWriter + // pre-merge lists to sort them in preparation for constrained SAMFileWriter readsNotToClean.addAll(readsToClean.getReads()); - for ( SAMRecord read : ReadUtils.coordinateSortReads(readsNotToClean) ) + ReadUtils.coordinateSortReads(readsNotToClean); + for ( SAMRecord read : readsNotToClean ) emit(read); readsToClean.clear(); readsNotToClean.clear(); diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index faf990b3e..3757120f8 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -216,17 +216,9 @@ public class ReadUtils { * @param reads * @return */ - public final static List coordinateSortReads(Collection reads) { - final int n = reads.size(); - - if ( n > 0 ) { - final SAMRecordComparator comparer = new SAMRecordCoordinateComparator(); - final Queue sorted = new PriorityQueue(reads.size(), comparer); - sorted.addAll(reads); - return new ArrayList(sorted); - } else { - return Collections.emptyList(); - } + public final static void coordinateSortReads(List reads) { + final SAMRecordComparator comparer = new SAMRecordCoordinateComparator(); + Collections.sort(reads, comparer); } public final static int getFirstInsertionOffset(SAMRecord read) { diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 7a3aa085f..2525e487a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -117,13 +117,4 @@ public class IndelRealignerIntegrationTest extends WalkerTest { executeTest(String.format("realigner [%s]", entry.getKey()), spec); } } - - @Test(expectedExceptions = { RuntimeException.class }, dependsOnMethods = { "testMaxReadsInMemory" }) - public void testFailure() { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + "--maxReadsInMemory 1000", - 1, - Arrays.asList("")); - executeTest("realigner failure", spec); - } }