diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index f3f54060f..b94b74748 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -919,19 +919,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In private void finalizeActiveRegion( final ActiveRegion activeRegion ) { if( DEBUG ) { logger.info("Assembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); } - final List finalizedReadList = new ArrayList<>(); - final FragmentCollection fragmentCollection = FragmentUtils.create( activeRegion.getReads() ); - activeRegion.clearReads(); - - // Join overlapping paired reads to create a single longer read - finalizedReadList.addAll( fragmentCollection.getSingletonReads() ); - for( final List overlappingPair : fragmentCollection.getOverlappingPairs() ) { - finalizedReadList.addAll( FragmentUtils.mergeOverlappingPairedFragments(overlappingPair) ); - } // Loop through the reads hard clipping the adaptor and low quality tails - final List readsToUse = new ArrayList<>(finalizedReadList.size()); - for( final GATKSAMRecord myRead : finalizedReadList ) { + final List readsToUse = new ArrayList<>(activeRegion.getReads().size()); + for( final GATKSAMRecord myRead : activeRegion.getReads() ) { final GATKSAMRecord postAdapterRead = ( myRead.getReadUnmappedFlag() ? myRead : ReadClipper.hardClipAdaptorSequence( myRead ) ); if( postAdapterRead != null && !postAdapterRead.isEmpty() && postAdapterRead.getCigar().getReadLength() > 0 ) { GATKSAMRecord clippedRead; @@ -962,6 +953,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In } } + activeRegion.clearReads(); activeRegion.addAll(DownsamplingUtils.levelCoverageByPosition(ReadUtils.sortReadsByCoordinate(readsToUse), maxReadsInRegionPerSample, minReadsPerAlignmentStart)); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 8394baa72..c1b8f8a70 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "e7b28ea087e8624f1e596c9d65381fea"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "03944bbedb012e2ac2026a84baa0560c"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -94,6 +94,6 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "2a72a9b5c6778b99bf155a7c5e90d11e"); + "7e9f99d4cba8087dac66ea871b910d7e"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index f9bab8ea7..da92f39fc 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -78,12 +78,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "f25b9cfc85995cbe8eb6ba5a126d713d"); + HCTest(CEUTRIO_BAM, "", "09d84bc1aef2dd9c185934752172b794"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "19d685727ec60b3568f313bc44f79b49"); + HCTest(NA12878_BAM, "", "5c074930b27d1f5c942fe755c2a8be27"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -94,7 +94,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "6da65f1d396b9c709eb6246cf3f615c1"); + "005a6d1933913a5d96fc56d01303fa95"); } @Test @@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "e3db7d56154e36eeb887259bea4b241d"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "9b6f667ad87e19c38d16fefe63c37484"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -186,7 +186,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("40416433baf96f4e84a058459717060b")); + Arrays.asList("a47ef09a8701128cfb301a83b7bb0728")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -194,7 +194,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testReducedBamWithReadsNotFullySpanningDeletion() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, - Arrays.asList("cf1461ce829023ea9920fbfeb534eb97")); + Arrays.asList("0cb99f6bb3e630add4b3486c496fa508")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } @@ -208,7 +208,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("45ca324be3917655e645d6c290c9280f")); + Arrays.asList("92f947cc89e4f50cf2ef3121d2fe308d")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -217,7 +217,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132 + " -L " + hg19Intervals + " -isr INTERSECTION", 1, - Arrays.asList("b7037770b7953cdf858764b99fa243ed")); + Arrays.asList("91877c8ea3eb0e0316d9ad11fdcc1a87")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index 857d0fc9e..d009550f4 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -61,7 +61,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest { List tests = new ArrayList(); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, "bd2a57e6b0cffb4cbdba609a6c1683dc"}); + tests.add(new Object[]{nct, "9da4cc89590c4c64a36f4a9c820f8609"}); } return tests.toArray(new Object[][]{});