diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java index 023acfc34..539e44b64 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java @@ -341,7 +341,7 @@ public class IntervalSharder { nextBin = null; while(wrappedIterator.hasNext() && nextBin == null) { Bin bin = wrappedIterator.next(); - if(index.getLevelForBin(bin) == index.getNumIndexLevels()-1) + if(index.getLevelForBin(bin) == AbstractBAMFileIndex.getNumIndexLevels()-1) nextBin = bin; } } diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java index 0a3c9b9c0..2740eae46 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java @@ -86,7 +86,7 @@ public class TraverseDuplicates extends TraversalEngine> uniqueReadSets(List reads) { - Set> readSets = new HashSet>(); + Set> readSets = new LinkedHashSet>(); // for each read, find duplicates, and either add the read to its duplicate list or start a new one for ( SAMRecord read : reads ) { diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java index bc06425d2..d062bd1b5 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java @@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { " -OQ -QT 4 -CR WRITE_Q0S" + " -o %s -ob %s", 2, - Arrays.asList("55c01ccc2e84481b22d3632cdb06c8ba", "12eeaaa8df3d742f68cdd8838b203825")); + Arrays.asList("55c01ccc2e84481b22d3632cdb06c8ba", "22db22749f811d30216215e047461621")); executeTest("clipOriginalQuals", spec); } } \ No newline at end of file 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 3ade9f186..69917e147 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerLod5() { - String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "c4ef635f2597b12b93a73199f07e509b"}; + String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "c4ef635f2597b12b93a73199f07e509b"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, @@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerLod50() { - String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "3735a510513b6fa4161d92155e026283"}; + String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "3735a510513b6fa4161d92155e026283"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, @@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testRealignerKnownsOnly() { - String[] md5s = {"7084d4e543bc756730ab306768028530", "74652bd8240291293ec921f8ecfa1622"}; + String[] md5s = {"70b657dcb654bd2c84c38d654c5af697", "74652bd8240291293ec921f8ecfa1622"}; WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly", 2, diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index 57abd4c4b..9e8b6f85e 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -52,10 +52,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibrator1() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "fd5eca3a40a971d5eabf9ab792bd0295" ); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e5d9fc628dcf4f0ae115a6e6cc5423fe"); - e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7ebdce416b72679e1cf88cc9886a5edc" ); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "b00679024ce8dcaf611907109a7e9a27" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "da79dcc74336a6333f75aeb231590436" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "6c5ac8f71a77f09eec3e38932ba274cf"); + e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b26a07cc3d3f6a607e786ebcc2c9c8ac" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "504152c1a94d6998af9785bcbddbb3d6" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -106,7 +106,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorMaxQ70() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "0e2bca11d09b1b93bfc4af5c185e0d1d" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "4d24b4683a9b20e93837da75fff2489f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -163,7 +163,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorSolidIndelsRemoveRefBias() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "a6eb2f8f531164b0a3cb19b4bb1d2f4f" ); + e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "85c0500f9f4ba0d613a77d34b5c84a64" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -276,7 +276,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoReadGroups() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "474e05b5a0f13776daebeb964a5e0e2b" ); + e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "a2d7b780052fe31b0d37fc6462ab58ca" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -331,7 +331,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoIndex() { HashMap e = new HashMap(); - e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "9733d0c5954dcdf5b9bb0ad0b6eb8232" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "4ae0b3d4e2f6a7c1c60ae64944afff5e" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java index 98d2cd956..e98dd13bf 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java @@ -20,8 +20,8 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest { List result = executeTest(name, spec).getFirst(); } - @Test public void testChr110Mb() { testCounter("testChr1-10mb", "-L chr1:1-10,000,000 --quietLocus", "fa8bfdd0b62a13a543bae90f7c674db7"); } - @Test public void testIntervalVerbose() { testCounter("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", "1ebcc10b85af16805a54391721776657"); } + @Test public void testChr110Mb() { testCounter("testChr1-10mb", "-L chr1:1-10,000,000 --quietLocus", "d3c329a634904d95c4b180d0d63eadfc"); } + @Test public void testIntervalVerbose() { testCounter("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", "5fbb930020df6ca7d0f724524fc43b3e"); } public void testCombiner(String name, String args, String md51, String md52) { WalkerTestSpec spec = new WalkerTestSpec( @@ -35,6 +35,6 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest { List result = executeTest(name, spec).getFirst(); } - @Test public void testIntervalCombine() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 50", "d41d8cd98f00b204e9800998ecf8427e", "e2501d7e20564df9f7519fadef8cf283"); } - @Test public void testIntervalCombineQ60() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 60", "d41d8cd98f00b204e9800998ecf8427e", "b23f6436d230f57f969502ddd8d48c18"); } + @Test public void testIntervalCombine() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 50", "d41d8cd98f00b204e9800998ecf8427e", "4541f57820637039bc2f5a97bcaadfe4"); } + @Test public void testIntervalCombineQ60() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 60", "d41d8cd98f00b204e9800998ecf8427e", "8c0350c0a697e4083aab6ead3f404de4"); } } \ No newline at end of file diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1459.jar b/settings/repository/edu.mit.broad/picard-private-parts-1562.jar similarity index 51% rename from settings/repository/edu.mit.broad/picard-private-parts-1459.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1562.jar index f64e1e0e5..25c7e8ae6 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1459.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1562.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1459.xml b/settings/repository/edu.mit.broad/picard-private-parts-1562.xml similarity index 58% rename from settings/repository/edu.mit.broad/picard-private-parts-1459.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1562.xml index fc44667c8..81a03fd6f 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1459.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1562.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.24.477.xml b/settings/repository/net.sf/picard-1.24.477.xml deleted file mode 100644 index 261a6c023..000000000 --- a/settings/repository/net.sf/picard-1.24.477.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/picard-1.24.477.jar b/settings/repository/net.sf/picard-1.29.571.jar similarity index 70% rename from settings/repository/net.sf/picard-1.24.477.jar rename to settings/repository/net.sf/picard-1.29.571.jar index 1bf801b52..32350c90e 100644 Binary files a/settings/repository/net.sf/picard-1.24.477.jar and b/settings/repository/net.sf/picard-1.29.571.jar differ diff --git a/settings/repository/net.sf/picard-1.29.571.xml b/settings/repository/net.sf/picard-1.29.571.xml new file mode 100644 index 000000000..fd00ca0c2 --- /dev/null +++ b/settings/repository/net.sf/picard-1.29.571.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.24.477.xml b/settings/repository/net.sf/sam-1.24.477.xml deleted file mode 100644 index 947d3c641..000000000 --- a/settings/repository/net.sf/sam-1.24.477.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/sam-1.24.477.jar b/settings/repository/net.sf/sam-1.29.571.jar similarity index 61% rename from settings/repository/net.sf/sam-1.24.477.jar rename to settings/repository/net.sf/sam-1.29.571.jar index 1bd1ac396..f75d0ed17 100644 Binary files a/settings/repository/net.sf/sam-1.24.477.jar and b/settings/repository/net.sf/sam-1.29.571.jar differ diff --git a/settings/repository/net.sf/sam-1.29.571.xml b/settings/repository/net.sf/sam-1.29.571.xml new file mode 100644 index 000000000..adee85dfa --- /dev/null +++ b/settings/repository/net.sf/sam-1.29.571.xml @@ -0,0 +1,3 @@ + + +