diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index 1f4875298..f7907649d 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -188,12 +188,12 @@ public class BQSRIntegrationTest extends WalkerTest { public Object[][] createPRTestData() { List tests = new ArrayList(); - tests.add(new Object[]{1, new PRTest(" -qq -1", "b8d296fb78adc5cff7ce12073a69d985")}); - tests.add(new Object[]{1, new PRTest(" -qq 6", "2ee0cedf84c1a33a807438172bc36c11")}); - tests.add(new Object[]{1, new PRTest(" -DIQ", "46cf74900bf8b13438e6a195b3085c48")}); + tests.add(new Object[]{1, new PRTest(" -qq -1", "fcc136b877fbde38791533b0f1ae39e4")}); + tests.add(new Object[]{1, new PRTest(" -qq 6", "f21b537c1689b8051b878ea5cc9b61a0")}); + tests.add(new Object[]{1, new PRTest(" -DIQ", "1d04a242bf825177d6a45eff9fbed647")}); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, new PRTest("", "88b88f006ebb1aade85089bfba5a9e8d")}); + tests.add(new Object[]{nct, new PRTest("", "b6f343ac69c63cdb49205c13e67297fc")}); } return tests.toArray(new Object[][]{}); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index eba9c7780..275ababda 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -60,8 +60,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest { private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; private static final String baseCommand = baseCommandPrefix + "-o %s "; - private static final String base_md5 = "7574ab7d0b1ee5d44a0b3f85b6e944e6"; - private static final String base_md5_with_SW_or_VCF = "a918d69d26d3c87b29002ed31f428c48"; + private static final String base_md5 = "a102dd55451799e5f053c784b762087e"; + private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d"; @Test public void testDefaults() { @@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec1 = new WalkerTestSpec( baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, 1, - Arrays.asList("36718f10d523dfb0fa2a709480f24bd4")); + Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192")); executeTest("realigner known indels only from VCF", spec1); } @@ -101,7 +101,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testLods() { HashMap e = new HashMap(); e.put( "-LOD 60", base_md5 ); - e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "9a75a0f7ad0442c78d0f8df260e733a4" ); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -117,7 +117,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", 1, - Arrays.asList("e98f51d71f0a82141b36a7e9f94db237")); + Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe")); executeTest("realigner long run", spec); } @@ -126,7 +126,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", 1, - Arrays.asList("58ac675d0699eb236d469b8e84513d11")); + Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d")); executeTest("realigner no output tags", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java index 13cd2be73..6b0422c6a 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java @@ -43,13 +43,13 @@ public class BAQIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testPrintReadsNoBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("d97340a2bba2c6320d1ebeb86024a27c")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("11af64ba020262d06b490bae2c5e08f8")); executeTest(String.format("testPrintReadsNoBAQ"), spec); } @Test public void testPrintReadsRecalBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("4ac691bde1ba1301a59857694fda6ae2")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("96ec97cf92f1f660bd5244c6b44539b3")); executeTest(String.format("testPrintReadsRecalBAQ"), spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java index ae4bce81b..b3d583ef1 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { } final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f"; - @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "33e781084379aae538954e30919e8fd3"); } - @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "67263a39d5127f2660a5b638ff32056a"); } + @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "12be03c817d94bab88457e5afe74256a"); } + @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "0bcfd177fe4be422898eda8e161ebd6c"); } - @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "764846d0592f346a33525af674fd7a10"); } - @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "3061cf742f9e5526a61130128ae761a3"); } + @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "aed836c97c6383dd80e39a093cc25e08"); } + @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "5f6e08bd44d6faf5b85cde5d4ec1a36f"); } - @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); } - @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); } + @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f3cb42759428df80d06e9789f9f9f762"); } + @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "44658c018378467f809b443d047d5778"); } - @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); } + @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "bae38f83eb9b63857f5e6e3c6e62f80c"); } - @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "2a1a3153e0942ab355fd8a6e082b30e0"); } - @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "50d43d63d8e39f67a87a6359963c6f52"); } + @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "3b32da2eaab7a2d4729fdb486cedbb2f"); } + @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "9d355b0f6d2076178e92bd7fcd8f5adb"); } @Test public void testUseOriginalQuals() { @@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { " -OQ -QT 4 -CR WRITE_Q0S" + " -o %s -os %s", 2, - Arrays.asList("22db22749f811d30216215e047461621", "55c01ccc2e84481b22d3632cdb06c8ba")); + Arrays.asList("c83b4e2ade8654a2818fe9d405f07662", "55c01ccc2e84481b22d3632cdb06c8ba")); executeTest("clipOriginalQuals", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java index 83f801a98..b509fc1df 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java @@ -54,17 +54,17 @@ public class PrintReadsIntegrationTest extends WalkerTest { @DataProvider(name = "PRTest") public Object[][] createPrintReadsTestData() { return new Object[][]{ - {new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "dc8e5451dd29757c336013146010f73a")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "fde82269c78c9e91e57286433531b4af")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "0531717b32a7e21c0de70b1526b0751f")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "cdc4ddf9ee1d2ecf37168da8ef23c270")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "fa9c66f66299fe5405512ac36ec9d0f2")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "488eb22abc31c6af7cbb1a3d41da1507")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "1510dc4429f3ed49caf96da41e8ed396")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "0e3d1748ad1cb523e3295cab9d09d8fc")}, // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance() - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "0a9ce949d07a84cb33a1a8e3358bf679")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e920b8505e7e95d67634b0905237dbc")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "13bb9a91b1d4dd2425f73302b8a1ac1c")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e920b8505e7e95d67634b0905237dbc")}, - {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "6caec4f8a25befb6aba562955401af93")}, - {new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "c43380ac39b98853af457b90e52f8427")} + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "e1cac555f3d720f611c47eec93e84bd9")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e2558317d409195eab3006dc9e5524c")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "2d32440e47e8d9d329902fe573ad94ce")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e2558317d409195eab3006dc9e5524c")}, + {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "349650b6aa9e574b48a2a62627f37c7d")}, + {new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "0c1cbe67296637a85e80e7a182f828ab")} }; } diff --git a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java index 7421767c7..9c9248669 100644 --- a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java @@ -38,7 +38,7 @@ public class GATKKeyIntegrationTest extends WalkerTest { public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s", publicTestDir + "exampleFASTA.fasta", publicTestDir + "exampleBAM.bam"); - public static final String MD5_UPON_SUCCESSFUL_RUN = "b9dc5bf6753ca2819e70b056eaf61258"; + public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b"; private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) { diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java index dc8a31945..98ecd0f43 100644 --- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java @@ -78,7 +78,7 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("748a38ed5eb0a043dfc7b82f0d1e8063",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("95e98192e5b90cf80eaa87a4ace263da",createTempFileFromBase(baseOutputFile.getAbsolutePath())); spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testUnmappedReadInclusion",spec); @@ -99,7 +99,7 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("083ef1e9ded868e0d12c05a1354c0319",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("3944b5a6bfc06277ed3afb928a20d588",createTempFileFromBase(baseOutputFile.getAbsolutePath())); spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testUnmappedReadInclusion",spec);