From f3c94a3c8751b4766e6842b78aeeb9e2ad1e776b Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 1 May 2013 15:48:05 -0400 Subject: [PATCH] Update expected test output for Java 7 -Changes in Java 7 related to comparators / sorting produce a large number of innocuous differences in our test output. Updating expectations now that we've moved to using Java 7 internally. -Also incorporate Eric's fix to the GATKSAMRecordUnitTest to prevent intermittent failures. --- .../VariantAnnotatorIntegrationTest.java | 12 ++++----- ...perGeneralPloidySuite1IntegrationTest.java | 4 +-- ...perGeneralPloidySuite2IntegrationTest.java | 6 ++--- ...dGenotyperIndelCallingIntegrationTest.java | 6 ++--- ...GenotyperNormalCallingIntegrationTest.java | 4 +-- ...dGenotyperReducedReadsIntegrationTest.java | 2 +- ...lexAndSymbolicVariantsIntegrationTest.java | 6 ++--- .../HaplotypeCallerIntegrationTest.java | 16 ++++++------ .../DepthOfCoverageIntegrationTest.java | 26 +++++++++---------- .../utils/crypt/GATKKeyIntegrationTest.java | 2 +- .../utils/sam/GATKSAMRecordUnitTest.java | 3 ++- 11 files changed, 44 insertions(+), 43 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 5866075a7..961a28bcf 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -78,7 +78,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("fbfbd4d13b7ba3d76e8e186902e81378")); + Arrays.asList("42889072698af972f2004ccfe8eae15e")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("19aef8914efc497192f89a9038310ca5")); + Arrays.asList("213560f395280e6a066d0b0497ce8881")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -112,7 +112,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("4f0b8033da18e6cf6e9b8d5d36c21ba2")); + Arrays.asList("7e755bb09169699b76850e76b71a5f5a")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("64ca176d587dfa2b3b9dec9f7999305c")); + Arrays.asList("d8089c5874ff35a7fd7e35ebd7d3b137")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("f33f417fad98c05d9cd08ffa22943b0f")); + Arrays.asList("e17596007d0db7673d138a9ae4890e82")); executeTest("test exclude annotations", spec); } @@ -136,7 +136,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("0c810f6c4abef9d9dc5513ca872d3d22")); + Arrays.asList("0ed4c7760f6e7a158b6d743d257300f3")); executeTest("test overwriting header", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index 34b19ed2d..88506fda3 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -69,7 +69,7 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testBOTH_GGA_Pools() { - executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "71f16e19b7d52e8edee46f4121e59f54"); + executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "dac2d7969e109aee9ad2dad573759f58"); } @Test(enabled = true) @@ -79,6 +79,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "603416111f34e2a735163fa97e1a8272"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "66a5a3eb657fac5c621bc0c228ea9caf"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index 8a165cbeb..e26822e07 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","13de8558acaa0b9082f2df477b45de9b"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9f960977b1b8d90ac75ba4306336553c"); } @Test(enabled = true) public void testMT_SNP_DISCOVERY_sp4() { - executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","3fc6f4d458313616727c60e49c0e852b"); + executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","296917e690616682b79229ec5f923bdb"); } @Test(enabled = true) public void testMT_SNP_GGA_sp10() { - executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "1bebbc0f28bff6fd64736ccca8839df8"); + executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "545d85ce79841f01886a5cf824a4a12c"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index 52970d70d..6b7631039 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("d8b0c5be39ec6b239641c2f2646d2bc3")); + Arrays.asList("ea4c4e020f59f48901d5820c8e4f6001")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("16d975480ff1e689113171805b916b62")); + Arrays.asList("79f7fc64da8f25eda1f1ee139ecdd657")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("60ed3f8d5bc3f765e6ce3fa698b68bb7")); + Arrays.asList("15508fcf61380a91b6611307f182447b")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index 8256a8496..5734d670f 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("09a1a4d4bf0289bcc5e8a958f783a989")); + Arrays.asList("21d1d3c6a50006c723cec738f19caeb6")); executeTest("test Multiple SNP alleles", spec); } @@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("57a1bb44967988f2b7ae7779127990ae")); + Arrays.asList("314b99eb146de1fdafed872ecbe1cfc2")); executeTest("test reverse trim", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java index f7ac87cda..5f9667cca 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java @@ -74,7 +74,7 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest { @Test public void testReducedBamINDELs() { - testReducedCalling("INDEL", "9a986b98ed014576ce923e07452447f4"); + testReducedCalling("INDEL", "19bc6a74250ec19efc4e1b4ee6515ac0"); } 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 d3f3a9936..90d7f493c 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", "", "27db36467d40c3cde201f5826e959d78"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "0bf5ae740bf9bd14c8d60d7849c45eb3"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "ed3b577e6f7d68bba6774a62d9df9cd9"); + "5954a46971b7546d30151b068cded42a"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "a594a28d8053c3e969c39de81a9d03d6"); + "b3684c670f68f5a3a348a7fd2b25f10a"); } } 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 50165bd01..03d3e8a17 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 @@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "aeab5f0d40852e6332b96481981a0e46"); + HCTest(CEUTRIO_BAM, "", "2e10ab97afd4492c2a153b85871a2c2d"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "18d5671d8454e8a0c05ee5f6e9fabfe3"); + HCTest(NA12878_BAM, "", "affed81386dfe60e0b0d4e7e0525918f"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -96,7 +96,7 @@ 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", - "28c3b1f276ec8198801aafe880e40fb6"); + "65188ec4e3b91796f62bfb5b965ccf1f"); } @Test @@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "bac6f98e910290722df28da44b41f06f"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "125e91ebe43108b2b514c58a9b6d3a4f"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -149,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "65e7b1b72a2411d6360138049914aa3a"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "2d295ce36066d9d8d9ee9c67e6e2cbd1"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cb190c935541ebb9f660f713a882b922")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("153d2251de7d22f423cd282b1505fbc0")); executeTest("HCTestStructuralIndels: ", spec); } @@ -188,7 +188,7 @@ 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("0df626cd0d76aca8a05a545d0b36bf23")); + Arrays.asList("0c29e4049908ec47a3159dce33d477c3")); executeTest("HC calling on a ReducedRead BAM", spec); } @@ -196,7 +196,7 @@ 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("8adfa8a27a312760dab50787da595c57")); + Arrays.asList("3306889b8d0735ce575bee281c1b8846")); executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 7171edf20..003ab6cf9 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -82,23 +82,23 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { // now add the expected files that get generated spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile); spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); - spec.addAuxFile("229b9b5bc2141c86dbc69c8acc9eba6a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); + spec.addAuxFile("520720a88ae7608257af51bc41c06b87", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); - spec.addAuxFile("e69ee59f447816c025c09a56e321cef8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); - spec.addAuxFile("fa054b665d1ae537ada719da7713e11b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); - spec.addAuxFile("28dec9383b3a323a5ce7d96d62712917", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); + spec.addAuxFile("6958004a8156f3f267caa6b04cf90f5f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("ebbfc9b9f4e12ac989c127061948c565", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); + spec.addAuxFile("e003bef6762833a5cebca25d94194616", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); - spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); + spec.addAuxFile("0732b6d2db9c94b0fcf18ca1f19772a8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); - spec.addAuxFile("4656c8797696cf5ef0cdc5971271236a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); - spec.addAuxFile("6f1d7f2120a4ac524c6026498f45295a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); - spec.addAuxFile("69c424bca013159942337b67fdf31ff8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); + spec.addAuxFile("3522f7380554b926c71a7258250c1d63", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); + spec.addAuxFile("2cd9d8c5e37584edd62ca6938659cf59", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); + spec.addAuxFile("78fdd35a63a7a4c6b3a043b946b04730", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); - spec.addAuxFile("a395dafde101971d2b9e5ddb6cd4b7d0", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); + spec.addAuxFile("aa00e3652dd518ccbae2caa00171835b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("185b910e499c08a8b88dd3ed1ac9e8ec", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("d5d11b686689467b5a8836f0a07f447d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("ad1a2775a31b1634daf64e691676bb96", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("0ce5ebfa46b081820d013bdbbfe42d34", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("c7c5bad6c6818995c634f350aa66fde9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("949c9ce745753cd98f337600d3931d09", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); execute("testBaseOutputNoFiltering",spec); } @@ -115,7 +115,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile); - spec.addAuxFile("7d87783b3d98b928cac16d383ceca807",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("4429d33ce8836c09ba2b5ddfae2f998e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); execute("testNoCoverageDueToFiltering",spec); } 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 9c9248669..ca7314ca9 100644 --- a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java @@ -130,7 +130,7 @@ public class GATKKeyIntegrationTest extends WalkerTest { { "corrupt_bad_isize_field.key", UserException.UnreadableKeyException.class }, { "corrupt_bad_crc.key", UserException.UnreadableKeyException.class }, { "corrupt_no_email_address.key", UserException.UnreadableKeyException.class }, - { "corrupt_no_sectional_delimiter.key", UserException.KeySignatureVerificationException.class }, + { "corrupt_no_sectional_delimiter.key", UserException.UnreadableKeyException.class }, { "corrupt_no_signature.key", UserException.UnreadableKeyException.class }, { "corrupt_bad_signature.key", UserException.KeySignatureVerificationException.class }, { "corrupt_non_gzipped_valid_key.key", UserException.UnreadableKeyException.class } diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java index eefc92799..e9af685a6 100644 --- a/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java @@ -42,7 +42,7 @@ public class GATKSAMRecordUnitTest extends BaseTest { GATKSAMRecord read, reducedRead; final static String BASES = "ACTG"; final static String QUALS = "!+5?"; - final private static int[] REDUCED_READ_COUNTS = new int[]{10, 20, 30, 40, 1}; + final private static int[] REDUCED_READ_COUNTS = new int[]{10, 20, 30, 40}; @BeforeClass public void init() { @@ -200,6 +200,7 @@ public class GATKSAMRecordUnitTest extends BaseTest { @Test public void testGetReducedCountsIsCorrect() { + reducedRead.setReducedReadCountsTag(REDUCED_READ_COUNTS); final int[] counts = reducedRead.getReducedReadCounts(); Assert.assertNotSame(counts, reducedRead.getAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG)); for ( int i = 0; i < counts.length; i++ )