diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index d72e2201c..aeb4a8dbb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -215,7 +215,6 @@ public class UnifiedGenotyper extends LocusWalker getSupportedHeaderStrings() { Set result = new HashSet(); result.add(new VCFFormatHeaderLine(GENOTYPE_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.String, "Genotype")); - result.add(new VCFFormatHeaderLine(GENOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Genotype Quality")); + result.add(new VCFFormatHeaderLine(GENOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Float, "Genotype Quality")); result.add(new VCFFormatHeaderLine(DEPTH_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Read Depth (only filtered reads used for calling)")); //result.add(new VCFFormatHeaderLine(HAPLOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Haplotype Quality")); return result; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java index 6aae27928..24866b11f 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java @@ -638,7 +638,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype { tempStr.append(rec.toStringEncoding(mAlts, genotypeFormatStrings)); gMap.remove(genotype); } else { - tempStr.append(VCFGenotypeRecord.EMPTY_GENOTYPE); + tempStr.append(VCFGenotypeRecord.stringEncodingForEmptyGenotype(genotypeFormatStrings)); } } if ( gMap.size() != 0 ) { diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java index f17675a73..680634efb 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java @@ -158,7 +158,10 @@ public class VCFUtils { record.setField(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount())); params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY); double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE); - record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual)); + if ( qual >= 0 ) + record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual)); + else + record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%d", VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY)); params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY); record.setVCFRecord(vcfrecord); @@ -186,7 +189,10 @@ public class VCFUtils { record.setField(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount())); params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY); double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE); - record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual)); + if ( qual >= 0 ) + record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual)); + else + record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%d", VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY)); params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY); return record; diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java index 52547fdb0..a01ffa3e0 100755 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java @@ -7,8 +7,6 @@ import org.junit.Test; import java.util.HashMap; import java.util.Map; import java.util.Arrays; -import java.util.List; -import java.io.File; public class VariantContextIntegrationTest extends WalkerTest { private static String cmdRoot = "-T TestVariantContext" + @@ -50,7 +48,7 @@ public class VariantContextIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B vcf,VCF," + validationDataLocation + "/yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", 2, // just one output file - Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "461960b26ee1f8998ccc47da9bd3913c")); + Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "62f06802c2cac1a41068a3d9b6330ad4")); executeTest("testToVCF", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java index 2e768b272..e7214d146 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java @@ -33,7 +33,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; - String md5_for_this_test = "4bd8a28bcbad107b102fc796918d5932"; + String md5_for_this_test = "c1116b3196cc9f553ae2442a4063bc5e"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); executeTest("Testing on E2 annotated but not Q2 annotated file ",spec); @@ -49,7 +49,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; - String md5_for_this_test = "3eee411119888fc4633870a91ed2093d"; + String md5_for_this_test = "a297259694ac88f769a45bce96a08e51"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); executeTest("Testing on bam file without 2bb annotations ",spec); @@ -61,7 +61,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { + " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" + " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf" + " -vcf %s -L chr15:46347148"; - String expected_md5 = "c70dfb30c3caa9184604f88bc7f62a07"; + String expected_md5 = "aac8f669a36092b70d9c083ad652a727"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); executeTest("Testing on locus with many indels", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 2d0e3b6c6..9141d68a9 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -50,7 +50,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("fecfec68226bbd9b458ede55d48e0762")); + Arrays.asList("bfb2566d062a03658e6d13467127aaca")); executeTest("test file has annotations, not asking for annotations, #1", spec); } @@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("36aaac8c38480b7f49766b8b88f9c537")); + Arrays.asList("98bcbd4dd9d0edc5aa1ae97877a7e8f8")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("c70cc6bb6b83748ec8d968dc3bf879c4")); + Arrays.asList("5c4287632573062778fc8a1483575b64")); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); } @@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("9fc6e8c5ee56a67f158bbf305470643d")); + Arrays.asList("437b45d2ee1a150f15c4479cb2cb5e8f")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java index 772687dce..6eded779a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java @@ -14,7 +14,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testSimpleVenn() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1, - Arrays.asList("c0376dcd60f1741eac2917f10b4bb7a4")); + Arrays.asList("cdd027a0d7bbfae2ba75480fcaa14356")); executeTest("testSimpleVenn", spec); } @@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testSNPConcordance() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1, - Arrays.asList("ffc13b79f6a18158f63cc9a8ee968f32")); + Arrays.asList("310bf0824fc407b2e40cbbaea234471e")); executeTest("testSNPConcordance", spec); } @@ -30,7 +30,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testNWayVenn() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1, - Arrays.asList("39717fb57526e54540e803a1f9c5d31b")); + Arrays.asList("179adafae6efdc879fc22442ab9e599f")); executeTest("testNWayVenn", spec); } @@ -38,7 +38,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testMulti() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1, - Arrays.asList("0b5b0c9ce7e21d1d2c38ebaad7765017")); + Arrays.asList("c8fe63633ef6ed2b6068958f06cddfe0")); executeTest("testMulti", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java index 419cd176e..2dfa478b4 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testNoAction() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("340e3a09d0571dc969557cc979a132b3")); + Arrays.asList("e8e1898d65eb77ec32b7eca6764864f3")); executeTest("test no action", spec); } @@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testClusteredSnps() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("53e2c4645bab58a4f039ff51d5bffb7e")); + Arrays.asList("25da669bc6411d31f585b01be85e8429")); executeTest("test clustered SNPs", spec); } @@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testMask() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("27dacba4bcc6beaac608a7b34b7206f0")); + Arrays.asList("bd08169351c4cc9a2d95f33a2a73c7fa")); executeTest("test mask", spec); } @@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilter1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("e1a17255db9aa17016457ce2d81c6fff")); + Arrays.asList("9e7631aeda1c174f5aac6712279ed861")); executeTest("test filter #1", spec); } @@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilter2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("18ef67575a76c2be74af8bd8b9fdf86e")); + Arrays.asList("9009742f5697c5a85f9e41e1d7d6f260")); executeTest("test filter #2", spec); } @@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilterWithSeparateNames() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("7de66cac85cfe8a70219e51a5f6c251c")); + Arrays.asList("6b280c5abd6e911df8e4fca58c7b216b")); executeTest("test filter with separate names #2", spec); } } \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 4484bce00..1a2302eb7 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -35,7 +35,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("5e0a92fbddeb9d6e35586d0488a1e5c7")); + Arrays.asList("2f928b1261963044ca1781601cae4bf7")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("68d00450e3c2129ea38c67171722b385")); + Arrays.asList("10fe265d0140243b52f500c3882230f2")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("8971ab1c9d2780e5e12e9bfc0b059cd1")); + Arrays.asList("5c455e1a33e3f82d13898b20ee71ac69")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); } @@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testParallelization() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1, - Arrays.asList("fb5d09eb8f1494d48032be7272699add")); + Arrays.asList("c827c74e59263b0f6b526089b050c100")); executeTest("test parallelization", spec); } @@ -77,11 +77,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testParameter() { HashMap e = new HashMap(); - e.put( "-genotype", "41af43f6eaab72de553d865a3089bf54" ); - e.put( "-all_bases", "7cc1609aef6d6cc3dd7822c52c403750" ); - e.put( "--min_base_quality_score 26", "9596e2102369ced181f2a87d686faf2e" ); - e.put( "--min_mapping_quality_score 26", "130efb2b8bd7b495bf65c6477bcf83c8" ); - e.put( "--max_mismatches_in_40bp_window 5", "18935308954cf390b628c9226eccbe94" ); + e.put( "-genotype", "8818584bf7053ecf52844f3b404ab630" ); + e.put( "-all_bases", "bf6ea1c04bf52002e3365c1f47103d4a" ); + e.put( "--min_base_quality_score 26", "3f192cd301f057698d0bc6c41841ce81" ); + e.put( "--min_mapping_quality_score 26", "2631025243ac6b52df852309235ec8d3" ); + e.put( "--max_mismatches_in_40bp_window 5", "e540a2057164e3b05a5d635805f1167e" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -95,7 +95,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1, - Arrays.asList("8c0e1fed37a2eac9eaaaa59e31350f43")); + Arrays.asList("bfa93ee89aa0807b9c4e4793363452b4")); executeTest("testConfidence", spec); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java index cd502631b..37aa3334e 100755 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java @@ -12,7 +12,7 @@ public class VCFIntegrationTest extends WalkerTest { // Read in and then emit each record WalkerTestSpec spec = new WalkerTestSpec( "-T PrintRODs -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:10,000,000-10,050,000 -o %s -B vcf,VCF," + validationDataLocation + "complexExample.vcf", 1, - Arrays.asList("26ad7a663d0f247ac26ce5490edd7ec0")); + Arrays.asList("68b123acca4975553297fcd776c70464")); executeTest("test vcf", spec); } } \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java index 521a1c187..a37610b03 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java @@ -309,7 +309,7 @@ public class VCFReaderTest extends BaseTest { if ( grec.getReadCount() == 4 ) Assert.assertTrue(grec.getFields().get("GQ").equals("-1")); else - Assert.assertTrue(grec.getFields().get("GQ").equals("5.85") && grec.getReadCount() == -1); + Assert.assertTrue(grec.getFields().get("GQ").equals("5.85") && grec.getReadCount() == -1); } }