diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index 6a4222c09..cfb29d272 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -408,7 +408,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In */ @Advanced @Argument(fullName="GVCFGQBands", shortName="GQB", doc="Emit experimental reference confidence scores", required = false) - protected List GVCFGQBands = Arrays.asList(5, 20, 60); + protected List GVCFGQBands = new ArrayList(70) {{ + for (int i=1; i<=60; ++i) add(i); + add(70); add(80); add(90); add(99); + }}; /** * This parameter determines the maximum size of an indel considered as potentially segregating in the diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 89b68114f..fca9b91fb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -69,10 +69,10 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // this functionality can be adapted to provide input data for whatever you might want in your data tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "9db87ae56df22456f3c08024384f3e5e"}); tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "4a006f9e39cacc3ae84384ad56ca22a2"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb048cbfa5cc058d680f9be5fd689767"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fe014592c9fa8d442508a96eb09e0c93"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d5c07fa3edca496a84fd17cecad06230"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "330685c734e277d70a44637de85ad54d"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e6ec90da053a612f0c615e221eb34baa"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "b01a2c222a3f00a675f5534c3b449919"}); return tests.toArray(new Object[][]{}); } @@ -137,7 +137,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testWrongGVCFNonVariantRecordOrderBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fecd24420579f321157e5605b6cd7f2")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d595dae0e3f993047c22c6e520e190aa")); spec.disableShadowBCF(); executeTest("testMissingGVCFIndexingStrategyException", spec); } @@ -149,7 +149,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testNoCallGVCFMissingPLsBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("95bae0b4a8fe9bfcf71762704b22a76e")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2a91768430a84dbae8d40242dee8c9b8")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); }