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Move htsjdk and picard to version 2.3.0

This commit is contained in:
Ron Levine 2016-04-26 13:56:05 -04:00
parent 8b338dd111
commit 35a06879f1
33 changed files with 251 additions and 252 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java
View File

@ -278,7 +278,7 @@ public class ConsensusAlleleCounter {
builder.noGenotypes();
if (doMultiAllelicCalls) {
vcs.add(builder.make());
if (vcs.size() >= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
if (vcs.size() >= GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
break;
} else if (curCnt > maxAlleleCnt) {
maxAlleleCnt = curCnt;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
View File

@ -407,14 +407,14 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
* @throws NullPointerException if {@code vc} is {@code null}.
*
* @return {@code true} iff there is too many alternative alleles based on
* {@link GenotypeLikelihoods#MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED}.
* {@link GenotypeLikelihoods#MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED}.
*/
@Requires("vc != null")
protected final boolean hasTooManyAlternativeAlleles(final VariantContext vc) {
// protect against too many alternate alleles that we can't even run AF on:
if (vc.getNAlleles() <= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
if (vc.getNAlleles() <= GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
return false;
logger.warn("Attempting to genotype more than "+GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED +
logger.warn("Attempting to genotype more than "+GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED +
" alleles. Site will be skipped at location "+vc.getChr()+":"+vc.getStart());
return true;
}

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
View File

@ -275,8 +275,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
UAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(UAC.CONTAMINATION_FRACTION_FILE, UAC.CONTAMINATION_FRACTION, sampleNameSet, logger));
// check for a bad max alleles value
if ( UAC.genotypeArgs.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
if ( UAC.genotypeArgs.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)
throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED);
// warn the user for misusing EMIT_ALL_SITES
if ( UAC.outputMode == OutputMode.EMIT_ALL_SITES &&

52
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -99,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("832861ecdc6344cfb7097d02903ffd4d"));
Arrays.asList("b63baada372925a76c3f279e16eb631d"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -107,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--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("d584454019f21729757ed7685ff8d02c"));
Arrays.asList("6f5856bc2d31f8aae4131717e5ab0b16"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("95a4be70c46496fb6791fdd0c3bcf8a3"));
Arrays.asList("7ec5470f742f80cdfbfb203213bea8cc"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -141,7 +141,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--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("fe6a7fdd3f7c1c77b31c2676aeb0ed8d"));
Arrays.asList("afc47e4f253d0999961f26920be8e834"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -150,7 +150,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testExcludeAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "-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("4995f77bedf7f476a15d46b5a8a392bd"));
Arrays.asList("a8a87e2a67436e14ed32ce9d355a3440"));
executeTest("test exclude annotations", spec);
}
@ -183,7 +183,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("de96b1e62f414b107430d179a154534d"));
Arrays.asList("fc7958261af93681fde73c1fc6b578a0"));
executeTest("test overwriting header", spec);
}
@ -191,7 +191,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("489a09a8531d9c8ef683ad8cc81db3e8"));
Arrays.asList("2d535a48ec1c66aa9c707f6d498fc81d"));
executeTest("not passing it any reads", spec);
}
@ -199,7 +199,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("a7af6774ea1f7622d999cae1b7f8ea32"));
Arrays.asList("a2a2f9ce8e6f9c933ad46906719ce402"));
executeTest("getting DB tag with dbSNP", spec);
}
@ -207,7 +207,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testMultipleIdsWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
Arrays.asList("de8cfffe3b61b7c8832096a399e9d954"));
Arrays.asList("ed351765d63d92b1913784fa47b3d859"));
executeTest("adding multiple IDs with dbSNP", spec);
}
@ -215,7 +215,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("25443af7099f7de184b8dcdfb659f62e"));
Arrays.asList("114d8300ec0fac613bb2e82f8951adc0"));
executeTest("getting DB tag with HM3", spec);
}
@ -223,7 +223,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTagWithTwoComps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("ea9b10d2b82a7846c01a017f6f3bb57e"));
Arrays.asList("af59185b6a03d4147d2755019dcc6bf9"));
executeTest("getting DB tag with 2 comps", spec);
}
@ -239,7 +239,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("f26d1f849cceca0ab115737f8db670ae"));
Arrays.asList("7bcbd8ad8388f371d1a990fde67d3273"));
executeTest("using expression", spec);
}
@ -247,7 +247,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionAlleleMisMatch() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resourceAlleleConcordance --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-mod.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty-mod.vcf", 1,
Arrays.asList("6f288c4b672ac3a22cb2385981f51d75"));
Arrays.asList("76f716569e33d88914e479b70e08ac88"));
executeTest("using expression allele mismatch", spec);
}
@ -255,7 +255,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionMultiAllele() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
Arrays.asList("af92a439f092f45da10adac0f9c8fc8f"));
Arrays.asList("0e3fc86349f5fd28159d00d22d278e84"));
executeTest("using expression with multi-alleles", spec);
}
@ -264,7 +264,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
/* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
Arrays.asList("d0a381375a407dd454637f78bb5b194f"));
Arrays.asList("6fe67e72232165a829fde7c3b12c2275"));
executeTest("annotate a vcf with the FILTER field of another vcf", spec);
}
@ -272,7 +272,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionWithID() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("58a86fe8a34c92127eb33e36107941dd"));
Arrays.asList("94b03ee63604ab8d61aacfd3297c5dca"));
executeTest("using expression with ID", spec);
}
@ -300,7 +300,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation +
"snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
1,
Arrays.asList("6618f3ae9dc6d4ce6ebd4eb8f9495103")
Arrays.asList("db0c5f273583a54d0cefc4b3c01aae9a")
);
executeTest("Testing SnpEff annotations", spec);
}
@ -313,7 +313,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
"--snpEffFile " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " +
"-L 1:10001292-10012424",
1,
Arrays.asList("7533645a3791ce30d7407f789e1ffbb0")
Arrays.asList("5f952cfcd25653edcffd3916d52e94ec")
);
executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec);
}
@ -326,14 +326,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
"--snpEffFile " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " +
"-L 1:10001292-10012424",
1,
Arrays.asList("0e201a91a2b2b130debcd5dd7d9328ab")
Arrays.asList("86fb28c2e3886eda194026b3b7d07c77")
);
executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec);
}
@Test(enabled = true)
public void testTDTAnnotation() {
final String MD5 = "9532ca341b52be650b35e32d7c765030";
final String MD5 = "cf65fdfbcd822279e84326989b2f6378";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@ -344,7 +344,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testChromosomeCountsPed() {
final String MD5 = "4ab0b4245ba2c5c62424775879f51379";
final String MD5 = "71045f20e4cd9f5fdaa367f6d7324e59";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@ -354,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testInbreedingCoeffPed() {
final String MD5 = "5cbf01dc895bff5a8dd9f6c46e0958c6";
final String MD5 = "0cf7c115316950abc0213935b20a653a";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" +
" -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1,
@ -364,7 +364,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testAlleleTrimming() {
final String MD5 = "90f9ee6c34c0820435dce7a0d63b4c1e";
final String MD5 = "5db0cd72ad0ffc711afb95df58de31fa";
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" +
" -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir + "exacAlleleTrim.vcf.gz -E exac.AC_Adj" +
@ -423,7 +423,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testStrandAlleleCountsBySample() {
final String MD5 = "dca6c2b416076ca89769a322cae65bb8";
final String MD5 = "564aeeefad92353d66dbb2a2222d5108";
final WalkerTestSpec spec = new WalkerTestSpec(
"-T HaplotypeCaller --disableDithering " +
String.format("-R %s -I %s ", REF, CEUTRIO_BAM) +
@ -510,7 +510,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " +
"-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --reference_window_stop 59 --no_cmdline_in_header -o %s", 1,
Arrays.asList("bda55495578147b2390d850d7fb25a12"));
Arrays.asList("f3166721ef0380636590b3e860aa06af"));
executeTest("Testing testHomopolymerRunWindow", spec);
}
@ -519,7 +519,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " +
"-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --no_cmdline_in_header -o %s", 1,
Arrays.asList("e20b12fd45f37a7bb31a2f2e91983477"));
Arrays.asList("3dba997d03779781c82a25ace69c838e"));
executeTest("Testing HomopolymerRunTooBig", spec);
}
}

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
View File

@ -121,7 +121,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
@Test
public void testMicroRegression() {
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "617054c6d056cad7448a463cb8d04a55");
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "a7658ccfb75bf1ce8d3d3cfbf3b552f0");
}
/**
@ -131,7 +131,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testTruePositivesDream3() {
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "f856432679e43445d2939772be4326cf");
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "91dee82a13275e5568f5d2e680e3162b");
}
/**
@ -140,7 +140,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
@Test
public void testTruePositivesDream3TrackedDropped() {
M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "",
"ee4786de29532ffd745048c449a9772a",
"4f1337df1de5dd4468e2d389403ca785",
"b536e76870326b4be01b8d6b83c1cf1c");
}
@ -150,7 +150,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testFalsePositivesDream3() {
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "11357aa543e7c6b2725cd330adba23a0");
M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "6be3fc318e2c22a28098f58b76c9a5a1");
}
/**
@ -158,7 +158,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testContaminationCorrection() {
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "1df41f2dd6d4715ae1b423bf295ec7c5");
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "b1010a6614b0332c41fd6da9d5f6b14e");
}
/**
@ -166,7 +166,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testTumorOnly(){
m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "8439d9a673b3a57aa5893af600125d3b");
m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "bb0cddfdc29500fbea68a0913d6706a3");
}
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -189,7 +189,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1,
Arrays.asList("0febd66699fcd7f521377d1d0d0016fb"));
Arrays.asList("b9fa012770831c984101d23420ef0c38"));
executeTest("testUnfilteredBecomesFilteredAndPass", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
View File

@ -133,7 +133,7 @@ public class UnifiedGenotyperEngineUnitTest extends BaseTest {
}
final VariantContext vc = new VariantContextBuilder("test", "chr1", 1000, 1000, alleles).make();
final boolean result = ugEngine.hasTooManyAlternativeAlleles(vc);
Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED));
Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED));
}
}

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
View File

@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testSNP_ACS_Pools() {
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "bf6012b6e7dec2d44b2bcb402c98c95e");
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "ebdf749d404aaef298780a53059a4f93");
}
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "1b834608171f67e52a4e7617458a3ba6");
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "c3826794a250e32b0497353ceb1deb26");
}
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "5b9e08bb141c48f826dc513066cb8a13");
executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "4eb0d8018da6612cd434491f338ed5a4");
}
@Test(enabled = true)
@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
//TODO the old MD5 is kept for the record.
//TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach.
// executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "988d421354869ec3b17f90bad695757a");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "c2fb9b05027c2b0ac9e338d9ddda69b1");
}
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
View File

@ -63,16 +63,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","1ad2b57af06e90679ce6476900d9cbbe");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","e22846de4567f576e08e00edda2931d0");
}
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","b9f5d1db0d2f5eb00eeb72ea29130de6");
executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","9757563c5e32f59cb47eb9b16f1016ac");
}
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "d90e41081b4a910a50116ff18c311245");
executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "37f8ccc683dc525c25dddc4f8dad505c");
}
}

22
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
View File

@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("8893a0ef99744757333ec6a85c31b753"));
Arrays.asList("32bece91e170d623092817738faddb4e"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("7fca7fe87afba84c1bece29ce7a402ef"));
Arrays.asList("897c6063236fcd7242c2ff5982585648"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("343307f432d2026e3c4cc44f64aad06f"));
Arrays.asList("dd66e5f8a6e43be0e473251185a4f38a"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -115,7 +115,7 @@ 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("618d6cdd823c9f88c03b58fc7ebf47b4"));
Arrays.asList("aa56ed44e77162efce45c936c485769e"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -125,7 +125,7 @@ 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("889e43aa0d2c9ce07064817268c965a4"));
Arrays.asList("a4b6434c59c4b119e480ddafc86de234"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
Arrays.asList("8052ee2044f3c5687859aadee2fe2a75"));
Arrays.asList("f9d848fe5e6e6762e0dd5b5d925f74f4"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -150,7 +150,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation +
"NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
Arrays.asList("6e8319e65fef1059c2092c05e6916257"));
Arrays.asList("41aa49e9c15198a006a1bc8e9638d6ec"));
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
}
@ -162,7 +162,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 20:10,000,000-10,100,000",
1,
Arrays.asList("745eb3eefa93aca72f724aab4734c7ef"));
Arrays.asList("e883a8863bdd44c559c4440183c87078"));
executeTest(String.format("test UG with base indel quality scores"), spec);
}
@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("8861c367dd20505e120af174a9d4f9f4"));
Arrays.asList("2a82d1586b2148e8d902da5cf8538210"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("a3bb6d95764d6f5a7d2f78e09699d4ef"));
Arrays.asList("3184a3f58b3aeafcd97280af708a04bb"));
executeTest("test minIndelFraction 0.25", spec);
}
@ -197,7 +197,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
public void testMinIndelFraction100() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 1", 1,
Arrays.asList("c7f190f7cea34a7f9c931cd8de110a48"));
Arrays.asList("990b838ef13b8ccf257eb6cbcc7c7741"));
executeTest("test minIndelFraction 1.0", spec);
}

32
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinBaseQualityScore() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
Arrays.asList("b4201a4d30b6ed5c6fc80248676be5ff"));
Arrays.asList("52a3064863b97e43d8df878edc29275c"));
executeTest("test min_base_quality_score 26", spec);
}
@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSLOD() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("06d166ecf40563c234902d1b340a3ff1"));
Arrays.asList("31790ea2bd2fa7e5cec78e3ffbc98c81"));
executeTest("test SLOD", spec);
}
@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNDA() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("0538b7363d271f1f37d73dc3bd5b0071"));
Arrays.asList("2f2d7dd623446fc3cae62a44a016c16d"));
executeTest("test NDA", spec);
}
@ -110,7 +110,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testCompTrack() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("f54dafe8e9ac1402d230e4d83766d6cf"));
Arrays.asList("7645a06b917efb1ee799bf21bdf08bc4"));
executeTest("test using comp track", spec);
}
@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "dfd11f2f33dc4da50a2725bfb6f64dba");
testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "a9c30d2bb179ea7a69dd0e7367fcd465");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f6937cc8ec068f2d38b5d277a92be34b");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "791fbabf4a8a7a1d0735d57c4c6b4a5a");
testOutputParameters("--output_mode EMIT_ALL_SITES", "1cddd7b1e730765c2b7b55d8a1d69b4c");
}
private void testOutputParameters(final String args, final String md5) {
@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("38a2f8e5542f78c324e89d09eb545f07"));
Arrays.asList("5c7d237e666439edb0ef8c697e37933c"));
executeTest("test confidence 1", spec1);
}
@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNoPrior() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1,
Arrays.asList("6f96d079f5889d8555880e6cb614a41d"));
Arrays.asList("24b550bbc3c9f0577e069b3fd3122d52"));
executeTest("test no prior 1", spec1);
}
@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testUserPrior() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.001 -inputPrior 0.495", 1,
Arrays.asList("6e48c44b58960954e7e49810d9e3b3ad"));
Arrays.asList("f60b6705daec1059ce3e533bf8e44c89"));
executeTest("test user prior 1", spec1);
}
@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void emitPLsAtAllSites() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
Arrays.asList("04630efda71e0e804cfa4b2e7461c083"));
Arrays.asList("ae778a64323abe0da5194f0b936f48aa"));
// GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
spec1.disableShadowBCF();
@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "3e6328e822a92911e591733438fe023c" );
testHeterozosity( 0.01, "6b8bdde9d303139806c5177fae53b1fd" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "e87e2ad4a6d86ba9cc627b397af9c681" );
testHeterozosity( 1.0 / 1850, "b1604d1ba68dfe2fcfb861ef6420a8ba" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("9363de1caf569d565e0c377fe234f170"));
Arrays.asList("7ed55f70feeacf8ecc6b36f0d741dfc7"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("5e9d48c296d50d553ae13f283b75e1ee"));
Arrays.asList("90224ac1c9e2ce9b77fee8dd6e044efe"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -310,7 +310,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
"-A SnpEff",
1,
Arrays.asList("52bac28a85b85d9596d668d3f934f792"));
Arrays.asList("e99f100fe71bb7f328b485204c16f14a"));
executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
}

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
View File

@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("46dd44e69ff078a48057ff08d278a293"));
Arrays.asList("c759b04ed0d948bda95008e29f3f5c2d"));
executeTest("test MultiSample Pilot1", spec);
}
@ -78,7 +78,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testWithAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("a19e5f74606cd980c3083d41d23b4acb"));
Arrays.asList("c35cadefda8a9f13c497f84193f9f841"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@ -86,7 +86,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testWithAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("fe3aec195ceb9180b6ffc474a4bb37b3"));
Arrays.asList("06b4ce476bf444305c8d76a765c5ddb6"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("4cc795e0e2ec1ce31fd6545fb24a850e"));
Arrays.asList("281db46f39e3367f207838c620a82bd2"));
executeTest("test SingleSample Pilot2", spec);
}
@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --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("0de8363482204fe2aedbe612782d1049"));
Arrays.asList("94ca1e00d4fad9c5279271c2779ff797"));
executeTest("test Multiple SNP alleles", spec);
}
@ -110,7 +110,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testBadRead() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
Arrays.asList("67dbab7d307d02b3d879eca8bd15a573"));
Arrays.asList("1d5c55b2df63eb24832de3486c020453"));
executeTest("test bad read", spec);
}
@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --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("e86ff5eb488f29aa77606309b2fd4fcb"));
Arrays.asList("87dbae957b1df41c1938906e23a88c5e"));
executeTest("test reverse trim", spec);
}
@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("d8b205bce4addb4ceff0b5a7ec36e3fe"));
Arrays.asList("c5aff2572ce09c413e7f5c9e1b3f92d6"));
executeTest("test mismatched PLs", spec);
}
}

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "39a1dfa5143e04f75ecd2b24f9c69578");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "32ce23b3830f5f2c693161b40de8b15e");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -84,7 +84,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
// TODO -- need a better symbolic allele test
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8a83ab27177f0b7adf50031f061f9cd7");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e158212aba1d7d229563db11b08b7974");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"af3a490e5f41e890c59927426ac0fe9a");
"8f8680bd8e1549ad88691c9c8af9977c");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"12b1826ee23243c64a002c3cbdfa569a");
"82b53501bc3254def885e09866377e7c");
}
private void HCTestComplexConsensusMode(String bam, String args, String md5) {
@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
"9765065daf3a008bd92c755d882c5f07");
"353f1895047b15b1fec22b559c9da0c1");
}
}

66
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -84,12 +84,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
//TODO this might need to be addressed at some point.
//TODO the following test is commented out for the record
//tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "1c1ca2d76bc5d7dd45a5e7aef756ad8f"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "7ddfd33f2efcd2617d896826434fb43c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "30accd7a171e9a13969fa543fde3fed1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "20d896bbf750739f937ccd2fb152d902"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "99dd66a5b36ba9e2d1b0f408ecfbb50b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "72d90fe0f5641b373744f75a21d4d14c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8d30370465d74fd549d76dd31adc4c0c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b7a5f4e40d5ebaf5f6c46a3d4355c817"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0f5e6f2584649a1b7386d94e3dc60f91"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2c67bdc08c8784f2114c2039270b9766"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "63fa5841a21e2c13f1e1a8e2d4ea3380"});
return tests.toArray(new Object[][]{});
}
@ -103,13 +103,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "9b2914cf121c411aad3a65cfdc98c1d4"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "259110565155a3a27ab3e98113bedef8"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "8058ce63339701d33425769217bffed1"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3abdde9d9ddbe9ec7cef28c65844a409"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "f5f0cef38a529e1542a8fd8bcce7ab1e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ae2c7e570855f6d6ca58ddd1089a970"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "22e03f01e91177011ac028d2347751ba"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb3f16bc10e1cc75f2093bec92145d18"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"});
final String NA12878bandedResolutionMD5 = "0f848ee7240ca48827bdfb85b455c1ad";
final String NA12878bandedResolutionMD5 = "8d4a51af32cd13ba4b3e33dd00c58398";
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@ -126,12 +126,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "1f99396292974df55ef6497be79b1917"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "eabb44785fd4a84ade3c674a0bda16d9"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "904feadac0e4a2a0c6b2cc7e55718f3b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "b430a401310b3812346d7496f9c62011"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "6e481747c50734b7fb0c4de39405044f"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cff5e49456d5ecc0dafd31cd014def4f"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0c87e26fdd7ab5629eb33f36833e3607"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "90b25f3050435c9e67aa0ee325c24167"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "5f329540dc5c4556ab029d0e2cfcabcb"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a0be095ed902a8acdb80fb56ca4e8fb4"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8123d8b68b6fa77ef084f292e191622a"});
return tests.toArray(new Object[][]{});
}
@ -144,12 +144,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals;
// 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, "50156c819a0096fa22ed1b9749affecc"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d91aace2100dc040659d77f366053a2e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "d86dc51757e69aa3f2608fbbfaa90069"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "27c73b8b1ec384a880bf60daf0b0f80e"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a6c70203e43d62b42c4b751fe9018410"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "7ebbbcab78d090d70a24819093812748"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0820ae1d19ba0a2da25737ded8e2c96f"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "70ee4e60d9f86b63aaab09075a71ddd3"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "700d79df3b0b481444e81471204e242e"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "09d1ae38586465b98dea0a0e432a7146"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "228e1d2ec2e729a5f79c37f3f2557708"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "2fc7020457dde4439b4133c098d9ab9b"});
return tests.toArray(new Object[][]{});
}
@ -275,7 +275,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testWrongGVCFNonVariantRecordOrderBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("1c3d390b467a9b0e1e307419796142fd"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6facd3d2cf9f52877182d627cef1c872"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@ -292,7 +292,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testNoCallGVCFMissingPLsBugFix() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c5a017f1cbd60219506be76f30fc4468"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d55ccf214fd5095e6d586c1547cb1a7a"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}
@ -325,7 +325,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("169c2145c9981b8a1bb1d64a6d776d66"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6f6b2fa85cd1bae7f8f72e144fe56c96"));
spec.disableShadowBCF();
executeTest(" testAlleleSpecificAnnotations", spec);
}
@ -334,7 +334,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testASMQMateRankSumAnnotation() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A AS_MQMateRankSumTest --disableDithering",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("75b78770469c5aaa73f1c95db8fda574"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9613ec1ec93547cfb0651673e914bee4"));
spec.disableShadowBCF();
executeTest(" testASMQMateRankSumAnnotation", spec);
}
@ -343,7 +343,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testASInsertSizeRankSum() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("4fd0fcf44b1121c15e9d38de4171002c"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a8765c11b9130c815aae4e06c1f90e45"));
spec.disableShadowBCF();
executeTest(" testASInsertSizeRankSum", spec);
}
@ -352,7 +352,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testHaplotypeCallerMultiAllelicNonRef() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample",
b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2bd863f0b54b9c9a5014097cd3d3f61a"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("87f9203f5ac637080469052b702c61c7"));
spec.disableShadowBCF();
executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
}
@ -361,7 +361,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testHaplotypeCallerMaxNumPLValues() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ea93210277fa4b590790a81c4b3994b"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a4b5c40b1993573c5efd992f3f0db8a9"));
spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValues", spec);
}
@ -378,7 +378,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e"));
spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec);
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
@ -403,7 +403,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e"));
spec.disableShadowBCF();
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec);
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log

64
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -106,92 +106,92 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeBAMOutFlags() throws IOException {
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "1ad8934dc0ea624ffeb89d3e877176b2", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756");
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "08943fb76d1cd5b5b8815e3991754911", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756");
}
@Test
public void testHaplotypeCallerMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "", "5d9b06d7bf88bb18aa3e8fa6322dff89");
HCTest(CEUTRIO_BAM, "", "ad472fbd63864caacf5bc018dcae9df9");
}
@Test
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "b35ba8b7ec8ddfe8268b82e77709c9ca");
HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe");
}
@Test
public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-ploidy 1", "84bd5a2ac22aa47b4436ecaf656b73b1");
HCTest(CEUTRIO_BAM, "-ploidy 1", "7ee30877f0153257afdc691c638e7684");
}
@Test
public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 1", "6e9855e22ed78a60eaaf0a06ed967b77");
HCTest(NA12878_BAM, "-ploidy 1", "9ca97bb743a369a1abb1e61168d63d69");
}
@Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "894b56fa3afd35e240a7db394da7b4ef");
HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806");
}
@Test
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "b35ba8b7ec8ddfe8268b82e77709c9ca");
HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe");
}
@Test
public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "6e9855e22ed78a60eaaf0a06ed967b77");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "9ca97bb743a369a1abb1e61168d63d69");
}
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "894b56fa3afd35e240a7db394da7b4ef");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "94dc1ca52ebe24ab118b13558e667253");
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ba0dc5f416d69558cb5dd3e0a0a5a084");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "8aae4fe36d14158ea2cbf5db151f39a1");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "129bca18bb9eec23004b2d28aa541de2");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ea4365e2dd6ae627d6347f2a53ceeaef");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "2b89c9e102a049e223bc0d91156a08a3");
}
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "626abc84e03d4488b781cfc5a5f50290");
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
"03a9fa3a1c7163c68807d8c713d8040c");
"6d3cea3ee76b6eba14c1dfe230cff96b");
}
@Test
public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"6120365c05e74a8e1e1c44d739cbf8cd");
"e60065998227f4ba8002165fb1729a71");
}
@Test
public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"a3a547a7bf7e488651733da08fd22049");
"9315d146a66c7baf3b615eb480c54dc1");
}
@Test
public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException {
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "da1f6b9a7e5913910531b00f3b35ce06");
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e98012fbad5f429b3b2abc3a7aa454");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -202,7 +202,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a048ea02eeb9610660e31f36e6114bf4");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3625167f0e788d409c7eab1898d5eafe");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -239,7 +239,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "796f4a44a29fc3c1a1461f90aef45846");
HCTestNearbySmallIntervals(NA12878_BAM, "", "591a58f16104fbb83ccf81c97cef931a");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -249,14 +249,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("188ce2d74ee42f4187c7b41a01a193bb"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("eb79b4c0bf9142c955f0a4501e9e6d8f"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, 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("034c6b151dfde537d5843f70880bf8a4"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8bddb7f343302ed20bc549df4b82825a"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -311,7 +311,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("5430b91902813cf64f5bb781b25d76c6"));
Arrays.asList("b56895e6d28ea0b9dadeecd0ff61687e"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -320,7 +320,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("8b775d84ea981f1e8207fa69a92b5e1f"));
Arrays.asList("7b52164df8bf76d789836f990bd6066a"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -328,7 +328,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestDBSNPAnnotationWGSGraphBased() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("f6f5b7e9348fc6dccd63110de0371d78"));
Arrays.asList("096826325215f79fe70661d984ae45a4"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -337,7 +337,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("82cd0142146521fd659905737dc6192c"));
Arrays.asList("ff3b24412090ce7693d66d750ae84ac9"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -360,7 +360,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestAggressivePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("c43caebd09b69dbc9d1e4b5f5f449712"));
Arrays.asList("c2dab66ad3740320004874c83051bbfc"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@ -368,7 +368,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestConservativePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("54e7595f6d82a69566f4c0163045688d"));
Arrays.asList("a8ea15ac136042891434ccb0b3c3b686"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}
@ -397,7 +397,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("8d44a2e1967e6e844f221960d6ea42bb"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5514cfbcf12954bb12c725b77eaac248"));
spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}
@ -406,7 +406,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testMissingKeyAlternativeHaplotypesBugFix() {
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cf8912f84153b2357a4d1ddb361f786f"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6d8c32585906122a6407cb40261d00d"));
spec.disableShadowBCF();
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
}
@ -429,7 +429,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
// but please make sure that both outputs get the same variant,
// alleles all with DBSNP ids
// We test here that change in active region size does not have an effect in placement of indels.
final String md5 = "6121d05f96eca3b1dbe3a881d968b6c5";
final String md5 = "87b687b5476eb38b11db6a156b4066c8";
final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5));
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec);
final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5));
@ -483,12 +483,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "57eed4eec7b49efa1269fd8d58bde718");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "34328c475325b7dfaa57ab5920478e0c");
}
@Test
public void testHBaseCountsBySample() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "5e5d064f2bb90e05e1ab28a087d8469d");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "f5ad4e03c0faaa806ee6ae536af8a479");
}
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -88,7 +88,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("af979bcb353edda8dee2127605c71daf","3934b5de598024496a5de0ec35bde5b0")
Arrays.asList("af979bcb353edda8dee2127605c71daf","7ed46f6aa4565b5012acde17119a1a31")
);
executeTest("testTrueNegativeMV", spec);
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -151,7 +151,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
" -o %s" +
" --no_cmdline_in_header",
1,
Arrays.asList("b251b4378fda9784f2175c7e3d80f032"));
Arrays.asList("0b47205ebdf2cf752ad91ff49e82c401"));
executeTest("Do not merge unphased SNPs", spec);
}
@ -166,7 +166,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
" -o %s" +
" --no_cmdline_in_header",
1,
Arrays.asList("630816da701b9ea8674c23c91fa61bec"));
Arrays.asList("1419d9292d6e5db6282204826cb53bf7"));
executeTest("Merge SNPs if on the same read", spec);
}
@ -184,7 +184,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
" -o %s" +
" --no_cmdline_in_header",
1,
Arrays.asList("b334de5ad35665f0d65034197ac05b32"));
Arrays.asList("8a3cd58dd6b1d04ab8c699f4e328dff4"));
executeTest("Don't merge symbolic SPAN_DEL (*) alleles (into the nonexistent ** MNP).", spec);
}
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -197,7 +197,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
"3ad7f55fb3b072f373cbce0b32b66df4", // tranches
"48c21792897bdbb9adcc64886d03c5d1", // recal file
"0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF
"93a6e7ab6cbd6ae24a5b2a6f0fd29d92"); // cut VCF
@DataProvider(name = "VRBCFTest")
public Object[][] createVRBCFTest() {
@ -359,7 +359,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -tranchesFile " + privateTestDir + "VQSR.AStest.snps.tranches" +
" -recalFile " + privateTestDir + "VQSR.AStest.snps.recal";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("cd087f2824fac5fe04c6c50cbdab1fab"));
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("dbcf0cb5c2a0eb2312e6ca7d4e3aeeda"));
final List<File> outputFiles = executeTest("testApplyRecalibrationAlleleSpecificSNPmode", spec).getFirst();
setPDFsForDeletion(outputFiles);
}
@ -377,7 +377,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -tranchesFile " + privateTestDir + "VQSR.AStest.indels.tranches" +
" -recalFile " + privateTestDir + "VQSR.AStest.indels.recal";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("b0d14f1c0647f46819018cd378036024"));
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("38d4b8e89dbf8acb6a36dfa1bb55c54c"));
final List<File> outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst();
setPDFsForDeletion(outputFiles);
}

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java
View File

@ -74,7 +74,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -L 20:10,000,000-10,001,432" +
" -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
1,
Arrays.asList("3e60ca3e04fecf5d6004c08d6f7503ca"));
Arrays.asList("43fa27382e654081af69ea05bd26e281"));
executeTest("testUsingDiscoveredAF", spec);
}
@ -89,7 +89,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -L 20:10,000,000-10,001,432" +
" -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
1,
Arrays.asList("1cca249ebc2599c7f24210d4f3204049"));
Arrays.asList("d63893f530fb749505ec685a5c57ff69"));
executeTest("testMissingPriors", spec);
}
@ -103,7 +103,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -V " + validationDataLocation + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" +
" -supporting " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf",
1,
Arrays.asList("cc59ceb6dab620a353edf03ef14090f1"));
Arrays.asList("a5d7bcad5a2a194441d00eb6574b8300"));
executeTest("testInputINDELs", spec);
}
@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -V " + CEUtrioTest +
" -supporting " + CEUtrioPopPriorsTest,
1,
Arrays.asList("c7d35ce5f3675528fc484baa1c5df7b4"));
Arrays.asList("98bf63fd2ae3fa1cc42e66fa6b4f50f5"));
executeTest("testFamilyPriors", spec);
}
@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -V " + getThreeMemberNonTrioTest +
" -skipPop",
1,
Arrays.asList("c523b99da1f7e0c0ea4090b916ae7379"));
Arrays.asList("e71420099fcfc824f1cf92ff2010b69e"));
executeTest("testFamilyPriors", spec);
}

28
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
View File

@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals",
1,
Arrays.asList("f3538bcaf27f5e8b036d4c1f8734e4c2"));
Arrays.asList("787aca81ad51cd40267f92f3309fa47e"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals",
1,
Arrays.asList("32cd060d6662bdc835f70a848d48fb0e"));
Arrays.asList("d52f018643ffed072f43dfd4d33ca082"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
@Test
public void testMD5s() throws Exception {
final String cmd = baseTestString(" -L 1:69485-69791");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("82fa951ce741451267dbf30335e0f71d"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("021ec495e70044039d092ebd5ef4b82a"));
spec.disableShadowBCF();
executeTest("testMD5s", spec);
}
@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
@Test
public void testBasepairResolutionOutput() throws Exception {
final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e1bfa842d53f86d46b2166574c0c66c"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5bc938a26cd197d9b1c80cb8dfefbba"));
spec.disableShadowBCF();
executeTest("testBasepairResolutionOutput", spec);
}
@ -206,7 +206,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
@Test
public void testBreakBlocks() throws Exception {
final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("76d78f83c7db247ce12087d6118dc5df"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("31c2f26e6b172a957a3f504734df5eff"));
spec.disableShadowBCF();
executeTest("testBreakBlocks", spec);
}
@ -217,7 +217,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
1,
Arrays.asList("cb46cb8fd6506ab3e80bd50f9231643c"));
Arrays.asList("097160606e65547722a1726e031529ec"));
spec.disableShadowBCF();
executeTest("testSpanningDeletions", spec);
}
@ -228,7 +228,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.many.g.vcf",
1,
Arrays.asList("5aeb14d64b9103b62d053aeb6158e5de"));
Arrays.asList("f517c2d361defeaac245916c835811d5"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsForOneSample", spec);
}
@ -239,7 +239,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.many.haploid.g.vcf",
1,
Arrays.asList("3fca32a67922bf30f72fe066fe7159fe"));
Arrays.asList("0a8d217b2833070dcaa3bbc1e7602b1c"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsForOneSampleHaploid", spec);
}
@ -250,7 +250,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.many.tetraploid.g.vcf",
1,
Arrays.asList("6891eaaef2991d7f967c7876fd2e4f5c"));
Arrays.asList("3fd437ad1f9e18303fec517653a30b6d"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsForOneSampleTetraploid", spec);
}
@ -259,7 +259,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
public void testWrongReferenceBaseBugFix() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
+ " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("224c3d6e06f7ce4bdb55411b2e376577"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("129879954e5b453d30326f100cbc2e83"));
spec.disableShadowBCF();
executeTest("testWrongReferenceBaseBugFix",spec);
@ -268,7 +268,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
@Test
public void testBasepairResolutionInput() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3244d99e9423b45099a220f19fac516"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5b4abe639081e6bf9c8970ca8405dbe"));
spec.disableShadowBCF();
executeTest("testBasepairResolutionInput", spec);
}
@ -277,7 +277,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f6a7fa62c33de963c55262820effe44a"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@ -286,7 +286,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
public void testASMateRankSumAnnotation() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest -V "
+ privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("005bf0087480cce364c20d67aab5ad59"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("2c264ed0057c93276c647f55998c4f25"));
spec.disableShadowBCF();
executeTest("testASMateRankSumAnnotation", spec);
}
@ -295,7 +295,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
public void testASInsertSizeRankSumAnnotation() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V "
+ privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("309ddf2a8b0c431cdabec8dafa4ab3a0"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("ff5ca958e81e406cfe010d5649b5c0d1"));
spec.disableShadowBCF();
executeTest("testASInsertSizeRankSumAnnotation", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
+ " -R " + b37KGReference
+ " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
1,
Arrays.asList("11aab642395645589e48edee1fb179e2"));
Arrays.asList("0f221847e76521250de1abcba535e49c"));
cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
}

63
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -84,7 +84,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
1,
Arrays.asList("beebc536d20d69a45c6f56fbb041c9bc"));
Arrays.asList("8d9788afd0de26bd9d9e55dd0e9fc3ed"));
executeTest("testUpdatePGT", spec);
}
@ -94,7 +94,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference),
1,
Arrays.asList("527d513874a787821daf54b8fc8a33e3"));
Arrays.asList("5dd4698da963a423446bb1e183eb75aa"));
executeTest("testUpdatePGTStrandAlleleCountsBySample", spec);
File file = new File(logFileName);
@ -109,7 +109,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000", b37KGReference),
1,
Arrays.asList("24ea3dd1f13b6636cf51aea7d5a4ce06"));
Arrays.asList("d3fab0d45f0054b71aa1d031876a4bbb"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -121,7 +121,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("3708b0d993a683e8c7421f60d7123cf4"));
Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -133,7 +133,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("7d7a65ea549fcd30553766ad4333f9e2"));
Arrays.asList("b1d93f4cd93093c208be2c9842f38d12"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -145,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
1,
Arrays.asList("65497a0711a33d131a165c9cfc8bc3cf"));
Arrays.asList("c2f30f25ba4a84e38c04aa49b95694e8"));
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@ -158,7 +158,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-20,000,000", b37KGReference),
1,
Arrays.asList("70dcdc1a111ebd048d32e7e61a9b7052"));
Arrays.asList("54a86ade63b84c87ff4e537e276987fc"));
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
}
@ -170,7 +170,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
1,
Arrays.asList("f911428f0f3bfba9b1d96a6b5ace3dee"));
Arrays.asList("1a2728e7295a6ffca6c2ba5a01af3593"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}
@ -180,7 +180,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
" -V " + privateTestDir + "gvcfExample1.vcf",
1,
Arrays.asList("84ad9c6e7582dbcc693deacdeff5984a"));
Arrays.asList("9ff344a5ab87a2c3b128e435e2e86db0"));
executeTest("testJustOneSample", spec);
}
@ -191,14 +191,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V " + privateTestDir + "gvcfExample1.vcf" +
" -V " + privateTestDir + "gvcfExample2.vcf",
1,
Arrays.asList("54b76f721811c9c7958e849c40b8d4e2"));
Arrays.asList("0c07ed795562ea96eab427e63a970384"));
executeTest("testSamplesWithDifferentLs", spec);
}
@Test(enabled = true)
public void testNoPLsException() {
// Test with input files with (1) 0/0 and (2) ./.
final String md5 = "276159213ddaaf82cd0e640cc7a77fc4";
final String md5 = "2f3d71272fdac19ac861cc7159edfb08";
WalkerTestSpec spec1 = new WalkerTestSpec(
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
@ -218,7 +218,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-nda"),
1,
Arrays.asList("3c9c84b78e7d3b358c8cb7e29a2d302b"));
Arrays.asList("ce064429e6cbcaa956d52ef22e102f2f"));
executeTest("testNDA", spec);
}
@ -227,7 +227,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-maxAltAlleles 1"),
1,
Arrays.asList("87ed70b8f910b662aa67e8ed1b2ed174"));
Arrays.asList("1f1c0605fc8a500c9646132e0d7420a0"));
executeTest("testMaxAltAlleles", spec);
}
@ -236,7 +236,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
1,
Arrays.asList("1d98fb542a39090db3a8f89ae232e1e5"));
Arrays.asList("0283e784ed49bc2dce32a26137c43409"));
executeTest("testStandardConf", spec);
}
@ -259,7 +259,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference),
1,
Arrays.asList("d8eb4a64a2ae7e7dad1efc4fe8b4b3ed"));
Arrays.asList("34d76dc8dabc6a97e6d8f5365d7531e5"));
spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC
executeTest("testStrandAlleleCountsBySample", spec);
}
@ -276,7 +276,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
" --uniquifySamples", b37KGReference),
1,
Arrays.asList("1c552a9d76a1bbba4b92a94532f54a1a"));
Arrays.asList("16d7374502fa3cf99863d15d31b5ef86"));
executeTest("testUniquifiedSamples", spec);
}
@ -448,7 +448,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
}
private static final String simpleSpanningDeletionsMD5 = "85c14341171548997e4503f7b5a9253f";
private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82";
@Test(enabled = true)
public void testSpanningDeletionsMD5() {
@ -478,7 +478,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf",
1,
Arrays.asList("6c5761ffb7a0c5252f3f5048d52f500e"));
Arrays.asList("7fe5364565585d31a0bb6a9dfa4a01d4"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsMD5", spec);
}
@ -489,7 +489,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
1,
Arrays.asList("c8414446dbac9a3639bfc2f347cc2c1d"));
Arrays.asList("057f9368f380bf3c12b539a749deac61"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@ -500,7 +500,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf",
1,
Arrays.asList("d1d8c3db65905b4ef79f960f9565ca94"));
Arrays.asList("e8f5186718050fe0784416e41425563f"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@ -523,7 +523,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "ad-bug-input.vcf",
1,
Arrays.asList("a8dcb9024e3701449ec2a1fe75e0d057"));
Arrays.asList("5ed5cb6aac68aa8943dc45b8b90eb508"));
spec.disableShadowBCF();
executeTest("testBadADPropagationHaploidBugTest", spec);
}
@ -534,7 +534,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf",
1,
Arrays.asList("01a9eee63801d46de8fcf1d6f80f8359"));
Arrays.asList("37eec6aedd26aa3430a15d90d7f8a011"));
spec.disableShadowBCF();
executeTest("testSAC", spec);
}
@ -545,7 +545,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf",
1,
Arrays.asList("8c79a16f6a524d49ff402b8c0b39b396"));
Arrays.asList("76532a74d4ba49f23362c149ad31a229"));
spec.disableShadowBCF();
executeTest("testSACMultisampleTetraploid", spec);
}
@ -556,8 +556,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" +
" -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" +
" -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames),
1,
Arrays.asList("6505d305441b4e6ff975a40ef5d352b5"));
Arrays.asList("b7106be316e43ca04204b78038f65c9f"));
executeTest("testSetZeroRGQsToNoCall", spec);
}
@ -565,7 +564,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d4dd179d8a53c4a550d4a22cc9ef1aa8"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("89712a9fe5b6db16be2257be2b0b4759"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@ -574,7 +573,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testASMateRankSumAnnotation() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V "
+ privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("515771fa88b0c4bc2a40e9c233806fb1"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e41a139600ab58a67910cdc60053726"));
spec.disableShadowBCF();
executeTest("testASMateRankSumAnnotation", spec);
}
@ -583,7 +582,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testASInsertSizeRankSumAnnotation() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("c8a096f2533d06c28ec115a24ffb7ca0"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b1334fbfbf21934aac1c1eda0b5062d5"));
spec.disableShadowBCF();
executeTest("testASInsertSizeRankSumAnnotation", spec);
}
@ -596,7 +595,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations_oneSample() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("558486182a84d0a274534fc00fee326e"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("7d86260e91fe74588e01339a2064b59c"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations_oneSample", spec);
}
@ -606,7 +605,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations_elevenSamples() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "multiSamples.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("84b5723c9c8eeb5549aaceb4fd4053b5"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a889fe6775575513e84905b4fa98f8b3"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
}
@ -615,7 +614,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testMonomorphicVCwithAlt() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V "
+ privateTestDir + "monomorphicGVCwithAlt.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("ddf0a386c007b797fce3eb4ddc204216"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8bf329a40637623515972dcc0e09a49e"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@ -624,7 +623,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testFractionInformativeReads() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("70fda103f68709e32d691393e9228a9b"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b338bf1807791b23255b8cb1947c01b2"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
View File

@ -136,7 +136,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split",
1,
Arrays.asList("1158324223c312e4767fcefe9dde2fe1"));
Arrays.asList("58c09033814d41fab5da4c152eab7fa2"));
executeTest("test left alignment with hard multiple alleles", spec);
}
@ -145,7 +145,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split",
1,
Arrays.asList("923cb1d06e2d0d9a98cda8f8f637d108"));
Arrays.asList("6d22a6b78d24ee2329b91f27a91751cf"));
executeTest("test left alignment with hard multiple alleles, don't trim", spec);
}
@ -154,7 +154,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split",
1,
Arrays.asList("f7be485b0cc7b8db75b7139f31c0708d"));
Arrays.asList("0acb354a2c28e250ef2853c1e0a0fafb"));
executeTest("test left alignment of multiple alleles with genoptypes", spec);
}
@ -163,7 +163,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt-het-noref.vcf --no_cmdline_in_header -split",
1,
Arrays.asList("cd686641ab7fe491a0acc7ff07535192"));
Arrays.asList("a335913de938082061d6bbb863626ee2"));
executeTest("test left alignment of multiple alleles with genoptypes, including het-noref", spec);
}
@ -172,7 +172,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC",
1,
Arrays.asList("5da4ca9705fbb63446c1d317f7b6cae0"));
Arrays.asList("67657ee509665fd0d7a2c9024981ba92"));
executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
}
}

30
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -369,7 +369,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("ce5168e2eadee2550188892b1ea444be")
Arrays.asList("9ad02f0df308eecb0634b3cd386956e9")
);
executeTest("testKeepOriginalDP--" + testFile, spec);
@ -395,7 +395,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("cc33eb41a821d9aebdfb99d309854db0")
Arrays.asList("c78a65b41edbdd386211042e8f65220b")
);
executeTest("testNoGTs--" + testFile, spec);
@ -408,7 +408,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile,
1,
Arrays.asList("b86340de516d6c37cc3a2eeb3bfb4821")
Arrays.asList("c963ca96d543ecccab8055295d2a4dab")
);
executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
}
@ -420,7 +420,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
"-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " +
"-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile,
1,
Arrays.asList("7807bb2bf8c70963f65a97f30c8deb39")
Arrays.asList("7f5484a74ab648608228eafea96f8ad3")
);
executeTest("test multi allelic annotation ordering --" + testfile, spec);
}
@ -471,19 +471,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf";
final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates "
+ "-V " + testFile + " -o %s --no_cmdline_in_header";
WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("354cd7aa25791465d0f4c7d53b81a3a3"));
WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("21d83006b012eeea84c6612976348d3c"));
executeTest("testAlleleTrimming", spec);
}
@DataProvider(name="unusedAlleleTrimmingProvider")
public Object[][] unusedAlleleTrimmingProvider() {
return new Object[][] {
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "354cd7aa25791465d0f4c7d53b81a3a3"},
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "5e81af1825aa207b0a352f5eeb5db700"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "339cca608ff18a355abc629bca448043"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "3e8e2ebbc576ceee717a7ce80e23dd35"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "2cbf4c8c991777254145aacf19cba508"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "14538e17d5aca22c655c42e130f8cebc"}
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "21d83006b012eeea84c6612976348d3c"},
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "8fc0c8a7de6bb579e1534b936f844090"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "595392b623b0869f1d87e46edf3de122"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "bba873b8eeeb4c01199140c37deb6f6b"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "93858f706dac876a8581f6b89bb85cc5"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "5d831401367eb8b0ab49ffa34e0dd278"}
};
}
@ -655,7 +655,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("f7fe7cbc84b3f2dfadcc40e19eeeb1f9"));
Arrays.asList("c68779547b28dfef39792598df8a93e9"));
executeTest("testMendelianViolationSelection--" + testFile, spec);
}
@ -668,7 +668,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 -invMv --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("865418a69ee57be4432f248c027e6aff"));
Arrays.asList("0ac6fda76228080bdb39c0e698440718"));
executeTest("testInvertMendelianViolationSelection--" + testFile, spec);
}
@ -758,7 +758,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -trimAlternates",
1,
Arrays.asList("c9d297e7758bf5681270029401cc97c2"));
Arrays.asList("d3bb7ea37a7c9dce8b34bf2020961619"));
spec.disableShadowBCF();
executeTest("testSACSimpleDiploid", spec);
}
@ -770,7 +770,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
1,
Arrays.asList("a8c23f4d6f93806a34d432dd2c7a0449"));
Arrays.asList("67a92b4d4174ff41f6f88ddf5ab6e422"));
spec.disableShadowBCF();
executeTest("testSACDiploid", spec);
}

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
View File

@ -95,12 +95,12 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
{ // new tests on b37 using testdir VCF
final String testfile = privateTestDir + "NA12878.hg19.example1.vcf";
final String args = "-select 'DP > 30' -V " + testfile;
new ParallelSelectTestProvider(b37KGReference, args, "b899cebdd30e6641437489b746301797", nt);
new ParallelSelectTestProvider(b37KGReference, args, "64f9258e9e3024b6361abbeeeefafee9", nt);
}
{ // AD and PL decoding race condition
final String testfile = privateTestDir + "race_condition.vcf";
final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
new ParallelSelectTestProvider(b37KGReference, args, "ace613ed2e4929f448d30d85110d6ced", nt);
new ParallelSelectTestProvider(b37KGReference, args, "f289f22aacf1a5638a9fb6b32c5cf6fb", nt);
}
}

2
public/external-example/pom.xml
View File

@ -136,7 +136,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<version>2.4.3</version>
<executions>
<execution>
<phase>${gatk.shade.phase}</phase>

8
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
View File

@ -758,8 +758,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@DataProvider(name = "vcfFeaturesData")
public Object[][] getVCFFeaturesData() {
return new Object[][]{
{"--sites_only", "6ef742ee6d9bcbc7b23f928c0e8a1d0e"},
{"--bcf", "cdea454ac0af9e9228147f9c2ed1e0a6"}
{"--sites_only", "99c07e55fc44694087af6a7d4795e1be"},
{"--bcf", "b300dd7a1300c55640d9f2e42520d086"}
};
}
@ -775,8 +775,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@DataProvider(name = "vcfFormatHandlingData")
public Object[][] getVCFFormatHandlingData() {
return new Object[][]{
{true, "870f39e19ec89c8a09f7eca0f5c4bcb9"},
{false, "baf9a1755d3b4e0ed25b03233e99ca91"}
{true, "7517264dd6eb0c1ac5ca8dfd103c94fb"},
{false, "4c69e6ae1d506ba3c029de3229de407b"}
};
}

8
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
View File

@ -41,16 +41,16 @@ public class CramIntegrationTest extends WalkerTest {
return new Object[][] {
{"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name
{"PrintReads", "exampleCRAM.cram", "", "cram", ""},
{"PrintReads", "exampleCRAM.cram", "", "bam", "247805098718dd74b8a871796424d359"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "a5b26631cd89f86f6184bcac7bc9c9ca"},
{"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"},
{"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
{"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
{"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
{"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "24dbd14b60220461f47ec5517962cb7f"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"},
{"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
{"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
{"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "84bee5063d8fa0d07e7c3ff7e825ae3a"},
{"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"},
{"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
{"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
};

2
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
View File

@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest {
File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath())); // Bypass MD5 check since the CRAM header stores the file name
spec.addAuxFile("ebbe6e311b6bb240554ec96ed9809216", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
spec.addAuxFile("4bd9185ce1c7d2e97e8c131b77f76aef", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
executeTest("testMultipleIntervalInclusionOnCRAM", spec);
}

10
public/gatk-root/pom.xml
View File

@ -24,8 +24,8 @@
<sourceEncoding>UTF-8</sourceEncoding>
<project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
<project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.committests.skipped>true</gatk.committests.skipped>
@ -44,8 +44,8 @@
<test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
<!-- Version numbers for picard and htsjdk -->
<htsjdk.version>2.0.0</htsjdk.version>
<picard.version>2.0.0</picard.version>
<htsjdk.version>2.3.0</htsjdk.version>
<picard.version>2.3.0</picard.version>
</properties>
<!-- Dependency configuration (versions, etc.) -->
@ -373,7 +373,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<version>2.4.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
View File

@ -66,7 +66,7 @@ public class PrintReadsIntegrationTest extends WalkerTest {
// See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "e9caf8a0e6ec947cdcbdfc48a4292eb5")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
{new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")},

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java
View File

@ -55,7 +55,7 @@ public class VCFIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testReadingAndWritingWitHNoChanges() {
String md5ofInputVCF = "3dc9ac85f2c0541df9bc57b4d81f480b";
String md5ofInputVCF = "a492a97a8d18ace8eeef02a6fe5f179b";
String testVCF = privateTestDir + "vcf4.1.example.vcf";
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

4
public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
View File

@ -80,9 +80,9 @@
<dependency>
<groupId>com.sun</groupId>
<artifactId>tools</artifactId>
<version>1.5.0</version>
<version>1.8.0</version>
<scope>system</scope>
<systemPath>${toolsjar}</systemPath>
<systemPath>${java.home}/lib/tools.jar</systemPath>
</dependency>
</dependencies>