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Move htsjdk & picard to rev 1.138

This commit is contained in:
Ron Levine 2015-08-12 17:48:57 -04:00
parent cd9db60ce2
commit beec624a63
63 changed files with 739 additions and 422 deletions
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8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
View File

@ -457,6 +457,14 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
return sb.toString();
}
}
/**
* Check the return from PrintStream.checkError() if underlying stream for a java.io.PrintStream
* @return false, no error since the underlying stream is not a java.io.PrintStream
*/
public boolean checkError(){
return false;
}
}

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java
View File

@ -341,4 +341,12 @@ public class GVCFWriter implements VariantContextWriter {
}
}
}
/**
* Check the return from PrintStream.checkError() if underlying stream is a java.io.PrintStream
* @return false, no error since the underlying stream is not a java.io.PrintStream
*/
public boolean checkError(){
return false;
}
}

58
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -84,7 +84,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("360610e4990860bb5c45249b8ac31e5b"));
Arrays.asList("b65bf866457f000926b76d0f9d40065e"));
executeTest("test file has annotations, not asking for annotations, #1", spec);
}
@ -92,7 +92,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --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("d69a3c92a0e8f44e09e7377e3eaed4e8"));
Arrays.asList("8e830da0bf34f1dc91bbc2fa64b8a518"));
executeTest("test file has annotations, not asking for annotations, #2", spec);
}
@ -100,7 +100,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("92eb47332dd9d7ee7fbe3120dc39c594"));
Arrays.asList("b829d22c62af2d77d595fbd246f5e6e9"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -108,7 +108,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--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("c367bf7cebd7b26305f8d4736788aec8"));
Arrays.asList("fde5bc227b3bd9a98b04d730ea8d8c2a"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -116,7 +116,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("540a9be8a8cb85b0f675fea1184bf78c"));
Arrays.asList("58793dec36f8aec2cd8894898ece7c4e"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
}
@ -126,7 +126,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
// they don't get reordered. It's a good test of the genotype ordering system.
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --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("f900e65b65ff0f9d9eb0891ef9b28c73"));
Arrays.asList("27745920cc780b04e8f5acba79f868ca"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
}
@ -134,7 +134,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("098dcad8d90d90391755a0191c9db59c"));
Arrays.asList("8af6faa01040e1d2ab57508ca4918657"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -142,7 +142,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--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("f3bbfbc179d2e1bae49890f1e9dfde34"));
Arrays.asList("5150f3d9ee092c734a7eba48fc7f1093"));
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() + standardAnnotations + "-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("7267450fc4d002f75a24ca17278e0950"));
Arrays.asList("d27f142e8d0fe64ca835a187603d4fd4"));
executeTest("test exclude annotations", spec);
}
@ -159,7 +159,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
String logFileName = new String("testAskingStrandAlleleCountsBySample.log");
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A StrandAlleleCountsBySample -log " + logFileName, 1,
Arrays.asList("0c0c4a219cb487598fb1fbb77db71eca"));
Arrays.asList("5c0fe344544a887acbb5cd83083d303b"));
executeTest("test file has annotations, adding StrandAlleleCountsBySample annotation", spec);
File file = new File(logFileName);
@ -170,7 +170,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testAskingGCContent() throws IOException{
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A GCContent", 1,
Arrays.asList("02f634fd978cf2a66738704581508569"));
Arrays.asList("82238b65dbd085baaec68be2975a9bf8"));
final File outputVCF = executeTest("test file has annotations, adding GCContent annotation", spec).getFirst().get(0);
final VCFCodec codec = new VCFCodec();
final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(outputVCF)));
@ -183,7 +183,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("18592c72d83ee84e1326acb999518c38"));
Arrays.asList("529d4a26cbabd0aa6a8b7b0dd7f45e15"));
executeTest("test overwriting header", spec);
}
@ -191,7 +191,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("6de950b381d2d92b21bab6144e8f0714"));
Arrays.asList("9a812a06362f17236bcc12d645875412"));
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 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("e0bd85747c87ea4df6ef67f593cbacbf"));
Arrays.asList("b68063c46b31bb8385bd0c92e8dbb325"));
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 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
Arrays.asList("194a942f17104292192fb564a3c96610"));
Arrays.asList("6808044cdd61c8eb868f598aee0e70e6"));
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" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("9e41ae733a76632b40eda38e3cef909d"));
Arrays.asList("aab4e2ff3b020a1dca927106e5b1582d"));
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 " + standardAnnotations + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("7b718bae0444f1896a6e86da80531218"));
Arrays.asList("80fe2973648b96b94ce1a58f2f217264"));
executeTest("getting DB tag with 2 comps", spec);
}
@ -231,7 +231,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoQuals() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
Arrays.asList("aea983adc01cd059193538cc30adc17d"));
Arrays.asList("b6321f3ce7a60d083be64d5ec9a54c1b"));
executeTest("test file doesn't have QUALs", spec);
}
@ -239,7 +239,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("0bed7b4f6ed0556c5e7d398353a9fa91"));
Arrays.asList("f01aee4b224520ca38f618f59e9f5343"));
executeTest("using expression", spec);
}
@ -247,7 +247,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionMultiAllele() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
Arrays.asList("195cf0f5b1aa5c7d00a0595dcca02f4c"));
Arrays.asList("c2f705658ef680b121568db0414c2c78"));
executeTest("using expression with multi-alleles", spec);
}
@ -255,13 +255,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testUsingExpressionWithID() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
Arrays.asList("b3fe9d3bdb18ca2629543f849a7d27ed"));
Arrays.asList("014f7e1e5b59429d12241b92c7b9e06f"));
executeTest("using expression with ID", spec);
}
@Test
public void testTabixAnnotationsAndParallelism() {
final String MD5 = "99938d1e197b8f10c408cac490a00a62";
final String MD5 = "c5beea399dadbba66a7fc46036eeafe5";
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
@ -283,7 +283,7 @@ 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("d9291845ce5a8576898d293a829a05b7")
Arrays.asList("6618f3ae9dc6d4ce6ebd4eb8f9495103")
);
executeTest("Testing SnpEff annotations", spec);
}
@ -296,7 +296,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
"--snpEffFile " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " +
"-L 1:10001292-10012424",
1,
Arrays.asList("7352cf23a4d45d3d2bb34ab44a4100ae")
Arrays.asList("7533645a3791ce30d7407f789e1ffbb0")
);
executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec);
}
@ -309,14 +309,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
"--snpEffFile " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " +
"-L 1:10001292-10012424",
1,
Arrays.asList("87cbf53c65ef4498b721f901f87f0161")
Arrays.asList("0e201a91a2b2b130debcd5dd7d9328ab")
);
executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec);
}
@Test(enabled = true)
public void testTDTAnnotation() {
final String MD5 = "427dfdc665359b67eff210f909ebf8a2";
final String MD5 = "9532ca341b52be650b35e32d7c765030";
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,
@ -327,7 +327,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testChromosomeCountsPed() {
final String MD5 = "6b5cbedf4a8b3385edf128d81c8a46f2";
final String MD5 = "4ab0b4245ba2c5c62424775879f51379";
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,
@ -337,7 +337,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testInbreedingCoeffPed() {
final String MD5 = "159a771c1deaeffb786097e106943893";
final String MD5 = "914e6882f01bae43f1d6ba1b0023cf91";
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,
@ -347,7 +347,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testAlleleTrimming() {
final String MD5 = "5f4b8dcbd4ec3b773486945e5b38e7f3";
final String MD5 = "90f9ee6c34c0820435dce7a0d63b4c1e";
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" +

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -196,12 +196,12 @@ public class BQSRIntegrationTest extends WalkerTest {
public Object[][] createPRTestData() {
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{1, new PRTest(" -qq -1", "ce09e16466151bb37305dbfd5dc88f35")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "2d12f3d48b1797ea0671e28a435527fe")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "f3dbf3ae2725f1e7aa8ae61a09beac51")});
tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, new PRTest("", "0746ae12c106a8af0b3b01f22e9efcba")});
tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")});
}
return tests.toArray(new Object[][]{});

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
View File

@ -71,11 +71,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testSingleSample() {
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "5cad1b8e3bf5582842bbeadbc173e8aa");
DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "13bfe41ef083d2716e07d35223916a4e");
}
@Test(enabled = true)
public void testMultiSample() {
DTTest("testMultiSample ", "-I " + multiSample, "c2a11ad34104fd5e4e65bdf049abe5e7");
DTTest("testMultiSample ", "-I " + multiSample, "64b4fa6cf4c4d16e822289990ee88240");
}
}

42
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -68,7 +68,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("a890cd298298e22bc04a2e5a20b71170"));
Arrays.asList("42a73683f2064a73d4b21a06c208205b"));
executeTest("test no action", spec);
}
@ -76,7 +76,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("f46b2fe2dbe6a423b5cfb10d74a4966d"));
Arrays.asList("5e5c03487b0b89169dafad327d8afd4a"));
executeTest("test clustered SNPs", spec);
}
@ -84,7 +84,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMask1() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask " + privateTestDir + "vcfexample2.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("86dbbf62a0623b2dc5e8969c26d8cb28"));
Arrays.asList("a286b5919ff373f454d24374a115c696"));
executeTest("test mask all", spec1);
}
@ -92,7 +92,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMask2() {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -maskName foo --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("2fb33fccda1eafeea7a2f8f9219baa39"));
Arrays.asList("c05349a096f6c4919ed24b293f40ffa8"));
executeTest("test mask some", spec2);
}
@ -100,7 +100,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMask3() {
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + privateTestDir + "vcfMask.vcf --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4351e00bd9d821e37cded5a86100c973"));
Arrays.asList("e45e4a287072cb6d4ec7596344fd0579"));
executeTest("test mask extend", spec3);
}
@ -108,7 +108,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMaskReversed() {
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -maskName outsideGoodSites -filterNotInMask --mask:BED " + privateTestDir + "goodMask.bed --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e65d27c13953fc3a77dcad27a4357786"));
Arrays.asList("35428e4348a11abc260a1d40049bdefd"));
executeTest("test filter sites not in mask", spec3);
}
@ -124,7 +124,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("2f056b50a41c8e6ba7645ff4c777966d"));
Arrays.asList("d7a9a49ed19bc0452595c293915a1480"));
executeTest("test filter #1", spec);
}
@ -132,7 +132,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b2a8c1a5d99505be79c03120e9d75f2f"));
Arrays.asList("0c0fddb0eb6f9d3f74556332cd498079"));
executeTest("test filter #2", spec);
}
@ -140,7 +140,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e350d9789bbdf334c1677506590d0798"));
Arrays.asList("45f90fd349d76b386fce4b9075d16b7e"));
executeTest("test filter with separate names #2", spec);
}
@ -148,7 +148,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testInvertFilter() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000 --invertFilterExpression", 1,
Arrays.asList("d478fd6bcf0884133fe2a47adf4cd765"));
Arrays.asList("c88c845108a26bebfeb09c420671c06f"));
executeTest("test inversion of selection of filter with separate names #2", spec);
}
@ -156,7 +156,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testInvertJexlFilter() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance >= 0.7' --filterName FSF -filter 'FisherStrand != 1.4' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("6fa6cd89bfc8b6b4dfc3da25eb36d08b")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
Arrays.asList("f5e03e4584f9b1d82f9d430543f06bd6")); // Differs from testInvertFilter() because their VCF header FILTER description uses the -filter argument. Their filter statuses are identical.
executeTest("test inversion of selection of filter via JEXL with separate names #2", spec);
}
@ -164,7 +164,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters1() {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("060e9e7b6faf8b2f7b3291594eb6b39c"));
Arrays.asList("ced70cfb4e6681a3aa0633cd0510ada0"));
executeTest("test genotype filter #1", spec1);
}
@ -172,7 +172,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilters2() {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("00f90028a8c0d56772c47f039816b585"));
Arrays.asList("837b6a3ce3fad3bd77ec3e870c4d2f10"));
executeTest("test genotype filter #2", spec2);
}
@ -180,7 +180,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testDeletions() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + privateTestDir + "twoDeletions.vcf", 1,
Arrays.asList("8077eb3bab5ff98f12085eb04176fdc9"));
Arrays.asList("32ed1e11fde63a57c1dfb7f83f5344f0"));
executeTest("test deletions", spec);
}
@ -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("8ed32a2272bab8043a255362335395ef"));
Arrays.asList("0febd66699fcd7f521377d1d0d0016fb"));
executeTest("testUnfilteredBecomesFilteredAndPass", spec);
}
@ -198,7 +198,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
Arrays.asList("a01f7cce53ea556c9741aa60b6124c41"));
Arrays.asList("c3eff7d167e1bfca5726a6e475e6b3ec"));
executeTest("testFilteringDPfromINFO", spec);
}
@ -207,7 +207,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
Arrays.asList("e10485c7c33d9211d0c1294fd7858476"));
Arrays.asList("260dd9d7e35737fe695b241b7a5a52a2"));
executeTest("testFilteringDPfromFORMAT", spec);
}
@ -216,7 +216,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf --invertGenotypeFilterExpression", 1,
Arrays.asList("d2664870e7145eb73a2295766482c823"));
Arrays.asList("907527b89d3f819cc3f6f88f51fcaaf6"));
executeTest("testInvertGenotypeFilterExpression", spec);
}
@ -225,7 +225,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --genotypeFilterExpression 'DP >= 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
Arrays.asList("8ddd8f3b5ee351c4ab79cb186b1d45ba")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
Arrays.asList("d79b2e5a7502a6d6e902bc40d74cc826")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
executeTest("testInvertJexlGenotypeFilterExpression", spec);
}
@ -234,7 +234,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf --setFilteredGtToNocall", 1,
Arrays.asList("9ff801dd726eb4fc562b278ccc6854b1"));
Arrays.asList("454d265ee8b425284ed7fca8ca4774be"));
executeTest("testSetFilteredGtoNocall", spec);
}
@ -245,7 +245,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("81b99386a64a8f2b857a7ef2bca5856e")
Arrays.asList("7771f07a9997296852ab367fac2c7a6c")
);
spec.disableShadowBCF();

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

@ -70,7 +70,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
for ( final int nt : Arrays.asList(1, 2) )
for ( final int nct : Arrays.asList(1, 2) ) {
tests.add(new Object[]{ "BOTH", "18418ddc2bdbe20c38ece6dd18535be7", nt, nct });
tests.add(new Object[]{ "BOTH", "52f590f6b37a1b3b12042ae917738965", nt, nct });
}
return tests.toArray(new Object[][]{});

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

@ -69,21 +69,21 @@ 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", "fa4f5e31d1f45193aa3a9b2a9a931ffd");
executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "f3ded70733e9bf52bbd368e3850ea992");
}
@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", "972c8db4b1cc971bd714fd9c1a72b65a");
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", "ba1412a226b7261b1430d1a2ad3ab5e2");
}
@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", "8096ec08219205af56bd4ea762412f7c");
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", "05834d7716eba5846aa6cbb51d4cd892");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "6007e0735aa5a680da92396345824077");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "4488717e2ab49bfc83abd6c49d3b1a08");
}
}

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","fdcdfbed14fb7d703cd991ee7d2821a6");
executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","984c5d3252b6efc82f87a51fafee2a83");
}
@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","7d533bea2ad3a151a1ec80e658e5756b");
executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7ef8e488a8125126a3411df7d3f6167a");
}
@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", "39ce89507ceb66ee7ae99ed68d50042d");
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", "b18e9c44b3c834d1ca8bf03951cf0c33");
}
}

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("8e0ba82e36df60fd0122818d0227041b"));
Arrays.asList("1d8b3a95f31364f8a88590b90e085558"));
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("02ed507c8c1d289b6c0092899b1b839e"));
Arrays.asList("f71ee7c0757b1c1fcf9390b2fbfc12ae"));
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("2b87723c03c46987dc3ee6d82f893c23"));
Arrays.asList("b75617d7557dd2b67fd8d74ed53b31ff"));
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("1bd415ee64fa01039e7b623fbd2ae838"));
Arrays.asList("e626454b67d56380b288671e57844616"));
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("4833c9b471cab8ce5bc5747f8cb1548d"));
Arrays.asList("1c66d5c77701f36182ead88a0bc8bed7"));
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("781d305993aedcc1a4c199a5c63ac54c"));
Arrays.asList("ed618b3c82e86cdf80f4865d838a7aaa"));
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("0bc38748e786259e7fd4e199ccdd7287"));
Arrays.asList("088ebba243dada6453bb8a9398e4ad24"));
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("0313e91607166767b7f1b1d6fcdf9263"));
Arrays.asList("9eaa295625e025099ce3b235590f7b6a"));
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("003243a8cc024cb297f86cc84de91be5"));
Arrays.asList("a6c3f664391f0f4a6e8afb3dfa68e871"));
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("d9fcd63e9eed692850eb49e124176648"));
Arrays.asList("acf4f7a8ebfaee05fc229340d1a3be7c"));
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("49821450356b4b398f3bcb688e13af36"));
Arrays.asList("1d1cd231a2eee6338bd3a320b01bac3c"));
executeTest("test minIndelFraction 1.0", spec);
}

34
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("a36d082235ad30bd343f6c0538b32d0b"));
Arrays.asList("24e3de56a64cf50e1ce159c640d2a914"));
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("4b80c1ef04831113f1911bf4a33a2931"));
Arrays.asList("500036226dd2dfb3593b8c203d818e28"));
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("c5a649ae11f5e45817d9877a97e0195d"));
Arrays.asList("f04503b889f4510023f00082afe65079"));
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("55c9e4ec4d1795b395b70bafc423c243"));
Arrays.asList("7c9a4c9283185d6d0e5263040cd04527"));
executeTest("test using comp track", spec);
}
@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "fc1d87645f2dc5e7a9355753df6e6acb");
testOutputParameters("-sites_only", "433df49e8ba3bfa3b32ff165b717ab51");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "406f48975e5232df4444416c2a570225");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "5628f9829474896fcc3a743d92f8300f");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "0899ffd439d9f4f61aad574f4a74b3de");
testOutputParameters("--output_mode EMIT_ALL_SITES", "4371fd83cc4904d60b943a7777e8e292");
}
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("6039ce16c722d9b133a1f76534c98a69"));
Arrays.asList("a1d212a5d23400f29517a4f25bff2fe2"));
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("ef478aae219a84a8a81b9c65fc24b67a"));
Arrays.asList("32b02c0315248dd69f19000f0a9687bb"));
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("ba1531d124436d2522c0a6335f57813b"));
Arrays.asList("5b6576518c62fab480252311dae8e716"));
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("38588b2aea153ae4a087a0804ada1e95"));
Arrays.asList("c9074a9ea9aa1ec42fc71cc1bc6b589f"));
// 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, "a89a1805344f71f299a50103a25d2117" );
testHeterozosity( 0.01, "c7f8684e4cb3175f274f91f80573d910" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "8fbf7fd8685e34f37d7c8e08d673a471" );
testHeterozosity( 1.0 / 1850, "1f067c6442dbccf5c341ea1a41e9d28b" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -238,7 +238,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "1f3fad09a63269c36e871e7ee04ebfaa";
String md5 = "398d3ad38834fea8961ab6f46a21dc4b";
final String myCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("051810b8e584a8c4718ea4d95551c768"));
Arrays.asList("ac54cc421a4c8a441179cd85653715a7"));
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("7b90d6ff043bf9fafbbb80a451261cdc"));
Arrays.asList("f561ce9ab992c99caea934fa7d649ee6"));
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("037ce3364668ee6527fba80c4f4bff95"));
Arrays.asList("42c2d98ed221b30b6a8986ce65b13066"));
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("b43bf9147e30cc68068a91a5e8405767"));
Arrays.asList("b0eee799738d0ffa007a368fb30d3f35"));
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("ce804ffdc146414f354bc9040ffffa87"));
Arrays.asList("3a080b1364f4daa1384a2be5aa445516"));
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("5d9bc104f1507433944176b58d75bbcf"));
Arrays.asList("96072b797cc1f9c5e728fa79127ba2fa"));
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("a4c7464ff35e5ca7291935abc71f0614"));
Arrays.asList("16341ab632b503f79cd14678aee76106"));
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("837847b512c8f60d7c572dd6a80239d8"));
Arrays.asList("fafb5e1fd44f51c523eb3650e8e79a76"));
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("2b3056f62f2da84c318e8809d8b3dd1a"));
Arrays.asList("26379bbc6b8d37800c35896299845c10"));
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("0fc44ff26d3f913e7012b000a4de9682"));
Arrays.asList("9ef30185c2ae2a4c7180cc500cc3b97c"));
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("0dba3bc42c0eb43fea205d528739e9da"));
Arrays.asList("a22ad5f0b5e4734f7ac441d09cbbffa1"));
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", "", "070729585401dda47838911928ffbd2f");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "b57861e1945f81b7f6a11f23243efbb3");
}
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, "", "2bddd2bf5427142bf2235daa8589efee");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "327b8a6d9ab5b92c036651cbf3192940");
}
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",
"64421f715e0258defc9efcfef56bdaab");
"0329146d969340fbfdd0182273837324");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"d2306f6ecfcee9340423ba251e0736a3");
"3af98489eeafc4379c8bcc409cb87d36");
}
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",
"22c4135a87be18940ff622ea7ff9cabc");
"a2b0fa398422df24f5e24b66da98226b");
}
}

52
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -75,12 +75,12 @@ 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, "3e440b1b755a21d7bd3ecb093af8f43e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ebe078a1e209a5b231aeeba6deebcb8a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "2ad9b5d87416c466292c2b97480e1f5c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ca1e6cb78157273a4a96ba00e6d4713"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8645c191ca5dbbae8dcb1389717f985a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "9606db453f9e8beae27669afcea288a1"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "468b2b827297422033ccd85050ac119f"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8f31fb899458aad4d8809e98c1b19e9c"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4f19785171b41fd01327f95af2d0385b"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "44be8f4f74a73632f2805efa6a8608e4"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "5a986c2c4f2f9b3bc1cb7bead4794d85"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cbe35a80d1988ab9693d6d32996a34ed"});
return tests.toArray(new Object[][]{});
}
@ -94,13 +94,13 @@ 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, "92c7415dd1a5793161032d839b88fc28"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b90d7c900ff4a8b5e58d6bd4ad64d750"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "8a1dcc091cb28e1fbbc86a1de85dfd4c"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "7e84e4562d8df6e593e58f017f697355"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "307ce5ada7c68e2f08664937bafa6281"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "20f149f41438c6cc64af829cb5cd6eb6"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "381e3fed6b1826047cda2ea990b7e41f"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1d5f6804e07590850601a515c821548a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "d2b86f9be8dde27038a964cb4b87d99f"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "75d10db3eb4a65037c652830f5865dcf"});
final String NA12878bandedResolutionMD5 = "d51df38ad52cf2b0ecbce362e60fb24e";
final String NA12878bandedResolutionMD5 = "b536f1e09d92d501fa6e891dbcafbad2";
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});
@ -117,12 +117,12 @@ 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, "f441aab92b07591281fa44748b7bd71e"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d54d7988552a13de90977ba06b094b74"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c3c12414059390f3d6e3e533502c1869"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "91164cf1247f5b187ad133b280aa1fd2"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b5c1b79550a8d8bb479895e2be38d945"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "79e913ab2ddf19b3cae75f2da9394239"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c9a85dd80f745d6433fff2c139c7158a"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "402fcd74bd6a880f7dd5b6b5acda6a33"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "ec2b1af010ba6c8e84aaa694adbee326"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1e58a154bb5f390d5a63a42955ac94da"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b998e52a00d97ad27fb196a211205009"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "f9fdc0054819f69df30e00268d926318"});
return tests.toArray(new Object[][]{});
}
@ -135,12 +135,12 @@ 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, "081d943a092b7ad71d1f1fa6ec191ace"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "93f95c7a51741f8e527f1308ffd91052"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1f2e5b5c06cb6d1196315c4308421f6d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3d8f4f849df0b9cddb1ec61279e91a83"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1fbe1435b860400ecae3115141453c9a"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "fe9e1992cc28b798dd3ee66aaba726aa"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c29c62be67c4a39a37a3bd1b4ca56c1d"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f969ca63fbb736ef0ef3a39bf9d5b48d"});
tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0272c2c5aae6aa8197711f450e604bbc"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "9ced0d30ddcabff1af2083a0fa944d9d"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "465b9ec2bfaca04adfd7abd54205a16f"});
tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "4e70638705b65c91a0a86771ec13ef74"});
return tests.toArray(new Object[][]{});
}
@ -266,7 +266,7 @@ 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("7fa0578150ea8ef333cb141f78cf4a5a"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e2de7ac5456a14122eaa910e6b3c4cc9"));
spec.disableShadowBCF();
executeTest("testMissingGVCFIndexingStrategyException", spec);
}
@ -283,7 +283,7 @@ 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("befa4bf150099b3faf44130a6c9cdbb9"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c8d5b833fa79da1270b7fe64ebea0763"));
spec.disableShadowBCF();
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
}

62
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -96,87 +96,87 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "", "e8a73b950d027239b780757d898c7334");
HCTest(CEUTRIO_BAM, "", "dd7580015e546e7311cfaa15ca1b3afc");
}
@Test
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "c741efeb6f3e412c4e707da3cabee621");
HCTest(NA12878_BAM, "", "6f3f96081b5e6c8489cc051269aacb9c");
}
@Test
public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-ploidy 1", "5bfcfdea258a3dafa04a99dd2b000c87");
HCTest(CEUTRIO_BAM, "-ploidy 1", "0036eaa05a1ac38764ad5445bf8b23cc");
}
@Test
public void testHaplotypeCallerSingleSampleHaploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 1", "304d2ade384406342655fdfd445576a3");
HCTest(NA12878_BAM, "-ploidy 1", "e751950efc7713d2ba64ad4316a74903");
}
@Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
HCTest(NA12878_BAM, "-ploidy 4", "139e0d3bbea7903f66941053f2b1a2fd");
}
@Test
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "c741efeb6f3e412c4e707da3cabee621");
HCTest(NA12878_BAM, "-mbq 15", "6f3f96081b5e6c8489cc051269aacb9c");
}
@Test
public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "304d2ade384406342655fdfd445576a3");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "e751950efc7713d2ba64ad4316a74903");
}
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "139e0d3bbea7903f66941053f2b1a2fd");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ffd2363d2f7afd694b8e9b23c51b0cea");
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "c0b7d3a147491445cbe7f2aef910d7f7");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "ab1630552bcc0a46431b3f6b7bd50bb5");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "6d4700884f9cbb1d65196d299370e056");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "31a21023efaf6f030478e5542ec652fe");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ea5ff9d7729147d63f7a99001cea7e43");
}
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "1c91ca0c8c04cbce1ace3e9884efd458");
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "7b303fcf907e4df7a3087778e2ccabeb");
}
@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,
"2944a830504b4e0b87bb8babc8ea39ae");
"b245ec43915c87a10ba081ed51bd34fa");
}
@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",
"b4da788ff173453d915a807149d9ab5d");
"612a8fcddd2cda58184d9a58a150af67");
}
@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",
"7a3a8a81c3f984d74e6e3e35f5e62aa3");
"5f12e02d06fdf7f4beee6ccdbe77f466");
}
@Test
public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException {
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e578f65ab2be60f31ee8395845607a");
HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "3f7d15c097d51c47c1d99927e4b8c7db");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -187,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "60df4797f86c1454c0eb76c5eaf2ad38");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a39b12f33f4b5f877195ff0c86eb6d3e");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -224,7 +224,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "7af25494bf2b05cc838ebf7055407c30");
HCTestNearbySmallIntervals(NA12878_BAM, "", "3145d5c494f19c8d56dcf93b9fe34d06");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -234,14 +234,14 @@ 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("3f01b3be2004f784a0fddc9e63aeba2a"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c6775f54873d9c37703f371caf7c6c9e"));
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("1ca9a141cb65c6070a93d5a2c55a9b3b"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2e389120877dc0770924441915d6e9e4"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -281,7 +281,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testLeftAlignmentBamOutBugFix() {
final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
+ " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c19f0e62f90794661f5927c360d50998"));
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c1840293b4565ce1cef393c6a0d5fc9a"));
executeTest("LeftAlignmentBamOutBugFix", spec);
}
@ -296,7 +296,7 @@ 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("e894e9f50112edad270f36f78e76a8e3"));
Arrays.asList("115d973436460efb99df2bf5de6a1e8d"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -305,7 +305,7 @@ 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("9e384f2bd2eb7a6d5ee1685ab5e75501"));
Arrays.asList("1282faeeb89a4cb9d0d04cb24669a1c8"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -313,7 +313,7 @@ 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("801a3af44153deee939370dcaaa110ab"));
Arrays.asList("445e4be6c21dadd81f68122a74704f86"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -322,7 +322,7 @@ 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("efac9fd7e7a92e3f130e7db9cbff4a45"));
Arrays.asList("418b054ed991c0ecd9ffd1c980a6c7dc"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@ -345,7 +345,7 @@ 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("c851be534595a2547a8ebf81f1b923d1"));
Arrays.asList("9ef202d2e6f9732b629f1876eb6395a0"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@ -353,7 +353,7 @@ 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("95a3f339a15b1398cfc9f9e933999ea9"));
Arrays.asList("c806855db1c464d2b6d3dd6a9b5ac152"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}
@ -373,7 +373,7 @@ 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("e6bc4d979ae90c35809a2030ad709b5e"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("ec9b548570fab2f9e9333e8639b463c1"));
spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}
@ -382,7 +382,7 @@ 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("e8ef8b17a7561dd056805c15baec285e"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("8c186ae7a94212aa186fb1f663b5e9e9"));
spec.disableShadowBCF();
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
}
@ -405,7 +405,7 @@ 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 = "df27ceb13e6cda2c97cacd23608c2f7f";
final String md5 = "ccdca73deac943ca9792a057b4359b54";
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));
@ -459,7 +459,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "1003c8c13efef8f4f439151460ccc32a");
}
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
View File

@ -69,7 +69,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
List<Object[]> tests = new ArrayList<>();
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, "8bcf149228e8845915733d6fd889a141"});
tests.add(new Object[]{nct, "07f969acede5e0ad7e1e94f4383af2a9"});
}
return tests.toArray(new Object[][]{});

14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -66,8 +66,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "458588d68c8ea7e54443ea722604b265";
private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4";
private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364";
@Test
public void testDefaults() {
@ -90,7 +90,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
1,
Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30"));
executeTest("realigner known indels only from VCF", spec1);
}
@ -107,7 +107,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put("-LOD 60", base_md5);
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "dea9bd14323b33348d9cf28e256415f2" );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "0c4597e48b4e194de32ebe494704ea6b" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -123,7 +123,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
1,
Arrays.asList("b91c0bf803247f703dc1cb6ccdc4f18f"));
Arrays.asList("19e6859b9ef09c7e0a79a19626908b17"));
executeTest("realigner long run", spec);
}
@ -132,7 +132,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
1,
Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
Arrays.asList("8f5684359d7b26acaacfa657ef395a0c"));
executeTest("realigner no output tags", spec);
}
@ -154,7 +154,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>();
e.put("--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11");
e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378");
e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) {

14
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","1ea9994f937012e8de599ec7bcd62a0e")
Arrays.asList("af979bcb353edda8dee2127605c71daf","3934b5de598024496a5de0ec35bde5b0")
);
executeTest("testTrueNegativeMV", spec);
}
@ -107,7 +107,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","547fdfef393f3045a96d245ef6af8acb")
Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","3260c4f7fda274aeb081744718cca829")
);
executeTest("testTruePositiveMV", spec);
}
@ -126,7 +126,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","9529e2bf214d72e792d93fbea22a3b91")
Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","14158702ed830ae022db69cbce83b3ed")
);
executeTest("testFalsePositiveMV", spec);
}
@ -145,7 +145,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("590ee56e745984296f73e4277277eac7","8c157d79dd00063d2932f0d2b96f53d8")
Arrays.asList("590ee56e745984296f73e4277277eac7","a0940a778e2e3b5454f99a54b40820ce")
);
executeTest("testSpecialCases", spec);
}
@ -167,7 +167,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","343e418850ae4a687ebef2acd55fcb07")
Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","3a45b5179dc32cb68f500ff78ef966a6")
);
executeTest("testPriorOption", spec);
}
@ -187,7 +187,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("9529e2bf214d72e792d93fbea22a3b91")
Arrays.asList("14158702ed830ae022db69cbce83b3ed")
);
executeTest("testMVFileOption", spec);
}
@ -208,7 +208,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-fatherAlleleFirst"
),
2,
Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","52ffa82428e63ade22ea37b72ae58492")
Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","c534df2b637d07bed96e3cd644b31554")
);
executeTest("testFatherAlleleFirst", spec);
}

16
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -77,7 +77,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:332341-382503",
1,
Arrays.asList("1bb034bd54421fe4884e3142ed92d47e"));
Arrays.asList("fd9810d1984fce38a78683124b6be933"));
executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
}
@ -87,7 +87,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:1232503-1332503",
1,
Arrays.asList("c12954252d4c8659b5ecf7517b277496"));
Arrays.asList("27c0e81c71f599685f6bdc433652645d"));
executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
}
@ -97,7 +97,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
+ " -L chr20:332341-382503",
1,
Arrays.asList("0b945e30504d04e9c6fa659ca5c25ed5"));
Arrays.asList("ca2556135efef75f04a0692afbce85bd"));
executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
}
@ -107,7 +107,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
+ " -L chr20:332341-382503",
1,
Arrays.asList("e9e8ef92d694ca71f29737fba26282f5"));
Arrays.asList("46507837790c71b4f8cba4f1551987a7"));
executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
}
@ -117,7 +117,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
+ " -L chr20:332341-482503",
1,
Arrays.asList("b9c9347c760a06db635952bf4920fb48"));
Arrays.asList("30a61a4853b1df1b6afb0a42fb01ca00"));
executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
}
@ -127,7 +127,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:652810-681757",
1,
Arrays.asList("02c3a903842aa035ae379f16bc3d64ae"));
Arrays.asList("acfcca2d271c3403dc42a16e0494f11b"));
executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
}
@ -137,7 +137,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
+ " -L chr20:332341-802503",
1,
Arrays.asList("ac41d1aa9c9a67c07d894f485c29c574"));
Arrays.asList("504e9af1f767db3d9da9bb6665daabcb"));
executeTest("Use trio-phased VCF, adding read-backed phasing information in HP tag (as is now standard for RBP) [TEST SEVEN]", spec);
}
@ -152,7 +152,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
" -o %s" +
" --no_cmdline_in_header",
1,
Arrays.asList("59ee67d657ee955477bca94d07014ac3"));
Arrays.asList("d7797171d9ca4e173fab6b5af1e6d539"));
executeTest("Do not merge unphased SNPs", spec);
}
}

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java
View File

@ -87,7 +87,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("2832abc680c6b5a0219702ad5bf22f01"));
Arrays.asList("72fbeb2043f005e1698e21563f0625a9"));
executeTest("test splits with overhangs", spec);
}
@ -95,7 +95,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsFixNDN() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "splitNCigarReadsSnippet.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS -fixNDN", 1,
Arrays.asList("4ee1c1a64847e2b2f660a3a86f9d7e32"));
Arrays.asList("add7012d5e814d6cfd32f6cac1eb8ce3"));
executeTest("test fix NDN", spec);
}
@ -103,7 +103,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangsNotClipping() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --doNotFixOverhangs -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("59783610006bf7a1ccae57ee2016123b"));
Arrays.asList("6a55ac0a945e010bf03e1dd8f7749417"));
executeTest("test splits with overhangs not clipping", spec);
}
@ -111,7 +111,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs0Mismatches() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --maxMismatchesInOverhang 0 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("7547a5fc41ebfd1bbe62ce854b37b6ef"));
Arrays.asList("8a577047955ff9edca3caf1f6e545d3e"));
executeTest("test splits with overhangs 0 mismatches", spec);
}
@ -119,7 +119,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs5BasesInOverhang() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --maxBasesInOverhang 5 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("f222eb02b003c08d4a606ab1bcb7931b"));
Arrays.asList("bdd822868b88063cf50c6336ed1a5e64"));
executeTest("test splits with overhangs 5 bases in overhang", spec);
}
}

14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("dd9e17a9c268578e903ecd4ca0a4a335"));
Arrays.asList("d929369b9095420a8aaff2595ec2f80a"));
executeTest("testVariants", spec);
}
@ -74,7 +74,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RL 70 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("d7388376ffd4d3826d48a5be0be70632"));
Arrays.asList("bbc65e4f8bd3a1656616476a1e190ecf"));
executeTest("testReadLength", spec);
}
@ -84,7 +84,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-ER 40 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("6c9bf583f4b2708d6b82f54516474b7b"));
Arrays.asList("cb0e4b11bbd1b5a154ad6c99541cd017"));
executeTest("testErrorRate", spec);
}
@ -94,7 +94,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RGPL SOLID -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("26db391f223ead74d786006a502029d8"));
Arrays.asList("2b5c6cda9a434c9e25e5da5599eeae51"));
executeTest("testPlatformTag", spec);
}
@ -105,7 +105,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag --useAFAsAlleleFraction -DP 100 -R " + b37KGReference + " -V " + publicTestDir + "forAlleleFractionSimulation.vcf -o %s",
1,
Arrays.asList("3425c807525dff71310d1517e00a4f7e"));
Arrays.asList("1ae2c354718b470e30b44d5e59cb9944"));
executeTest("testAlleleFraction", spec);
}
@ -116,7 +116,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
1,
Arrays.asList("bb412c1fc8f95523dd2fc623d53dbeec"));
Arrays.asList("5c069bff8efb988660c7f6d28a3117fc"));
executeTest("testLongInsertFailure", spec);
}
@ -126,7 +126,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RL 269 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
1,
Arrays.asList("9236320c470cd8d6759c21b79206f63f"));
Arrays.asList("0657f6a692d22b5e2b7f5832710042e4"));
executeTest("testLongInsertSuccess", spec);
}

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java
View File

@ -84,7 +84,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqUnif + "--variant " + testfile),
1,
Arrays.asList("19fe0e3297bfd502911608490222a2fd")
Arrays.asList("d52bc5a7d99916ddda2d281694a733e2")
);
executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
@ -96,7 +96,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqAF + "--variant " + testfile),
1,
Arrays.asList("91a7f3bf452241040646e61ee6ab1a23")
Arrays.asList("a509bacf1920bd080fc8a9026d187bf7")
);
executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
@ -108,7 +108,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqUnif + "--variant " + testfile),
1,
Arrays.asList("faae3baf1feb76877fcb81c01b5d44f3")
Arrays.asList("dcb50e6c733b791bb79720a418d5683f")
);
executeTest("testPolyGTFreqUniform--" + testfile, spec);
@ -120,7 +120,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqAF + "--variant " + testfile),
1,
Arrays.asList("d2ba4e3e76f87e2c1a12d82e7a3dc595")
Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
);
executeTest("testPolyGTFreqAF--" + testfile, spec);
@ -132,7 +132,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGL + freqAF + "--variant " + testfile),
1,
Arrays.asList("d2ba4e3e76f87e2c1a12d82e7a3dc595")
Arrays.asList("c8a3892a8074d0ee5050119cc239fb76")
);
executeTest("testPolyGLFreqAF--" + testfile, spec);

22
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -94,14 +94,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
"41e2d951a17de433fe378bb3d9ec75d4", // tranches
"19c77724f08d90896914d3d348807399", // recal file
"c6a186a1a9271f5de35f1e5aeb8749a6"); // cut VCF
"3fe87e69c6a613addb7eff5449e86aa1", // recal file
"78b8f1934d77341df2f6a9fdbd30fa74"); // cut VCF
VRTest lowPassPlusExomes = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf",
"ce4bfc6619147fe7ce1f8331bbeb86ce", // tranches
"b7cad6a0bbbf0330e0ac712a80c3144f", // recal file
"bee399765991636461599565c9634bcf"); // cut VCF
"5a298554e9175961f63506c4e42ea78b", // recal file
"f284c0cbb00407cc5273c6f1a871513e"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
@ -196,8 +196,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
"3ad7f55fb3b072f373cbce0b32b66df4", // tranches
"e91a5b25ea1eefdcff488e0326028b51", // recal file
"e6a0c5173d8c8fbd08afdc5e5e7d3a78"); // cut VCF
"73489f9365e4884b2dd89477350a7fe0", // recal file
"0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF
@DataProvider(name = "VRBCFTest")
public Object[][] createVRBCFTest() {
@ -251,14 +251,14 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest indelUnfiltered = new VRTest(
validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
"9a331328370889168a7aa3a625f73620", // tranches
"689c7853fe2e63216da3b0d47e27740e", // recal file
"4147373ec8e0aba7ace3658677007990"); // cut VCF
"d8f68f41c8fbdff84f909f4de4a67476", // recal file
"ca376c261dc041faa4dfa31e53fed1e2"); // cut VCF
VRTest indelFiltered = new VRTest(
validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
"9a331328370889168a7aa3a625f73620", // tranches
"689c7853fe2e63216da3b0d47e27740e", // recal file
"8dd8ea31e419f68d80422b34b14e24e4"); // cut VCF
"d8f68f41c8fbdff84f909f4de4a67476", // recal file
"c968a943ef24520de6ed15c830ab5ac4"); // cut VCF
@DataProvider(name = "VRIndelTest")
public Object[][] createTestVariantRecalibratorIndel() {
@ -316,7 +316,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -o %s" +
" -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
" -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
Arrays.asList("cd42484985179c7f549e652f0f6a94d0"));
Arrays.asList("41d5c363bd311677ae1fcf98f4a18487"));
final List<File> outputFiles = executeTest("testApplyRecalibrationSnpAndIndelTogether", 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("afe5c06ef62612e4c663a3f8e9f5cd60"));
Arrays.asList("3e60ca3e04fecf5d6004c08d6f7503ca"));
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("de153b79fd1c0e1c1f769ec4a9fb01e0"));
Arrays.asList("1cca249ebc2599c7f24210d4f3204049"));
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("7876c43e9fc13723bd890b8adc5d053d"));
Arrays.asList("cc59ceb6dab620a353edf03ef14090f1"));
executeTest("testInputINDELs", spec);
}
@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -V " + CEUtrioTest +
" -supporting " + CEUtrioPopPriorsTest,
1,
Arrays.asList("781f85f56dac9074c96ace31b09e0f59"));
Arrays.asList("c7d35ce5f3675528fc484baa1c5df7b4"));
executeTest("testFamilyPriors", spec);
}
@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
" -V " + getThreeMemberNonTrioTest +
" -skipPop",
1,
Arrays.asList("abfa4332bce9aba911ad2eba34ee9924"));
Arrays.asList("c523b99da1f7e0c0ea4090b916ae7379"));
executeTest("testFamilyPriors", spec);
}

22
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("7b3153135e4f8e1d137d3f4beb46f182"));
Arrays.asList("f3538bcaf27f5e8b036d4c1f8734e4c2"));
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("4f546634213ece6f08ec9258620b92bb"));
Arrays.asList("32cd060d6662bdc835f70a848d48fb0e"));
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("b7c753452ab0c05f9cee538e420b87fa"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("82fa951ce741451267dbf30335e0f71d"));
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("bb6420ead95da4c72e76ca4bf5860ef0"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e1bfa842d53f86d46b2166574c0c66c"));
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("dd31182124c4b78a8a03edb1e0cf618b"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("76d78f83c7db247ce12087d6118dc5df"));
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("58984edf9a3a92c9fc97039b97755861"));
Arrays.asList("cb46cb8fd6506ab3e80bd50f9231643c"));
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("5c88e10211def13ba847c29d0fe9e191"));
Arrays.asList("5aeb14d64b9103b62d053aeb6158e5de"));
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("76fc5f6b949ac0b893061828af800bf8"));
Arrays.asList("3fca32a67922bf30f72fe066fe7159fe"));
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("0ec79471550ec5e30540f68cb0651b14"));
Arrays.asList("6891eaaef2991d7f967c7876fd2e4f5c"));
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("c0fdba537399cf28b28771963e2c5174"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("224c3d6e06f7ce4bdb55411b2e376577"));
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("6aeb88ca94cb5223f26175da72b985f2"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3244d99e9423b45099a220f19fac516"));
spec.disableShadowBCF();
executeTest("testBasepairResolutionInput", spec);
}

42
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -132,30 +132,30 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
cvExecuteTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec, true);
}
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6469fce8a5cd5a0f77e5ac5d9e9e192b", " -U LENIENT_VCF_PROCESSING"); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "a4cedaa83d54e34cafc3ac4b80acf5b4", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "ac58a5fde17661e2a19004ca954d9781", " -setKey null -U LENIENT_VCF_PROCESSING"); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "67a8076e30b4bca0ea5acdc9cd26a4e0"); } // official project VCF files in tabix format
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e3dbdfa14aefb2f6bd1213287d34a2e5", " -U LENIENT_VCF_PROCESSING"); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "d727fab83b4265859c4a902f6e66ac3d", " -setKey foo -U LENIENT_VCF_PROCESSING"); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "42fc3d2c68415a61ff15e594a63d9349", " -setKey null -U LENIENT_VCF_PROCESSING"); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "a3994d6145bb3813950939238db4c592"); } // official project VCF files in tabix format
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "909c6dc74eeb5ab86f8e74073eb0c1d6"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "381875b3280ba56eef0152e56f64f68d"); }
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "e7fd959312e2aff0b4231963ee690aec"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "23439a1f0108b57a14e18efe9482cc88"); }
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "f0ce3fb83d4ad9ba402d7cb11cd000c3"); }
@Test public void combineWithPLs() { combinePLs("combine.3.vcf", "combine.4.vcf", "27aa46cdb022be3959e7240a0d7ac794"); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "4efdf983918db822e4ac13d911509576"); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "848d4408ee953053d2307cefebc6bd6d"); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "629656bfef7713c23f3a593523503b2f"); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "6344953a82a422115bd647ec1d696b94"); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c4b995405872b22ded76c0a9e183c52d"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e54d0dcf14f90d5c8e58b45191dd0219"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); }
@Test public void uniqueSNPs() {
// parallelism must be disabled because the input VCF is malformed (DB=0) and parallelism actually fixes this which breaks the md5s
//both of these files have the YRI trio and merging of duplicate samples without priority must be specified with UNSORTED merge type
combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "e5ea6ac3905bd9eeea1a2ef5d2cb5af7", true);
combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", " -genotypeMergeOptions UNSORTED", "5aece78046bfb7d6ee8dc4d551542e3a", true);
}
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "def52bcd3942bbe39cd7ebe845c4f206"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5f61145949180bf2a0cd342d8e064860"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "0897efcc0046bd94760315838d4d0fa5"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "8b12b09a6ec4e3fde2352bbf82637f1e"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
@ -169,7 +169,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("58e6281df108c361e99673a501ee4749"));
Arrays.asList("8f8ba6d671f67386883c11873df3cf95"));
cvExecuteTest("threeWayWithRefs", spec, true);
}
@ -186,17 +186,17 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true);
}
@Test public void complexTestFull() { combineComplexSites("", "9d989053826ffe5bef7c4e05ac51bcca"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "4f38d9fd30a7ae83e2a7dec265a28772"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "46bbbbb8fc9ae6467a4f8fe35b8d7d14"); }
@Test public void complexTestFull() { combineComplexSites("", "3a702773e31674b14a1073d455f6f1ce"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "cabad0e328f1c967d44aaf2085da5dcf"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "31f6f62664cc5891e9a8e228dbb6278d"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "31f6f62664cc5891e9a8e228dbb6278d"); }
@Test
public void combineDBSNPDuplicateSites() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
1,
Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6"));
Arrays.asList("b0d4b86702b44fc4faa527c34adf6239"));
cvExecuteTest("combineDBSNPDuplicateSites:", spec, true);
}
@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
+ " -R " + b37KGReference
+ " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
1,
Arrays.asList("f8c014d0af7e014475a2a448dc1f9cef"));
Arrays.asList("11aab642395645589e48edee1fb179e2"));
cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
}

40
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -82,7 +82,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
1,
Arrays.asList("c67b9378b28c7dd0ffc095efb7e029ea"));
Arrays.asList("9424ae7832fd53790372578423392468"));
executeTest("testUpdatePGT", spec);
}
@ -91,7 +91,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample", b37KGReference),
1,
Arrays.asList("1d6bcc23db3d099efd430c50968d059b"));
Arrays.asList("5deed67f8eb10cbd4429d70e0c26ef7c"));
executeTest("testUpdatePGT, adding StrandAlleleCountsBySample annotation", spec);
}
@ -103,7 +103,7 @@ 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("cb239f8b9bc97bff320034c988ac8ff2"));
Arrays.asList("6df12487566b55c4cdbc0993ddf4a75e"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -115,7 +115,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("599394c205c1d6641b9bebabbd29e13c"));
Arrays.asList("e0a51868271fb7b399478b9c63ede291"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("f7d5344a85e6d7fc2437d4253b424cb0"));
Arrays.asList("1e4be55f727c7a9376a7a37406f06cee"));
executeTest("combineSingleSamplePipelineGVCF", spec);
}
@ -139,7 +139,7 @@ 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("c9e4d1e52ee1f3a5233f1fb100f24d5e"));
Arrays.asList("92513f9a6f34829ef455a379e87e09cd"));
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
}
@ -152,7 +152,7 @@ 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("ca587157c9f34e33aa0dfb087c4ccd76"));
Arrays.asList("95e21516ef7a71de9b299d502e83268e"));
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
}
@ -164,7 +164,7 @@ 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("c3da307d0991376b098d85d5a708f23d"));
Arrays.asList("f352d0204a37a7adc4000318d5f24cb8"));
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
}
@ -174,7 +174,7 @@ 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("4b4d3386ac6d3b7a113c9389a1061416"));
Arrays.asList("88ef27a16fc44a3caa700677d5b78df5"));
executeTest("testJustOneSample", spec);
}
@ -185,14 +185,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V " + privateTestDir + "gvcfExample1.vcf" +
" -V " + privateTestDir + "gvcfExample2.vcf",
1,
Arrays.asList("50e497153a7932e590a5b9f6c193fa8b"));
Arrays.asList("45d9c291a74897cf3c3aaf52af5a08f8"));
executeTest("testSamplesWithDifferentLs", spec);
}
@Test(enabled = true)
public void testNoPLsException() {
// Test with input files with (1) 0/0 and (2) ./.
final String md5 = "c7a81b1fba1e14f2607c56036647b625";
final String md5 = "2dd285987047f37c730060734ca76038";
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",
@ -212,7 +212,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-nda"),
1,
Arrays.asList("033cb91830de7d783986d47fcf88b742"));
Arrays.asList("b7fda2981a2367764b83df7aa3b3b3e7"));
executeTest("testNDA", spec);
}
@ -221,7 +221,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-maxAltAlleles 1"),
1,
Arrays.asList("a91df2010eeb111c7adfe367e4030b44"));
Arrays.asList("0c26cabfcebfb0b662185b233e0cd976"));
executeTest("testMaxAltAlleles", spec);
}
@ -230,7 +230,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
1,
Arrays.asList("49694b40a2d2f0ca8251a7b9564734c4"));
Arrays.asList("102c33e8b2a7200972d58fc6bae8bd3b"));
executeTest("testStandardConf", spec);
}
@ -274,7 +274,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
" --uniquifySamples", b37KGReference),
1,
Arrays.asList("3785b362b78c92f9dd9fa16cd603e92b"));
Arrays.asList("1f6321464371ecffb06108fb86ffab49"));
executeTest("testUniquifiedSamples", spec);
}
@ -446,7 +446,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
}
private static final String simpleSpanningDeletionsMD5 = "2aeec92ff1598dfdc1c86be04f062668";
private static final String simpleSpanningDeletionsMD5 = "9ccf64721dba002bef08046f02eb5ee9";
@Test(enabled = true)
public void testSpanningDeletionsMD5() {
@ -476,7 +476,7 @@ 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("d112d14eaefb2bba2434ab954deae768"));
Arrays.asList("80de258cf5c73e0805e15347ef82d4be"));
spec.disableShadowBCF();
executeTest("testMultipleSpanningDeletionsMD5", spec);
}
@ -487,7 +487,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
1,
Arrays.asList("02cca337e097b86c5471929036ad4b64"));
Arrays.asList("b16ae4b8e87bc87cd689929c28aff3de"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@ -498,7 +498,7 @@ 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("46169d08f93e5ff57856c7b64717314b"));
Arrays.asList("586e814c0578e245352cbb4647b5a46a"));
spec.disableShadowBCF();
executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
}
@ -521,7 +521,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
" -V " + privateTestDir + "ad-bug-input.vcf",
1,
Arrays.asList("51319e24f460c71d484242967d2acd57"));
Arrays.asList("027f96584e91ca8255764fbf38293963"));
spec.disableShadowBCF();
executeTest("testBadADPropagationHaploidBugTest", spec);
}

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

@ -66,7 +66,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header",
1,
Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
Arrays.asList("dd238fe14b4a495a489907c1e021221e"));
executeTest("test left alignment", spec);
}
@ -75,7 +75,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -trim -split",
1,
Arrays.asList("d12468cf08cfd14354f781d5f42b279f"));
Arrays.asList("534bea653d4a0e59e74f4107c1768558"));
executeTest("test left alignment with trimming and hard multiple alleles", spec);
}

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LiftoverVariantsIntegrationTest.java
View File

@ -67,7 +67,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("7d5f91fcf419211ae9eca6c66dcec0e6"));
Arrays.asList("eb38adfffb7913fa761c5c579b885ea2"));
executeTest("test b36 to hg19", spec);
}
@ -76,7 +76,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + privateTestDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("29dab3555e7f1ee6a60e267b00215a11"));
Arrays.asList("f40e078fd5fb1d4107738a4f2f602902"));
executeTest("test b36 to hg19, unsorted samples", spec);
}
@ -85,7 +85,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + privateTestDir + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
1,
Arrays.asList("7e7bad0e1890753a01303c09a38ceb8d"));
Arrays.asList("186a675c9758c1b83a1232399e18d8fe"));
executeTest("test hg18 to hg19, unsorted", spec);
}
@ -94,7 +94,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T FilterLiftedVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "liftover_indel_test.vcf --no_cmdline_in_header",
1,
Arrays.asList("0909a953291a5e701194668c9b8833ab"));
Arrays.asList("303e3df3bf737feaff397b4eeb037ecb"));
executeTest("test liftover filtering of indels", spec);
}

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

@ -66,7 +66,7 @@ public class RegenotypeVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T RegenotypeVariants -R " + b36KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
Arrays.asList("88118ebd39d6576aa1171082d8f37cd8")
);
executeTest("testRegenotype--" + testFile, spec);

76
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -64,10 +64,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args;
}
private static final String SAMPLE_EXCLUSION_MD5 = "eea22fbf1e490e59389a663c3d6a6537";
private static final String INVERT_SELECTION_MD5 = "831bc0a5a723b0681a910d668ff3757b";
private static final String MAX_FILTERED_GT_SELECTION_MD5 = "0365de1bbf7c037be00badace0a74d02";
private static final String MIN_FILTERED_GT_SELECTION_MD5 = "fcee8c8caa0696a6675961bb12664878";
private static final String SAMPLE_EXCLUSION_MD5 = "2e52f21e7dcc67151a51630807a4eef2";
private static final String INVERT_SELECTION_MD5 = "26d192b868746ab14133f145ae812e7c";
private static final String MAX_FILTERED_GT_SELECTION_MD5 = "f83ac0deb7a8b022d6d40a85627a71ec";
private static final String MIN_FILTERED_GT_SELECTION_MD5 = "346620b7a5d66dabf89d3f42d6e27db7";
@Test
public void testDiscordanceNoSampleSpecified() {
@ -78,7 +78,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
+ b37hapmapGenotypes + " -disc " + testFile
+ " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
1,
Arrays.asList("954415f84996d27b07d00855e96d33a2")
Arrays.asList("9e08f761d2ba9a2bae9c279701aabc70")
);
spec.disableShadowBCF();
@ -92,7 +92,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
1,
Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57")
Arrays.asList("792962a5cc830e86dfc89caffbda1707")
);
executeTest("testRepeatedLineSelection--" + testfile, spec);
@ -107,7 +107,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
+ b37hapmapGenotypes + " -disc " + testFile
+ " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
1,
Arrays.asList("ca1b5226eaeaffb78d4abd9d2ee10c43")
Arrays.asList("c9aa80cabf036a268a032a61d398cdd5")
);
spec.disableShadowBCF();
@ -122,7 +122,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
1,
Arrays.asList("4386fbb258dcef4437495a37f5a83c53")
Arrays.asList("8090c349d12549b437a80e29c285fdd5")
);
spec.disableShadowBCF();
executeTest("testComplexSelection--" + testfile, spec);
@ -136,7 +136,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES -sn A -se '[CDH]' -sn Z -sn T -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile),
1,
Arrays.asList("4386fbb258dcef4437495a37f5a83c53")
Arrays.asList("8090c349d12549b437a80e29c285fdd5")
);
spec.disableShadowBCF();
executeTest("testComplexSelectionWithNonExistingSamples--" + testfile, spec);
@ -149,7 +149,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
1,
Arrays.asList("44e77cea624cfff2b8acc3a4b30485cb") // should yield empty vcf because the foo!=0 will yield complete expression false
Arrays.asList("e7ec1f2c8077d07b54721e68b603d42c") // should yield empty vcf because the foo!=0 will yield complete expression false
);
spec.disableShadowBCF();
executeTest("testNonExistingSelection--" + testfile, spec);
@ -166,7 +166,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile,
1,
Arrays.asList("1f5c72951a35667c4bdf1be153787e27")
Arrays.asList("30aabc865634bf887cad0c02cdcde042")
);
spec.disableShadowBCF();
@ -184,7 +184,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s --no_cmdline_in_header -xl_sf " + samplesFile + " --variant " + testfile,
1,
Arrays.asList("875d7e00ac8081e87ab9fb1b20c83677")
Arrays.asList("1afba8d53094bdef63db1e39d52be5aa")
);
spec.disableShadowBCF();
@ -252,7 +252,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
+ b37hapmapGenotypes + " --variant " + testFile
+ " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
1,
Arrays.asList("946e7f2e0ae08dc0e931c1634360fc46")
Arrays.asList("24114c01b81fc0052ee36523ccd1d338")
);
spec.disableShadowBCF();
@ -269,7 +269,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
);
executeTest("testVariantTypeSelection--" + testFile, spec);
@ -285,7 +285,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --maxIndelSize 2",
1,
Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
);
executeTest("testMaxIndelLengthSelection--" + testFile, spec);
@ -301,7 +301,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -selectType INDEL --variant " + testFile + " -o %s --no_cmdline_in_header --minIndelSize 2",
1,
Arrays.asList("fa5f3eb4f0fc5cedc93e6c519c0c8bcb")
Arrays.asList("ed9dc00d0551630a2eed9e81a2a357d3")
);
executeTest("testMinIndelLengthSelection--" + testFile, spec);
@ -314,7 +314,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
);
executeTest("testUsingDbsnpName--" + testFile, spec);
@ -327,7 +327,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
Arrays.asList("86d97e682b2dccff75d079f3b5d17f4b")
);
executeTest("testRemoveMLE--" + testFile, spec);
@ -340,7 +340,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalAC -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("ad7e8b25e431a3229a78cec063876559")
Arrays.asList("6f26cf5a7fd20682e1de193e5bb5f61f")
);
executeTest("testKeepOriginalAC--" + testFile, spec);
@ -353,7 +353,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalAC -env -trimAlternates -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("4695c99d96490ed4e5b1568c5b52dea6")
Arrays.asList("e0ac2b37387048bf51ac2914bdd2e178")
);
executeTest("testKeepOriginalACAndENV--" + testFile, spec);
@ -366,7 +366,7 @@ 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("e897097a47aee5516dc4f1c0b9d69037")
Arrays.asList("ce5168e2eadee2550188892b1ea444be")
);
executeTest("testKeepOriginalDP--" + testFile, spec);
@ -379,7 +379,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("44f7c47395ca5b2afef5313f592c8cea")
Arrays.asList("bfbfefbd4a84b093ee0b63eab8cc1be9")
);
executeTest("testMultipleRecordsAtOnePosition--" + testFile, spec);
@ -392,7 +392,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("ef3c5f75074a5dd2b2cd2715856a2542")
Arrays.asList("cc33eb41a821d9aebdfb99d309854db0")
);
executeTest("testNoGTs--" + testFile, spec);
@ -405,7 +405,7 @@ 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("69862fb97e8e895fe65c7abb14b03cee")
Arrays.asList("b86340de516d6c37cc3a2eeb3bfb4821")
);
executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
}
@ -417,7 +417,7 @@ 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("8fe7cdca8638461909262cb0769b2527")
Arrays.asList("7807bb2bf8c70963f65a97f30c8deb39")
);
executeTest("test multi allelic annotation ordering --" + testfile, spec);
}
@ -468,19 +468,19 @@ 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("9df942000eb18b12d9008c7d9b5c4178"));
WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("354cd7aa25791465d0f4c7d53b81a3a3"));
executeTest("testAlleleTrimming", spec);
}
@DataProvider(name="unusedAlleleTrimmingProvider")
public Object[][] unusedAlleleTrimmingProvider() {
return new Object[][] {
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "9df942000eb18b12d9008c7d9b5c4178"},
{ privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "981b757e3dc6bf3864ac7e493cf9d30d"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "8ded359dd87fd498ff38736ea0fa4c28"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "a7e7288dcd779cfac6983069de45b79c"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "2e726d06a8d317199e8dda74691948a3"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "1e5585f86c347da271a79fbfc61ac849"}
{ 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", "8650d66b2199a4f8ce0acc660b2091cd"},
{ privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "14538e17d5aca22c655c42e130f8cebc"}
};
}
@ -603,7 +603,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -IDs " + idFile + " --variant " + testFile),
1,
Arrays.asList("2c50ab2ae96fae40bfc2b8398fc5e54e")
Arrays.asList("41dda9f4b9ec9f9b0f3593b2cbd82cd5")
);
spec.disableShadowBCF();
executeTest("testKeepSelectionID--" + testFile, spec);
@ -620,7 +620,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -xlIDs " + idFile + " --variant " + testFile),
1,
Arrays.asList("77514a81233e1bbc0f5e47b0fb76a89a")
Arrays.asList("6c1e8591c134519bfc202b4ec7ef1f71")
);
spec.disableShadowBCF();
executeTest("testExcludeSelectionID--" + testFile, spec);
@ -636,7 +636,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -xlSelectType SNP --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("fa5f3eb4f0fc5cedc93e6c519c0c8bcb")
Arrays.asList("ed9dc00d0551630a2eed9e81a2a357d3")
);
executeTest("testExcludeSelectionType--" + testFile, spec);
@ -650,7 +650,7 @@ 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("406243096074a417d2aa103bd3d13e01"));
Arrays.asList("f7fe7cbc84b3f2dfadcc40e19eeeb1f9"));
executeTest("testMendelianViolationSelection--" + testFile, spec);
}
@ -663,7 +663,7 @@ 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("35921fb2dedca0ead83027a66b725794"));
Arrays.asList("865418a69ee57be4432f248c027e6aff"));
executeTest("testInvertMendelianViolationSelection--" + testFile, spec);
}
@ -727,7 +727,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("81b99386a64a8f2b857a7ef2bca5856e")
Arrays.asList("7771f07a9997296852ab367fac2c7a6c")
);
spec.disableShadowBCF();

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
View File

@ -90,17 +90,17 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
String args = " -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant " + testfile;
new ParallelSelectTestProvider(b36KGReference, args, "4386fbb258dcef4437495a37f5a83c53", nt);
new ParallelSelectTestProvider(b36KGReference, args, "8090c349d12549b437a80e29c285fdd5", nt);
}
{ // 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, "c64b45a14d41b1e5cddbe036b47e7519", nt);
new ParallelSelectTestProvider(b37KGReference, args, "b899cebdd30e6641437489b746301797", 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, "e86c6eb105ecdd3ff026999ffc692821", nt);
new ParallelSelectTestProvider(b37KGReference, args, "ace613ed2e4929f448d30d85110d6ced", nt);
}
}

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

@ -87,7 +87,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --no_cmdline_in_header " +
" -o %s",
1,
Arrays.asList("283f434b3efbebb8e10ed6347f97d104")
Arrays.asList("f9f6418698f967ba7ca451ac1fb4cc8d")
);
executeTest("testSimpleVCFStreaming", spec);

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

@ -66,7 +66,7 @@ public class VariantsToAllelicPrimitivesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantsToAllelicPrimitives -o %s -R " + b37KGReference + " -V " + privateTestDir + "vcfWithMNPs.vcf --no_cmdline_in_header",
1,
Arrays.asList("c5333d2e352312bdb7c5182ca3009594"));
Arrays.asList("db9929eef707d7dff0aef576f49e4a0d"));
executeTest("test MNPs To SNPs", spec);
}
}

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

@ -70,7 +70,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("22373883afa2221b5a4f75a50f30f26b");
md5.add("c73bcc3658b4a4d8bd9d794069d41dbd");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -88,7 +88,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>();
md5.add("738eb66dbc400dcd1786cd9e49902e8c");
md5.add("a1771924b58dd633620114ef0f462acb");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -106,7 +106,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingHapMapInput() {
List<String> md5 = new ArrayList<String>();
md5.add("67656672acc264156f5a3e01e5cac61a");
md5.add("970157c9e15c53a6e50faaad41227487");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
@ -123,7 +123,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>();
md5.add("21084d32ce7ac5df3cee1730bfaaf71c");
md5.add("975830cb2bff58c7df426bbf09a08244");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java
View File

@ -90,6 +90,10 @@ public class GVCFWriterUnitTest extends BaseTest {
public void add(VariantContext vc) {
emitted.add(vc);
}
public boolean checkError(){
return false;
}
}
private MockWriter mockWriter;

19
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/storage/VariantContextWriterStorage.java
View File

@ -154,6 +154,16 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
return writer;
}
/**
* Check the return from PrintStream.checkError() if underlying stream is a java.io.PrintStream
* @return true if PrintStream.checkError() returned true, false otherwise
*/
public boolean checkError(){
if ( stream instanceof PrintStream )
return ((PrintStream) stream).checkError();
return false;
}
private final static class TestWriter implements VariantContextWriter {
final List<VariantContextWriter> writers;
@ -175,6 +185,14 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
public void add(final VariantContext vc) {
for ( final VariantContextWriter writer : writers ) writer.add(vc);
}
/**
* Check the return from PrintStream.checkError() if underlying stream for a java.io.PrintStream
* @return false, no error since the underlying stream is not a java.io.PrintStream
*/
public boolean checkError(){
return false;
}
}
public void add(VariantContext vc) {
@ -225,4 +243,5 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
}
}
}

10
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.java
View File

@ -246,6 +246,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
setWriteFullFormatField(argumentCollection.neverTrimVCFFormatField);
}
@Override
public void writeHeader(VCFHeader header) {
vcfHeader = header;
@ -274,6 +275,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
/**
* @{inheritDoc}
*/
@Override
public void close() {
outputTracker.getStorage(this).close();
}
@ -300,4 +302,12 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
getOutputFile() != null && // that are going to disk
engine.getArguments().generateShadowBCF; // and we actually want to do it
}
/**
* Check the return from PrintStream.checkError() if underlying stream for a java.io.PrintStream
* @return true if PrintStream.checkError() returned true, false otherwise
*/
public boolean checkError(){
return genotypeStream.checkError();
}
}

20
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
View File

@ -324,12 +324,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@Test()
public void testDefaultBaseQualities20() {
executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "7d254a9d0ec59c66ee3e137f56f4c78f"));
executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26"));
}
@Test()
public void testDefaultBaseQualities30() {
executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "0f50def6cbbbd8ccd4739e2b3998e503"));
executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26"));
}
@Test(expectedExceptions = Exception.class)
@ -731,12 +731,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@Test
public void testSAMWriterFeatures() {
testBAMFeatures("-compress 0", "bb4b55b1f80423970bb9384cbf0d8793");
testBAMFeatures("-compress 9", "b85ee1636d62e1bb8ed65a245c307167");
testBAMFeatures("-simplifyBAM", "38f9c30a27dfbc085a2ff52a1617d579");
testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139");
testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b");
testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964");
//Validate MD5
final String expectedMD5 = "6627b9ea33293a0083983feb94948c1d";
final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd";
final File md5Target = testBAMFeatures("--generate_md5", expectedMD5);
final File md5File = new File(md5Target.getAbsoluteFile() + ".md5");
md5File.deleteOnExit();
@ -758,8 +758,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@DataProvider(name = "vcfFeaturesData")
public Object[][] getVCFFeaturesData() {
return new Object[][]{
{"--sites_only", "94bf1f2c0946e933515e4322323a5716"},
{"--bcf", "03f2d6988f54a332da48803c78f9c4b3"}
{"--sites_only", "6ef742ee6d9bcbc7b23f928c0e8a1d0e"},
{"--bcf", "285549ca1a719a09fa95cfa129520621"}
};
}
@ -775,8 +775,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@DataProvider(name = "vcfFormatHandlingData")
public Object[][] getVCFFormatHandlingData() {
return new Object[][]{
{true, "95b6262efbd40b6b72f44f808f3e4c45"},
{false, "333232e08b8cdd3303309e438c44277f"}
{true, "870f39e19ec89c8a09f7eca0f5c4bcb9"},
{false, "baf9a1755d3b4e0ed25b03233e99ca91"}
};
}

10
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
View File

@ -39,15 +39,15 @@ public class CramIntegrationTest extends WalkerTest {
@DataProvider(name="cramData")
public Object[][] getCRAMData() {
return new Object[][] {
{"PrintReads", "exampleBAM.bam", "", "cram", "fc6e3919a8a34266c89ef66e97ceaba9"},
{"PrintReads", "exampleCRAM.cram", "", "cram", "fc6e3919a8a34266c89ef66e97ceaba9"},
{"PrintReads", "exampleCRAM.cram", "", "bam", "d89efbc3bd867749a2864ebd2d2cd6e1"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "072435e8272411c31b2234f851706384"},
{"PrintReads", "exampleBAM.bam", "", "cram", "95cce9111a377d8e84fd076f7f0744df"},
{"PrintReads", "exampleCRAM.cram", "", "cram", "95cce9111a377d8e84fd076f7f0744df"},
{"PrintReads", "exampleCRAM.cram", "", "bam", "7c716d5103c20e95a8115b3c2848bf0d"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "5cc9cac96f7f9819688d47a28ed97778"},
{"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", "9598062587ad8d2ec596a8ecb19be979"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "2e1b175c9b36154e2bbd1a23ebaf4c22"},
{"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
{"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
};

21
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
View File

@ -48,21 +48,6 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testAllIntervalsImplicit",spec);
}
// '-L all' is no longer supported
// @Test(enabled = true)
// public void testAllExplicitIntervalParsing() {
// String md5 = "7821db9e14d4f8e07029ff1959cd5a99";
// WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
// "-T TestCountLociWalker" +
// " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
// " -R " + hg18Reference +
// " -L all" +
// " -o %s",
// 1, // just one output file
// Arrays.asList(md5));
// executeTest("testAllIntervalsExplicit",spec);
// }
@Test
public void testUnmappedReadInclusion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -77,7 +62,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("95e98192e5b90cf80eaa87a4ace263da",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);
@ -103,7 +88,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion", ".cram");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("36b3dfdcc3a5ab4e240a6e3237101489", createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("0f11cc035455cd68fb388e33aaf5feff", createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("ebbe6e311b6bb240554ec96ed9809216", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
executeTest("testUnmappedReadInclusionCRAM", spec);
@ -124,7 +109,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("3944b5a6bfc06277ed3afb928a20d588",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);

2
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/crypt/GATKKeyIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class GATKKeyIntegrationTest extends WalkerTest {
public static final String BASE_COMMAND = String.format("-T TestPrintReadsWalker -R %s -I %s -o %%s",
publicTestDir + "exampleFASTA.fasta",
publicTestDir + "exampleBAM.bam");
public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b";
public static final String MD5_UPON_SUCCESSFUL_RUN = "69b6432aed2d0cebf02e5d414f654425";
private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) {

4
public/gatk-root/pom.xml
View File

@ -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>1.134</htsjdk.version>
<picard.version>1.133</picard.version>
<htsjdk.version>1.138</htsjdk.version>
<picard.version>1.138</picard.version>
</properties>
<!-- Dependency configuration (versions, etc.) -->

22
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java
View File

@ -91,25 +91,25 @@ public class CatVariantsIntegrationTest {
final File catVariantsTempList1 = BaseTest.createTempListFile("CatVariantsTest1", CatVariantsVcf1.getAbsolutePath());
final File catVariantsTempList2 = BaseTest.createTempListFile("CatVariantsTest2", CatVariantsVcf2.getAbsolutePath());
new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "6a57fcbbf3cae490896d13a288670d83");
new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
for (String extension1 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
for (String extension2 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
final File file1 = new File(CatVariantsDir, "CatVariantsTest1.vcf" + extension1);
final File file2 = new File(CatVariantsDir, "CatVariantsTest2.vcf" + extension2);
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "6a57fcbbf3cae490896d13a288670d83");
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "33f728ac5c70ce2994f3619a27f47088");
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3");
new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
}
new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "33f728ac5c70ce2994f3619a27f47088");
new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "f1a55575f59707f80b8c17e2591fbf53");
new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576");
new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "b9f31b6a00226c58181c19d421503693");
}
//Test list parsing functionality
new CatVariantsTestProvider(catVariantsTempList1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
new CatVariantsTestProvider(CatVariantsVcf1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
new CatVariantsTestProvider(catVariantsTempList1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "d0d81eb7fd3905256c4ac7c0fc480094");
new CatVariantsTestProvider(catVariantsTempList1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
new CatVariantsTestProvider(CatVariantsVcf1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
new CatVariantsTestProvider(catVariantsTempList1, catVariantsTempList2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1");
return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
}
@ -130,7 +130,7 @@ public class CatVariantsIntegrationTest {
@DataProvider(name = "SortOrderTest")
public Object[][] makeSortOrderTestProvider() {
new CatVariantsTestProvider(CatVariantsVcf3, CatVariantsVcf4, BaseTest.createTempFile("CatVariantsSortOrderTest", ".vcf"), "7bfe34c78b9f1b56a28cc33262cdfd97");
new CatVariantsTestProvider(CatVariantsVcf3, CatVariantsVcf4, BaseTest.createTempFile("CatVariantsSortOrderTest", ".vcf"), "fb0b4ebe98ca23862b45fcd672fbfc3e");
return CatVariantsTestProvider.getTests(CatVariantsTestProvider.class);
}

4
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
View File

@ -43,13 +43,13 @@ public class BAQIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testPrintReadsNoBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("d1f74074e718c82810512bf40dbc7f72"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb"));
executeTest(String.format("testPrintReadsNoBAQ"), spec);
}
@Test
public void testPrintReadsRecalBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("96ec97cf92f1f660bd5244c6b44539b3"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df"));
executeTest(String.format("testPrintReadsRecalBAQ"), spec);
}
}

4
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
View File

@ -48,7 +48,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
1,
Arrays.asList("5bafc5a99ea839e686e55de93f91fd5c"));
Arrays.asList("a1de53ac340f4ca02367c40680628251"));
executeTest("Test symbolic alleles", spec);
}
@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
1,
Arrays.asList("30f66a097987330d42e87da8bcd6be21"));
Arrays.asList("c8b294089832bb1a2c450b550318a471"));
executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
}
}

26
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
View File

@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
}
final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "12be03c817d94bab88457e5afe74256a"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "0bcfd177fe4be422898eda8e161ebd6c"); }
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "aed836c97c6383dd80e39a093cc25e08"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "5f6e08bd44d6faf5b85cde5d4ec1a36f"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f3cb42759428df80d06e9789f9f9f762"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "44658c018378467f809b443d047d5778"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "906871df304dd966682e5798d59fc86b"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "bae38f83eb9b63857f5e6e3c6e62f80c"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "b41995fea04034ca0427c4a71504ef83"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "3b32da2eaab7a2d4729fdb486cedbb2f"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "9d355b0f6d2076178e92bd7fcd8f5adb"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
@Test
public void testUseOriginalQuals() {
@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
" -OQ -QT 4 -CR WRITE_Q0S" +
" -o %s -os %s",
2,
Arrays.asList("c83b4e2ade8654a2818fe9d405f07662", "55c01ccc2e84481b22d3632cdb06c8ba"));
Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba"));
executeTest("clipOriginalQuals", spec);
}
}

30
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
View File

@ -59,27 +59,27 @@ public class PrintReadsIntegrationTest extends WalkerTest {
@DataProvider(name = "PRTest")
public Object[][] createPrintReadsTestData() {
return new Object[][]{
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "5aee1c592f7b0505430df4d4452b8000")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "62a542230502c9e54124ebd46242e252")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "a054a6618ffa8cd2d1113b005335922b")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "0e3d1748ad1cb523e3295cab9d09d8fc")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")},
// See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "d7f23fd77d7dc7cb50d3397f644c6d8a")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "c601db95b20248d012b0085347fcb6d1")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "b16f6ed6cc1e7640b08bf9bcc86f1596")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "2d32440e47e8d9d329902fe573ad94ce")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "c601db95b20248d012b0085347fcb6d1")},
{new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "349650b6aa9e574b48a2a62627f37c7d")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "0c1cbe67296637a85e80e7a182f828ab")},
{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.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
{new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "0387c61303140d8899fcbfdd3e72ed80")},
// Tests for filtering options
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
"", "b3ae15c8af33fd5badc1a29e089bdaac")},
"", "ad56da66be0bdab5a8992de9617ae6a5")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -readGroup SRR359098", "8bd867b30539524daa7181efd9835a8f")},
" -readGroup SRR359098", "c3bfe28722a665e666098dbb7048a9f1")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -readGroup 20FUK.3 -sn NA12878", "93a7bc1b2b1cd27815ed1666cbb4d0cb")},
" -readGroup 20FUK.3 -sn NA12878", "8191f8d635d00b1f4d0993b785cc46c5")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -sn na12878", "52e99cfcf03ff46285d1ba302f8df964")},
" -sn na12878", "92a85b4223ec45e114f12a1fe6ebbaeb")},
};
}

4
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java
View File

@ -47,13 +47,13 @@ public class ReadAdaptorTrimmerIntegrationTest extends WalkerTest {
@Test
public void testBasicTrimmer() {
WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest.bam"), 1, Arrays.asList("1d42414e12b45d44e6f396d97d0f60fe"));
WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest.bam"), 1, Arrays.asList("c7d7f69e6b532ec693bfbd821c2e9766"));
executeTest(String.format("testBasicTrimmer"), spec);
}
@Test
public void testSkippingBadPairs() {
WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest2.bam")+" -removeUnpairedReads", 1, Arrays.asList("5e796345502fbfc31134f7736ce68868"));
WalkerTestSpec spec = new WalkerTestSpec( getBaseCommand("shortInsertTest2.bam")+" -removeUnpairedReads", 1, Arrays.asList("f7aa76d1a2535774764e06ba610c21de"));
executeTest(String.format("testSkippingBadPairs"), spec);
}

6
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
View File

@ -43,9 +43,9 @@ public class SplitSamFileIntegrationTest extends WalkerTest {
" --outputRoot " + prefix,
Collections.<String>emptyList()
);
addSplitOutput(spec, prefix, "NA12878", "ffb8a1e76798fa78c9ffe46abc02e92f");
addSplitOutput(spec, prefix, "NA12891", "42154dc36451dfe98922a579d329bbe2");
addSplitOutput(spec, prefix, "NA12892", "6abb5d11e615310987da22212dd9fc84");
addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b");
addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
executeTest("testSplitSamFile", spec);
}

18
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 = "d991abe6c6a7a778a60a667717903be0";
String md5ofInputVCF = "3dc9ac85f2c0541df9bc57b4d81f480b";
String testVCF = privateTestDir + "vcf4.1.example.vcf";
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
@ -76,7 +76,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("13329ba7360a8beb3afc02569e5a20c4"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("b8b18a9a015cba1f3a44af532bf45338"));
executeTest("Test reading and writing breakpoint VCF", spec1);
}
@ -87,7 +87,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e0e308a25e56bde1c664139bb44ed19d"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("89daaa81f64e96cf4d9aa0abf9be0b76"));
executeTest("Test reading VCF with lower-case bases", spec1);
}
@ -98,7 +98,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("bdab26dd7648a806dbab01f64db2bdab"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("5d91e685c760f7e869cb06596d741116"));
executeTest("Test reading and writing 1000G Phase I SVs", spec1);
}
@ -109,7 +109,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("38697c195e7abf18d95dcc16c8e6d284"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("122340e3dc333d2b4b79c5c0c443a3fe"));
executeTest("Test reading and writing samtools vcf", spec1);
}
@ -118,7 +118,7 @@ public class VCFIntegrationTest extends WalkerTest {
String testVCF = privateTestDir + "ex2.vcf";
String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e8f721ce81e4fdadba13c5291027057f"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("db565efb14b2fe5f00a11762751d2476"));
executeTest("Test writing samtools WEx BCF example", spec1);
}
@ -127,7 +127,7 @@ public class VCFIntegrationTest extends WalkerTest {
String testVCF = privateTestDir + "ex2.bcf";
String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0439e2b4ccc63bb4ba7c283cd9ab1b25"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0ca1a078d4801886ef4abac327df7104"));
executeTest("Test reading samtools WEx BCF example", spec1);
}
@ -144,7 +144,7 @@ public class VCFIntegrationTest extends WalkerTest {
@Test
public void testPassingOnVCFWithoutHeadersWithLenientProcessing() {
runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true);
runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "a8f4be8ad9820286ea13a28a675133f1", null, true);
}
private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
@ -360,7 +360,7 @@ public class VCFIntegrationTest extends WalkerTest {
" -o %s ";
final String name = "testBlockCompressedInput: " + testSpec.toString();
final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("3b60668bd973e43783d0406de80d2ed2"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("ce9c0bf31ee9452ac4a12a59d5814545"));
executeTest(name, spec);
}

11
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java
View File

@ -112,6 +112,8 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
private final static Set<String> HEADER_IDs = new HashSet<String>(Arrays.asList("marker", "I"));
private static final String delimiterRegex = "\\s+";
// codec file extension
protected static final String FILE_EXT = "beagle";
/**
* The parser to use when resolving genome-wide locations.
@ -212,6 +214,7 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
private static Pattern MARKER_PATTERN = Pattern.compile("(.+):([0-9]+)");
@Override
public BeagleFeature decode(String line) {
String[] tokens;
@ -273,4 +276,12 @@ public class BeagleCodec extends AsciiFeatureCodec<BeagleFeature> implements Ref
return bglFeature;
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
}

10
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java
View File

@ -77,6 +77,8 @@ public class RawHapMapCodec extends AsciiFeatureCodec<RawHapMapFeature> {
private static final int minimumFeatureCount = 11;
private String headerLine;
// codec file extension
protected static final String FILE_EXT = "hapmap";
public RawHapMapCodec() {
super(RawHapMapFeature.class);
@ -110,6 +112,14 @@ public class RawHapMapCodec extends AsciiFeatureCodec<RawHapMapFeature> {
headerLine);
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
@Override
public Object readActualHeader(final LineIterator lineIterator) {
this.headerLine = lineIterator.next();

10
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java
View File

@ -74,6 +74,8 @@ import java.util.ArrayList;
*/
public class RefSeqCodec extends AsciiFeatureCodec<RefSeqFeature> implements ReferenceDependentFeatureCodec {
// codec file extension
protected static final String FILE_EXT = "refseq";
/**
* The parser to use when resolving genome-wide locations.
*/
@ -163,6 +165,14 @@ public class RefSeqCodec extends AsciiFeatureCodec<RefSeqFeature> implements Ref
return feature;
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
@Override
public Object readActualHeader(LineIterator lineIterator) {
// No header for this format

11
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java
View File

@ -128,6 +128,9 @@ public class SAMPileupCodec extends AsciiFeatureCodec<SAMPileupFeature> {
private static final String baseT = "T";
private static final String emptyStr = ""; // we will use this for "reference" allele in insertions
// codec file extension
protected static final String FILE_EXT = "samp";
public SAMPileupCodec() {
super(SAMPileupFeature.class);
}
@ -240,6 +243,14 @@ public class SAMPileupCodec extends AsciiFeatureCodec<SAMPileupFeature> {
return feature;
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
@Override
public Object readActualHeader(LineIterator lineIterator) {
// No header for this format

11
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java
View File

@ -57,6 +57,8 @@ public class SAMReadCodec extends AsciiFeatureCodec<SAMReadFeature> {
// the number of tokens we expect to parse from a read line
private static final int expectedTokenCount = 11;
// codec file extension
protected static final String FILE_EXT = "samr";
public SAMReadCodec() {
super(SAMReadFeature.class);
@ -67,6 +69,7 @@ public class SAMReadCodec extends AsciiFeatureCodec<SAMReadFeature> {
* @param line line to decode.
* @return A SAMReadFeature modeling that line.
*/
@Override
public SAMReadFeature decode(String line) {
// we may be asked to process a header line; ignore it
if (line.startsWith("@")) return null;
@ -115,6 +118,14 @@ public class SAMReadCodec extends AsciiFeatureCodec<SAMReadFeature> {
qualities);
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
@Override
public Object readActualHeader(LineIterator lineIterator) {
// No header for this format

18
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java
View File

@ -65,10 +65,12 @@ import java.util.Collections;
* @since 2009
*/
public class TableCodec extends AsciiFeatureCodec<TableFeature> implements ReferenceDependentFeatureCodec {
final static protected String delimiterRegex = "\\s+";
final static protected String headerDelimiter = "HEADER";
final static protected String igvHeaderDelimiter = "track";
final static protected String commentDelimiter = "#";
protected final static String delimiterRegex = "\\s+";
protected final static String headerDelimiter = "HEADER";
protected final static String igvHeaderDelimiter = "track";
protected final static String commentDelimiter = "#";
// codec file extension
protected final static String FILE_EXT = "tbl";
protected ArrayList<String> header = new ArrayList<String>();
@ -100,6 +102,14 @@ public class TableCodec extends AsciiFeatureCodec<TableFeature> implements Refer
return new TableFeature(genomeLocParser.parseGenomeLoc(split[0]),Arrays.asList(split), header);
}
/**
* Can the file be decoded?
* @param path path the file to test for parsability with this codec
* @return true if the path has the correct file extension, false otherwise
*/
@Override
public boolean canDecode(final String path) { return path.endsWith("." + FILE_EXT); }
@Override
public Object readActualHeader(final LineIterator reader) {
boolean isFirst = true;

42
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java 100644
View File

@ -0,0 +1,42 @@
/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.codecs.beagle;
import org.testng.Assert;
import org.testng.annotations.Test;
public class BeagleCodecUnitTest {
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
BeagleCodec codec = new BeagleCodec();
Assert.assertTrue(codec.canDecode("filename." + BeagleCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + BeagleCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + BeagleCodec.FILE_EXT + EXTRA_CHAR));
Assert.assertFalse(codec.canDecode("filename" + BeagleCodec.FILE_EXT));
}
}

12
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
View File

@ -142,7 +142,7 @@ public class HapMapUnitTest extends BaseTest {
codec.readHeader(reader);
line = reader.next();
RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
Assert.assertEquals(feature.getSampleIDs().length,87);
Assert.assertEquals(feature.getSampleIDs().length, 87);
} catch (IOException e) {
Assert.fail("IOException " + e.getMessage());
@ -151,6 +151,16 @@ public class HapMapUnitTest extends BaseTest {
}
}
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
RawHapMapCodec codec = new RawHapMapCodec();
Assert.assertTrue(codec.canDecode("filename." + RawHapMapCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + RawHapMapCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + RawHapMapCodec.FILE_EXT + EXTRA_CHAR));
Assert.assertFalse(codec.canDecode("filename" + RawHapMapCodec.FILE_EXT));
}
public LineIterator getLineIterator() {
try {

42
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java 100644
View File

@ -0,0 +1,42 @@
/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.codecs.refseq;
import org.testng.Assert;
import org.testng.annotations.Test;
public class RefSeqCodecUnitTest {
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
RefSeqCodec codec = new RefSeqCodec();
Assert.assertTrue(codec.canDecode("filename." + RefSeqCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + RefSeqCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + RefSeqCodec.FILE_EXT + EXTRA_CHAR));
Assert.assertFalse(codec.canDecode("filename" + RefSeqCodec.FILE_EXT));
}
}

42
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java 100644
View File

@ -0,0 +1,42 @@
/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.codecs.sampileup;
import org.testng.Assert;
import org.testng.annotations.Test;
public class SAMPileupCodecUnitTest {
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
SAMPileupCodec codec = new SAMPileupCodec();
Assert.assertTrue(codec.canDecode("filename." + SAMPileupCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + SAMPileupCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + SAMPileupCodec.FILE_EXT + "1"));
Assert.assertFalse(codec.canDecode("filename" + SAMPileupCodec.FILE_EXT));
}
}

42
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java 100644
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@ -0,0 +1,42 @@
/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.codecs.samread;
import org.testng.Assert;
import org.testng.annotations.Test;
public class SAMReadCodecUnitTest {
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
SAMReadCodec codec = new SAMReadCodec();
Assert.assertTrue(codec.canDecode("filename." + SAMReadCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + SAMReadCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + SAMReadCodec.FILE_EXT + "1"));
Assert.assertFalse(codec.canDecode("filename" + SAMReadCodec.FILE_EXT));
}
}

42
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java 100644
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/*
* Copyright 2012-2015 Broad Institute, Inc.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.codecs.table;
import org.testng.Assert;
import org.testng.annotations.Test;
public class TableCodecUnitTest {
@Test
public void testCanDecode() {
final String EXTRA_CHAR = "1";
TableCodec codec = new TableCodec();
Assert.assertTrue(codec.canDecode("filename." + TableCodec.FILE_EXT));
Assert.assertTrue(codec.canDecode("filename" + EXTRA_CHAR + "." + TableCodec.FILE_EXT));
Assert.assertFalse(codec.canDecode("filename." + TableCodec.FILE_EXT + EXTRA_CHAR));
Assert.assertFalse(codec.canDecode("filename" + TableCodec.FILE_EXT));
}
}