diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index 74faef31b..212a09937 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -33,7 +33,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation; import org.broad.tribble.util.variantcontext.*; import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker; import org.broadinstitute.sting.utils.*; -import org.broad.tribble.vcf.VCFCodec; +import org.broad.tribble.vcf.VCFCodecUtils; import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -566,7 +566,7 @@ public class VariantContextUtils { VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? maxACAttributes : attributes) ); // Trim the padded bases of all alleles if necessary - merged = VCFCodec.createVariantContextWithTrimmedAlleles(merged); + merged = VCFCodecUtils.createVariantContextWithTrimmedAlleles(merged); if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged); return merged; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index a80549460..b86831cd3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; import org.broad.tribble.bed.BEDCodec; import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.util.variantcontext.VariantContext; +import org.broad.tribble.vcf.VCF3Codec; import org.broad.tribble.vcf.VCFCodec; import org.broadinstitute.sting.commandline.Gather; import org.broadinstitute.sting.commandline.Output; @@ -192,6 +193,7 @@ public class CountCovariatesWalker extends LocusWalker expectations = new HashMap(); static { @@ -47,7 +47,7 @@ public class VariantContextIntegrationTest extends WalkerTest { public void testToVCF() { // this really just tests that we are seeing the same number of objects over all of chr1 - WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", + WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", 2, // just one output file Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "e6673737acbb6bfabfcd92c4b2268241")); executeTest("testToVCF", spec); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java index 50c52cd99..218948c52 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java @@ -28,6 +28,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; +import org.broad.tribble.vcf.VCF3Codec; import org.broad.tribble.vcf.VCFCodec; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -82,7 +83,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest { public void testBuilderIndexUnwriteable() { File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/relic.vcf"); try { - builder.loadIndex(vcfFile, new VCFCodec()); + builder.loadIndex(vcfFile, new VCF3Codec()); } catch (IOException e) { e.printStackTrace(); Assert.fail("IO exception unexpected" + e.getMessage()); @@ -118,7 +119,7 @@ public class RMDTrackBuilderUnitTest extends BaseTest { Index ind = null; try { - ind = builder.loadIndex(vcfFile, new VCFCodec()); + ind = builder.loadIndex(vcfFile, new VCF3Codec()); } catch (IOException e) { e.printStackTrace(); Assert.fail("IO exception unexpected" + e.getMessage()); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 9ecd3cdbe..50d19830d 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -14,7 +14,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347")); executeTest("test file has annotations, not asking for annotations, #1", spec); } @@ -22,7 +22,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("1de8e943fbf55246ebd19efa32f22a58")); executeTest("test file has annotations, not asking for annotations, #2", spec); } @@ -30,7 +30,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("11fab4bbd26e0428e6d7b53284a34388")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -38,7 +38,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("4fb98442f2c09247fab296872abb5655")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -46,7 +46,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("4b48e7d095ef73e3151542ea976ecd89")); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); } @@ -54,7 +54,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("28dfbfd178aca071b948cd3dc2365357")); executeTest("test file doesn't have annotations, not asking for annotations, #2", spec); } @@ -62,7 +62,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("4bcc71f014def02d0fe9237176cc99af")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -70,7 +70,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("c92e614ec796a5b39c5fdcc426410a9b")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, + baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, Arrays.asList("019d6b1bb7b367759fc42fbdb14b8bf7")); executeTest("not passing it any reads", spec); } @@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, + baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, Arrays.asList("92a29447f222eadb549dc05ddd11b45e")); executeTest("getting DB tag with dbSNP", spec); } @@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, + baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, Arrays.asList("067dde55de98a631225e0e084f0fcc1a")); executeTest("getting DB tag with HM3", spec); } @@ -110,7 +110,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1, + baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1, Arrays.asList("e55b457426d6ba7f8ccea085c23c1350")); executeTest("using expression", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java index f5233330e..c4f6d5ebc 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java @@ -32,7 +32,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest { String[] md5WithDashSArg = {"3d3b61a83c1189108eabb2df04218099"}; WalkerTestSpec specWithSArg = new WalkerTestSpec( "-T GenomicAnnotator -R " + b36KGReference + - " -B:variant,vcf /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" + + " -B:variant,vcf3 /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" + " -B:dbsnp,AnnotatorInputTable /humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt" + " -m" + //generate many records from one input record if necessary " -o %s" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 5234c992c..70c34e729 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -37,7 +37,7 @@ public class BeagleIntegrationTest extends WalkerTest { public void testBeagleOutput() { WalkerTestSpec spec = new WalkerTestSpec( "-T BeagleOutputToVCF -R " + hg19Reference + " " + - "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " + + "-B:variant,VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " + "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " + "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " + @@ -49,7 +49,7 @@ public class BeagleIntegrationTest extends WalkerTest { public void testBeagleInput() { WalkerTestSpec spec = new WalkerTestSpec( "-T ProduceBeagleInput -R " + hg19Reference + " " + - "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " + + "-B:variant,VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-o %s", 1, Arrays.asList("a01c704246f3dd1b9c65774007e51e69")); executeTest("test BeagleInput", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java index 2899ecedb..840b29b37 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testNoAction() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347")); executeTest("test no action", spec); } @@ -23,7 +23,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testClusteredSnps() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -window 10 -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -window 10 -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("ada5540bb3d9b6eb8f1337ba01e90a94")); executeTest("test clustered SNPs", spec); } @@ -31,7 +31,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testMask() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -mask foo -B:mask,VCF3 " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("b0fcac4af3526e3b2a37602ab4c0e6ae")); executeTest("test mask", spec); } @@ -39,7 +39,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("7a40795147cbfa92941489d7239aad92")); executeTest("test filter #1", spec); } @@ -47,7 +47,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("e9dd4991b1e325847c77d053dfe8ee54")); executeTest("test filter #2", spec); } @@ -55,7 +55,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilterWithSeparateNames() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("9ded2cce63b8d97550079047051d80a3")); executeTest("test filter with separate names #2", spec); } @@ -63,7 +63,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testGenotypeFilter1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("6696e3f65a62ce912230d47cdb0c129b")); executeTest("test genotype filter #1", spec); } @@ -71,7 +71,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testGenotypeFilter2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("26e5b4ee954c9e0b5eb044afd4b88ee9")); executeTest("test genotype filter #2", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index dd7af78a3..e11e600a2 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -204,7 +204,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp,VCF " + validationDataLocation + "vcfexample3.vcf" + + " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + " -L 1:10,000,000-10,200,000" + @@ -228,7 +228,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:anyNameABCD,VCF " + validationDataLocation + "vcfexample3.vcf" + + " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 337afb26f..0f046f96a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -18,13 +18,13 @@ public class VariantEvalIntegrationTest extends WalkerTest { private static String root = cmdRoot + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; + " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + + " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; private static String rootGZ = cmdRoot + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + - " -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + - " -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; + " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + + " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; // TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB] // private static String[] testsEnumerations = {root, rootGZ}; @@ -355,7 +355,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testVEGenotypeConcordance() { String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"}; for (String vcfFile : vcfFiles) { - WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", + WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, Arrays.asList("732d32997b19d9c4f0291287858c56d2")); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); @@ -388,7 +388,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { HashMap expectations = new HashMap(); String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator -ST CpG" + " -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" + - " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; + " -B:comp_hapmap,VCF3 " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; expectations.put("", "700eba07bac9fba4ed963bbbdcab0e29"); @@ -410,7 +410,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { - String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf"; + String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e68272d2f3b7a6439c4949cf0e34beeb")); executeTestParallel("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 0992657e0..8371acce9 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -39,42 +39,42 @@ public class CombineVariantsIntegrationTest extends WalkerTest { return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args; } - public void test1InOut(String file, String md5) { - test1InOut(file, md5, ""); + public void test1InOut(String file, String md5, boolean vcf3) { + test1InOut(file, md5, "", vcf3); } - public void test1InOut(String file, String md5, String args) { + public void test1InOut(String file, String md5, String args, boolean vcf3) { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -priority v1 -B:v1,VCF " + validationDataLocation + file + args), + baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args), 1, Arrays.asList(md5)); executeTest("testInOut1--" + file, spec); } - public void combine2(String file1, String file2, String args, String md5) { + public void combine2(String file1, String file2, String args, String md5, boolean vcf3) { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -priority v1,v2 -B:v1,VCF " + validationDataLocation + file1 + " -B:v2,VCF " + validationDataLocation + file2 + args), + baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args), 1, Arrays.asList(md5)); executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec); } - @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c"); } - @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo"); } - @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null"); } - @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308"); } // official project VCF files in tabix format + @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); } + @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); } + @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); } + @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format - @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12"); } - @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d"); } + @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); } + @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); } - @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3"); } // 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", "802977fdfd2f4905b501bb06800f60af"); } // 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", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a"); } + @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // 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", "802977fdfd2f4905b501bb06800f60af", false); } // 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", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); } - @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53"); } + @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); } - @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48"); } + @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); } @Test public void threeWayWithRefs() { WalkerTestSpec spec = new WalkerTestSpec( diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index 1dfdf5831..d32ab6282 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testb36Tohg19() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "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", + "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "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("37e23efd7d6471fc0f807b31ccafe0eb")); executeTest("test b36 to hg19", spec); @@ -47,7 +47,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testb36Tohg19UnsortedSamples() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf " + validationDataLocation + "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", + "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "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("b6ef4a2f026fd3843aeb9ed764a66921")); executeTest("test b36 to hg19, unsorted samples", spec); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 235e16cc1..23fd43b01 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF3 " + testfile + " -NO_HEADER"), 1, Arrays.asList("1df84e2b755cce19f1876710ec38dd2c") ); @@ -29,7 +29,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testfile = validationDataLocation + "test.dup.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -sn A -sn B -sn C -B:variant,VCF " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -sn B -sn C -B:variant,VCF3 " + testfile + " -NO_HEADER"), 1, Arrays.asList("fe6963e5fea1d3854634dcf3defd7b92") ); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java index 814530719..15733e104 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -56,7 +56,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants" + " -R " + b36KGReference + - " -B:variant,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() + + " -B:variant,vcf3,storage=STREAM " + tmpFifo.getAbsolutePath() + " --NO_HEADER" + " -o %s", 1, @@ -80,7 +80,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { WalkerTestSpec selectTestSpec = new WalkerTestSpec( "-T SelectVariants" + " -R " + b36KGReference + - " -B:variant,vcf,storage=STREAM " + testFile + + " -B:variant,vcf3,storage=STREAM " + testFile + " --NO_HEADER" + " -select 'QD > 2.0'" + " -o " + tmpFifo.getAbsolutePath(), @@ -93,7 +93,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { selectTestSpec = new WalkerTestSpec( "-T VariantEval" + " -R " + b36KGReference + - " -B:eval,vcf " + testFile + + " -B:eval,vcf3 " + testFile + " -B:comp,vcf,storage=STREAM " + tmpFifo.getAbsolutePath() + " -EV CompOverlap -noEV -noST" + " -o %s", diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java index 61cd3c8fe..67c4297b1 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -42,7 +42,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString("validationExampleGood.vcf", "ALL"), 0, - Arrays.asList("") + Arrays.asList("d41d8cd98f00b204e9800998ecf8427e") ); executeTest("test good file", spec); diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java index c17b3ea26..fa9d0afbb 100644 --- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java @@ -21,7 +21,7 @@ public class ValidateRODForReadsIntegrationTest extends WalkerTest { @Test public void testSimpleVCFPileup() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:vcf,vcf " + vcfFile, 1, + baseTestString() + " -B:vcf,vcf3 " + vcfFile, 1, Arrays.asList("f7919e9dc156fb5d3ad0541666864ea5")); executeTest("testSimpleVCFPileup", spec); } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java index 79af15e12..4202c1e46 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java @@ -29,8 +29,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest { @Test public void testSimpleVCFPileup() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf", 1, - Arrays.asList("5d84c75746738833b6c9441d9d614553")); + baseTestString1KG() + " -B:eval,VCF3 " + validationDataLocation + "MultiSample.vcf", 1, + Arrays.asList("7dc521914d1fd39cc0cab0220b6187f4")); executeTest("testSimpleVCFPileup", spec); } @@ -40,8 +40,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest { if (vcf.exists()) vcf.delete(); WalkerTestSpec spec = new WalkerTestSpec( - baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "justHeader.vcf", 1, - Arrays.asList("b3e80d77f8c05edf2a385b0a87708670")); + baseTestString1KG() + " -B:eval,VCF3 " + validationDataLocation + "justHeader.vcf", 1, + Arrays.asList("fa30619829498040414b45ec78151079")); executeTest("testEmptyVCF", spec); } @@ -49,32 +49,32 @@ public class RodSystemValidationIntegrationTest extends WalkerTest { @Test public void testComplexVCFPileup() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" + + baseTestString1KG() + " -B:eval,VCF3 " + validationDataLocation + "MultiSample.vcf" + " -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" , 1, - Arrays.asList("8d97cbc29f73a0027267858f961e6fe5")); + Arrays.asList("ad9d697a015860089774452886cc1028")); executeTest("testComplexVCFPileup", spec); } @Test public void testBTIWithROD() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" + + baseTestString1KG() + " -B:eval,VCF3 " + validationDataLocation + "MultiSample.vcf" + " -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval" , 1, - Arrays.asList("ccfc0389a3c614f7892dbe972543f0ec")); + Arrays.asList("92adff4129bc4c6abb96fb67b8bf61b6")); executeTest("testBTIWithROD", spec); } @Test public void testLargeComplexVCFPileup() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" + - " -B:eval2,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" + - " -B:eval3,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" + + baseTestString1KG() + " -B:eval,VCF3 " + validationDataLocation + "MultiSample.vcf" + + " -B:eval2,VCF3 " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" + + " -B:eval3,VCF3 " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" + " -L 1 -L 2 -L 20" , 1, - Arrays.asList("8805912af2c38ec8d1cbc8d82532725e")); + Arrays.asList("2069cc9155af2ec10028acc8df4523b3")); executeTest("testLargeComplexVCFPileup", spec); } @@ -83,7 +83,7 @@ public class RodSystemValidationIntegrationTest extends WalkerTest { final String vcfName = validationDataLocation + "bgzipped_vcfs/vcfexample.vcf"; WalkerTestSpec spec = new WalkerTestSpec( baseTestString1KG() + " -B:eval,VCF " + vcfName + - " -B:eval2,VCF " + vcfName + ".gz" + + " -B:eval2,VCF3 " + vcfName + ".gz" + " --PerLocusEqual" , 1, Arrays.asList("ab3da32eae65e8c15a9f4a787a190a37"));