diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 991f8015b..8b3d05675 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -252,6 +252,7 @@ public class GenomeAnalysisEngine { for (String str : rodNames.keySet()) if (str.equals(rodName)) { + logger.info("Adding interval list from track (ROD) named " + rodName); RMDIntervalGenerator intervalGenerator = new RMDIntervalGenerator(rodNames.get(str).getReferenceOrderedData()); ret.addAll(intervalGenerator.toGenomeLocList()); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index a74a4f36c..d26ebd4fb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -25,10 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broad.tribble.vcf.VCFGenotypeRecord; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFInfoHeaderLine; -import org.broad.tribble.vcf.VCFRecord; +import org.broad.tribble.vcf.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -156,7 +153,7 @@ public class UnifiedGenotyper extends LocusWalker args = new HashSet(); diff --git a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java index 501b92d2e..78f999da8 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.genotype; import net.sf.samtools.SAMFileHeader; import org.broad.tribble.vcf.VCFHeaderLine; import org.broad.tribble.vcf.VCFGenotypeRecord; +import org.broad.tribble.vcf.VCFHeaderVersion; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.genotype.geli.*; import org.broadinstitute.sting.utils.genotype.glf.*; @@ -68,7 +69,7 @@ public class GenotypeWriterFactory { // VCF if ( writer instanceof VCFGenotypeWriter ) { if ( headerInfo == null ) - headerInfo = new HashSet(VCFGenotypeRecord.getSupportedHeaderStrings()); + headerInfo = new HashSet(VCFGenotypeRecord.getSupportedHeaderStrings(VCFHeaderVersion.VCF3_3)); ((VCFGenotypeWriter)writer).writeHeader(sampleNames, headerInfo); } // GELI diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java index 4bae2afc5..2f9fef96a 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java @@ -1,9 +1,6 @@ package org.broadinstitute.sting.utils.genotype.vcf; -import org.broad.tribble.vcf.VCFFormatHeaderLine; -import org.broad.tribble.vcf.VCFHeader; -import org.broad.tribble.vcf.VCFHeaderLine; -import org.broad.tribble.vcf.VCFRecord; +import org.broad.tribble.vcf.*; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; import org.apache.log4j.Logger; @@ -57,7 +54,7 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter { // set up the header fields Set hInfo = new TreeSet(); - hInfo.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION)); + hInfo.add(new VCFHeaderLine(VCFHeaderVersion.VCF3_3.getFormatString(), VCFHeaderVersion.VCF3_3.getVersionString())); // set up the allowed genotype format fields if ( headerInfo != null ) { diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java index f2deeae47..fba1303ac 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.genotype.vcf; import org.broad.tribble.vcf.VCFHeader; import org.broad.tribble.vcf.VCFHeaderLine; +import org.broad.tribble.vcf.VCFHeaderVersion; import org.broad.tribble.vcf.VCFRecord; import java.io.*; @@ -52,11 +53,11 @@ public class VCFWriter { // the fileformat field needs to be written first TreeSet nonFormatMetaData = new TreeSet(); for ( VCFHeaderLine line : header.getMetaData() ) { - if ( line.getKey().equals(VCFHeader.FILE_FORMAT_KEY) ) { + if ( line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ) { mWriter.write(VCFHeader.METADATA_INDICATOR + line.toString() + "\n"); } - else if ( line.getKey().equals(VCFHeader.OLD_FILE_FORMAT_KEY) ) { - mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeader.FILE_FORMAT_KEY + line.toString().substring(VCFHeader.OLD_FILE_FORMAT_KEY.length()) + "\n"); + else if ( line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) ) { + mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF3_2.getFormatString() + "=" + VCFHeaderVersion.VCF3_2.getVersionString() + "\n"); } else { nonFormatMetaData.add(line); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java index ce1cefe74..de8b64c7c 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java @@ -70,7 +70,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { @Test public void testGenotypesToVCFUsingVCFInput() { List md5 = new ArrayList(); - md5.add("92d661a3789e55078197666eb9ee7020"); + md5.add("3f920c6a443764b183e4765b4e4d00b0"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + oneKGLocation + "reference/human_b36_both.fasta" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java index a0fcc2274..bc4a098ed 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java @@ -63,7 +63,7 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { + " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" + " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf" + " -o %s -L chr15:46347148"; - String expected_md5 = "465f92e689110afeb308c201cb6e8c5a"; + String expected_md5 = "f4aff94a713fcf4dc5750d6a6a884ad3"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); executeTest("Testing on locus with many indels", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 71e5b5319..992b36ad6 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -30,7 +30,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { case 2: return "-L chr22:20660081-20660083 -L chr22:29198100-29198104 -L chr22:29821330-29821334"; default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo); } - } + } public static String secondBaseTestmd5( int testNo ) { switch ( testNo ) { @@ -50,7 +50,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("5a91f6b50fc136d7d3f8735dbc64defe")); + Arrays.asList("92369e62b3bade625992bc1741e9367a")); executeTest("test file has annotations, not asking for annotations, #1", spec); } @@ -58,7 +58,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("0a561b161a06e68b88417ff5fe365871")); + Arrays.asList("1a394cdace4ff7698b603c2252ee9365")); executeTest("test file has annotations, not asking for annotations, #2", spec); } @@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("dff7c888fbd142b6eff27c3233c1292d")); + Arrays.asList("5a8c9c18da89b052e7f3797cd391bff6")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("45c9d5136900d9ab347f489d6f442bb4")); + Arrays.asList("0c8607c69d761bd058b944d1e98708b6")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("16e578597eed68609268c00886f2842a")); + Arrays.asList("006642aabd41e806d3ea64bf5441f1d2")); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); } @@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("0e947087c44479faefe616f6b6f7d272")); + Arrays.asList("c66ed83d2a981c43546d05120809ed57")); executeTest("test file doesn't have annotations, not asking for annotations, #2", spec); } @@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("7c13af3226a92bfc3826c37b30f179e0")); + Arrays.asList("3b570e13bd0e1cb5750da268178ce656")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { 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, - Arrays.asList("369ad538eacdc0943b58a807d92d823c")); + Arrays.asList("42e9c57cd5d266fd7837354fc8495176")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -114,7 +114,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("07af9983127c62e96accc03db2fb523e")); + Arrays.asList("374da32e1b9540bfe8ee6ea5b896babd")); executeTest("not passing it any reads", spec); } @@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTag() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, - Arrays.asList("286887826ab99bb2864f7f4db195e59e")); + Arrays.asList("05a9dcb87efc65e5c726c201460192d9")); executeTest("getting DB tag", spec); } } \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java index 5b86f8edc..81ac7b734 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java @@ -14,7 +14,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testSimpleVenn() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1, - Arrays.asList("d9124d2b0fb5bec5bc50c26a16b4e900")); + Arrays.asList("a1970effe9c51923d52af9034e778de4")); executeTest("testSimpleVenn", spec); } @@ -22,7 +22,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testSNPConcordance() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1, - Arrays.asList("df1fbc744947f316f65f51a21368b0e4")); + Arrays.asList("e7a0d52c266ba3c76283111674c7168f")); executeTest("testSNPConcordance", spec); } @@ -30,7 +30,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testNWayVenn() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1, - Arrays.asList("aa835ae5368b35f376b844d7f8ef2976")); + Arrays.asList("e65fc811137fca7d6c32125240c7468f")); executeTest("testNWayVenn", spec); } @@ -38,7 +38,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testMulti() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1, - Arrays.asList("c9ef68cc3b7dc08f1d2b49170e6560ab")); + Arrays.asList("ddc2507590e28743e9cb4b132cb066e7")); executeTest("testMulti", spec); } @@ -46,7 +46,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { public void testComplex() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B set1,VCF," + validationDataLocation + "complexExample.vcf -B set2,VCF," + validationDataLocation + "complexExample.vcf -CT NWayVenn", 1, - Arrays.asList("7bc72ec5f8b0fda5d59ebd2526b53e48")); + Arrays.asList("250df7bde7a8cf9c7ee7c5704183ea88")); executeTest("testComplex", 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 b98648a31..55e831fed 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testNoAction() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("af14c7d03e3516b61f2702c9e4a7780f")); + Arrays.asList("d2f0a3c6e598d9054de9ea7bd914a12d")); executeTest("test no action", spec); } @@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testClusteredSnps() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("b2b18929289bb47f07bcc23d4cec94c4")); + Arrays.asList("4dad2ddfb74785c5c80c2a73709e543a")); executeTest("test clustered SNPs", spec); } @@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testMask() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("af048053eaef84fc4d61c51c50be1e0a")); + Arrays.asList("70fc964e73fda55ed3f2c0b0ae4bcec1")); executeTest("test mask", spec); } @@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilter1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("43a580d9c684a496f21d0d42939dd910")); + Arrays.asList("bde496530822a81197df31f5ecf98033")); executeTest("test filter #1", spec); } @@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilter2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("2bd1e8975d8105dec2fb6055fbf00569")); + Arrays.asList("750f5076e906901dabec78f804f035fa")); executeTest("test filter #2", spec); } @@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { public void testFilterWithSeparateNames() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, - Arrays.asList("3479158ffd02a45371b5103277a30a53")); + Arrays.asList("7f876c9187948d27c0cd39f5a0395e0e")); executeTest("test filter with separate names #2", spec); } } \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 2b2c11f27..7a67bf8ce 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -39,7 +39,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testVariantRecalibrator() { HashMap e = new HashMap(); - e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "412bdb2eb4ca8f7ee9dfb39cda676c95" ); + e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "cf8dac86df97d55f866dd379434bbdc2" ); for ( Map.Entry entry : e.entrySet() ) { String vcf = entry.getKey(); diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index c1162b9fa..97fcf1e30 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -66,8 +66,8 @@ public class VCFWriterUnitTest extends BaseTest { * @return a fake VCF header */ public static VCFHeader createFakeHeader(Set metaData, Set additionalColumns) { - metaData.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION)); - metaData.add(new VCFHeaderLine("two", "2")); + metaData.add(new VCFHeaderLine(VCFHeaderVersion.VCF3_3.getFormatString(), VCFHeaderVersion.VCF3_3.getVersionString(),VCFHeaderVersion.VCF3_3)); + metaData.add(new VCFHeaderLine("two", "2",VCFHeaderVersion.VCF3_3)); additionalColumns.add("FORMAT"); additionalColumns.add("extra1"); additionalColumns.add("extra2");