diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 716bff0aa..f048dbb88 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -331,9 +331,9 @@ public class GATKArgumentCollection { // // -------------------------------------------------------------------------------------------------------------- - @Argument(fullName="also_generate_bcf",doc="If provided, whenever we create a VCFWriter we will also write out a BCF file alongside it, for testing purposes",required=false) + @Argument(fullName="generateShadowBCF",doc="If provided, whenever we create a VCFWriter we will also write out a BCF file alongside it, for testing purposes",required=false) @Hidden - public boolean alsoGenerateBCF = false; - // TODO -- remove all code tagged with TODO -- remove me when argument alsoGenerateBCF is removed + public boolean generateShadowBCF = false; + // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed } diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index b04608a62..2ca7b46de 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -103,7 +103,7 @@ public class VariantContextWriterStorage implements Storage SUPPORTED_ZIPPED_SUFFIXES = new HashSet(); @@ -96,7 +96,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { @Override public List createArgumentDefinitions( ArgumentSource source ) { - return Arrays.asList( createDefaultArgumentDefinition(source),createNoHeaderArgumentDefinition(),createSitesOnlyArgumentDefinition()); + return Arrays.asList( createDefaultArgumentDefinition(source), createNoCommandLineHeaderArgumentDefinition(),createSitesOnlyArgumentDefinition()); } /** @@ -144,12 +144,12 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { // Should we compress the output stream? boolean compress = isCompressed(writerFileName); - boolean skipWritingHeader = argumentIsPresent(createNoHeaderArgumentDefinition(),matches); + boolean skipWritingCmdLineHeader = argumentIsPresent(createNoCommandLineHeaderArgumentDefinition(),matches); boolean doNotWriteGenotypes = argumentIsPresent(createSitesOnlyArgumentDefinition(),matches); // Create a stub for the given object. - VariantContextWriterStub stub = (writerFile != null) ? new VariantContextWriterStub(engine, writerFile, compress, argumentSources, skipWritingHeader, doNotWriteGenotypes) - : new VariantContextWriterStub(engine, defaultOutputStream, compress, argumentSources, skipWritingHeader, doNotWriteGenotypes); + VariantContextWriterStub stub = (writerFile != null) ? new VariantContextWriterStub(engine, writerFile, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes) + : new VariantContextWriterStub(engine, defaultOutputStream, compress, argumentSources, skipWritingCmdLineHeader, doNotWriteGenotypes); // WARNING: Side effects required by engine! parsingEngine.addTags(stub,getArgumentTags(matches)); @@ -162,7 +162,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { * Creates the optional compression level argument for the BAM file. * @return Argument definition for the BAM file itself. Will not be null. */ - private ArgumentDefinition createNoHeaderArgumentDefinition() { + private ArgumentDefinition createNoCommandLineHeaderArgumentDefinition() { return new ArgumentDefinition( ArgumentIOType.ARGUMENT, boolean.class, NO_HEADER_ARG_NAME, diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index e649397cf..8018db4e6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -87,7 +87,7 @@ public class VariantContextWriterStub implements Stub, Var /** * Should the header be written out? A hidden argument. */ - private final boolean skipWritingHeader; + private final boolean skipWritingCommandLineHeader; /** * Should we not write genotypes even when provided? @@ -107,16 +107,16 @@ public class VariantContextWriterStub implements Stub, Var * @param genotypeFile file to (ultimately) create. * @param isCompressed should we compress the output stream? * @param argumentSources sources. - * @param skipWritingHeader skip writing header. + * @param skipWritingCommandLineHeader skip writing header. * @param doNotWriteGenotypes do not write genotypes. */ - public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, boolean isCompressed, Collection argumentSources, boolean skipWritingHeader, boolean doNotWriteGenotypes) { + public VariantContextWriterStub(GenomeAnalysisEngine engine, File genotypeFile, boolean isCompressed, Collection argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) { this.engine = engine; this.genotypeFile = genotypeFile; this.genotypeStream = null; this.isCompressed = isCompressed; this.argumentSources = argumentSources; - this.skipWritingHeader = skipWritingHeader; + this.skipWritingCommandLineHeader = skipWritingCommandLineHeader; this.doNotWriteGenotypes = doNotWriteGenotypes; } @@ -127,16 +127,16 @@ public class VariantContextWriterStub implements Stub, Var * @param genotypeStream stream to (ultimately) write. * @param isCompressed should we compress the output stream? * @param argumentSources sources. - * @param skipWritingHeader skip writing header. + * @param skipWritingCommandLineHeader skip writing header. * @param doNotWriteGenotypes do not write genotypes. */ - public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, boolean isCompressed, Collection argumentSources, boolean skipWritingHeader, boolean doNotWriteGenotypes) { + public VariantContextWriterStub(GenomeAnalysisEngine engine, OutputStream genotypeStream, boolean isCompressed, Collection argumentSources, boolean skipWritingCommandLineHeader, boolean doNotWriteGenotypes) { this.engine = engine; this.genotypeFile = null; this.genotypeStream = new PrintStream(genotypeStream); this.isCompressed = isCompressed; this.argumentSources = argumentSources; - this.skipWritingHeader = skipWritingHeader; + this.skipWritingCommandLineHeader = skipWritingCommandLineHeader; this.doNotWriteGenotypes = doNotWriteGenotypes; } @@ -205,17 +205,13 @@ public class VariantContextWriterStub implements Stub, Var public void writeHeader(VCFHeader header) { vcfHeader = header; - // Check for the command-line argument header line. If not present, add it in. - if (!skipWritingHeader && header.isWriteEngineHeaders()) { - - if (header.isWriteCommandLine()) { - VCFHeaderLine commandLineArgHeaderLine = getCommandLineArgumentHeaderLine(); - boolean foundCommandLineHeaderLine = false; - for (VCFHeaderLine line: vcfHeader.getMetaData()) { - if ( line.getKey().equals(commandLineArgHeaderLine.getKey()) ) - foundCommandLineHeaderLine = true; - } - if ( !foundCommandLineHeaderLine ) + if ( header.isWriteEngineHeaders() ) { + // skip writing the command line header if requested + if ( ! skipWritingCommandLineHeader && header.isWriteCommandLine() ) { + // Check for the command-line argument header line. If not present, add it in. + final VCFHeaderLine commandLineArgHeaderLine = getCommandLineArgumentHeaderLine(); + final boolean foundCommandLineHeaderLine = vcfHeader.getMetaDataLine(commandLineArgHeaderLine.getKey()) != null; + if ( ! foundCommandLineHeaderLine ) vcfHeader.addMetaDataLine(commandLineArgHeaderLine); } @@ -251,12 +247,12 @@ public class VariantContextWriterStub implements Stub, Var /** * Should we also write a BCF file alongside our VCF file for testing * - * TODO -- remove me when argument alsoGenerateBCF is removed + * TODO -- remove me when argument generateShadowBCF is removed * * @return */ public boolean alsoWriteBCFForTest() { - return ! isCompressed() && getFile() != null && engine.getArguments().alsoGenerateBCF; + return ! isCompressed() && getFile() != null && engine.getArguments().generateShadowBCF; } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java index 707ddb39a..2b47b0d12 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java @@ -198,6 +198,20 @@ public class VCFHeader { return Collections.unmodifiableSet(lines); } + /** + * Get the VCFHeaderLine whose key equals key. Returns null if no such line exists + * @param key + * @return + */ + public VCFHeaderLine getMetaDataLine(final String key) { + for (final VCFHeaderLine line: getMetaData()) { + if ( line.getKey().equals(key) ) + return line; + } + + return null; + } + /** * get the genotyping sample names * diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java index e7169321c..f7b527772 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java @@ -15,7 +15,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest { " -genotypeMergeOptions REQUIRE_UNIQUE" + " -setKey null" + " -o %s" + - " -NO_HEADER"; + " --no_cmdline_in_header"; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index a3cd2d39f..757ae92f7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -9,7 +9,7 @@ import java.util.Arrays; public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantAnnotator -R " + b36KGReference + " -NO_HEADER -o %s"; + return "-T VariantAnnotator -R " + b36KGReference + " --no_cmdline_in_header -o %s"; } @Test @@ -155,7 +155,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final String MD5 = "bb9a148716fc69d706c5be146c1afa00"; 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_HEADER", 1, + baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1, Arrays.asList(MD5)); executeTest("Testing lookup vcf tabix vs. vcf tribble", spec); } @@ -164,7 +164,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testSnpEffAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( - "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " + + "-T VariantAnnotator -R " + hg19Reference + " --no_cmdline_in_header -o %s -A SnpEff --variant " + 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, @@ -176,7 +176,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testSnpEffAnnotationsUnsupportedVersion() { WalkerTestSpec spec = new WalkerTestSpec( - "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " + + "-T VariantAnnotator -R " + hg19Reference + " --no_cmdline_in_header -o %s -A SnpEff --variant " + validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation + "snpEff.AFR.unfiltered.unsupported.version.vcf -L 1:1-1,500,000", 1, @@ -190,7 +190,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final String MD5 = "a78c1e950740d3c13c0258960c5fa8e1"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" + - " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, + " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, Arrays.asList(MD5)); executeTest("Testing TDT annotation ", spec); } @@ -201,7 +201,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final String MD5 = "32df3ceb63c277df442ed55fb8684933"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" + - " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, + " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, Arrays.asList(MD5)); executeTest("Testing ChromosomeCounts annotation with PED file", spec); } @@ -211,7 +211,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final String MD5 = "7f1314fada5cb1f35ba1996f8a7a686b"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" + - " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, + " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1, Arrays.asList(MD5)); executeTest("Testing InbreedingCoeff annotation with PED file", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 9aae1f0ae..f31c3c4f5 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest { "--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " + "--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " + "--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " + - "-o %s -NO_HEADER", 1, Arrays.asList("6d0f213918e3b9ea33bc2f8a51a462f1")); + "-o %s --no_cmdline_in_header", 1, Arrays.asList("6d0f213918e3b9ea33bc2f8a51a462f1")); executeTest("test BeagleOutputToVCF", spec); } @@ -59,7 +59,7 @@ public class BeagleIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T ProduceBeagleInput --variant:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+ "--validation:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+ - "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2, + "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta --no_cmdline_in_header ",2, Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166")); executeTest("test BeagleInputWithBootstrap",spec); } @@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest { "--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+ "--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+ "--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+ - "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("ddbf490f1d9f37cc79fe414c8d40886f")); + "-L 20:1-70000 -o %s --no_cmdline_in_header ",1,Arrays.asList("ddbf490f1d9f37cc79fe414c8d40886f")); executeTest("testBeagleChangesSitesToRef",spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java index 2c04cebd4..d917a4147 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -8,7 +8,7 @@ import java.util.Arrays; public class VariantFiltrationIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantFiltration -o %s -NO_HEADER -R " + b36KGReference; + return "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b36KGReference; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index d031d393c..6cbbbc924 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -17,9 +17,9 @@ import java.util.Map; public class UnifiedGenotyperIntegrationTest extends WalkerTest { - private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl -NO_HEADER -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; - private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl -NO_HEADER -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; - private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132; + private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; + private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; + private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132; // -------------------------------------------------------------------------------------------------------------- // @@ -61,7 +61,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1, + "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1, Arrays.asList("ec907c65da5ed9b6046404b0f81422d4")); executeTest("test Multiple SNP alleles", spec); } @@ -69,7 +69,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testBadRead() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH -I " + validationDataLocation + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, + "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + validationDataLocation + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, Arrays.asList("7678827a2ee21870a41c09d28d26b996")); executeTest("test bad read", spec); } @@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, + "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --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("a70593bbb5042e2d0e46e3c932cae170")); executeTest("test reverse trim", spec); } @@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b36KGReference + " -NO_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, + "-T UnifiedGenotyper -R " + b36KGReference + " --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("e9d23a08472e4e27b4f25e844f5bad57")); executeTest("test SLOD", spec); } @@ -164,7 +164,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + b36KGReference + " -NO_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, + "-T UnifiedGenotyper -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("71251d8893649ea9abd5d9aa65739ba1")); executeTest("test using comp track", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 48be3264f..d84666416 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -20,7 +20,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + TNTest, "-ped "+ goodFamilyFile, @@ -39,7 +39,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + TPTest, "-ped "+ goodFamilyFile, @@ -58,7 +58,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + FPTest, "-ped "+ goodFamilyFile, @@ -77,7 +77,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + SpecialTest, "-ped "+ goodFamilyFile, @@ -98,7 +98,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + FPTest, "-ped "+ goodFamilyFile, @@ -120,7 +120,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + FPTest, "-ped "+ goodFamilyFile, @@ -139,7 +139,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T PhaseByTransmission", - "-NO_HEADER", + "--no_cmdline_in_header", "-R " + b37KGReference, "--variant " + TPTest, "-ped "+ goodFamilyFile, diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java index b78e76e07..4e515688a 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java @@ -16,7 +16,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " --maxPhaseSites " + maxPhaseSites + " --phaseQualityThresh " + phaseQualityThresh + " -o %s" + - " -NO_HEADER"; + " --no_cmdline_in_header"; } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java index 1a4de3e87..9bfa6b96b 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java @@ -14,7 +14,7 @@ import java.util.Arrays; */ public class ValidationSiteSelectorIntegrationTest extends WalkerTest { public static String baseTestString(String args) { - return "-T ValidationSiteSelector -R " + b36KGReference + " -L 1 -o %s -NO_HEADER -numSites 100 " + args; + return "-T ValidationSiteSelector -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header -numSites 100 " + args; } private static String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 79a58c820..95c47b3a5 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -63,7 +63,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { "-R " + b37KGReference + " -T ApplyRecalibration" + " -L 20:12,000,000-30,000,000" + - " -NO_HEADER" + + " --no_cmdline_in_header" + " -input " + params.inVCF + " -o %s" + " -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) + @@ -110,7 +110,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -T ApplyRecalibration" + " -L 20:12,000,000-30,000,000" + " -mode INDEL" + - " -NO_HEADER" + + " --no_cmdline_in_header" + " -input " + params.inVCF + " -o %s" + " -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) + @@ -126,7 +126,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -T ApplyRecalibration" + " -L 20:1000100-1000500" + " -mode BOTH" + - " -NO_HEADER" + + " --no_cmdline_in_header" + " -input " + validationDataLocation + "VQSR.mixedTest.input" + " -o %s" + " -tranchesFile " + validationDataLocation + "VQSR.mixedTest.tranches" + diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 649a76941..4b53ae4f7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -35,7 +35,7 @@ import java.util.Arrays; */ public class CombineVariantsIntegrationTest extends WalkerTest { public static String baseTestString(String args) { - return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args; + return "-T CombineVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + b36KGReference + args; } public void test1InOut(String file, String md5) { @@ -62,7 +62,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { String file1 = "1000G_omni2.5.b37.sites.vcf"; String file2 = "hapmap_3.3.b37.sites.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference + "-T CombineVariants --no_cmdline_in_header -o %s -R " + b37KGReference + " -L 1:1-10,000,000 -V:omni " + validationDataLocation + file1 + " -V:hm3 " + validationDataLocation + file2 + args, 1, @@ -72,7 +72,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { public void combinePLs(String file1, String file2, String md5) { WalkerTestSpec spec = new WalkerTestSpec( - "-T CombineVariants -NO_HEADER -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 " + validationDataLocation + file2, + "-T CombineVariants --no_cmdline_in_header -o %s -R " + b36KGReference + " -priority v1,v2 -V:v1 " + validationDataLocation + file1 + " -V:v2 " + validationDataLocation + file2, 1, Arrays.asList(md5)); executeTest("combine PLs 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec); @@ -119,7 +119,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { String file1 = "combine.1.vcf"; String file2 = "combine.2.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference + "-T CombineVariants --no_cmdline_in_header -o %s -R " + b37KGReference + " -V:one " + validationDataLocation + file1 + " -V:two " + validationDataLocation + file2 + args, 1, @@ -135,7 +135,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { @Test public void combineDBSNPDuplicateSites() { WalkerTestSpec spec = new WalkerTestSpec( - "-T CombineVariants -NO_HEADER -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132, + "-T CombineVariants --no_cmdline_in_header -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132, 1, Arrays.asList("a838dc241cf357466cd4331fd298c73a")); executeTest("combineDBSNPDuplicateSites:", spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java index 942bedc82..c7c7a4b15 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java @@ -38,7 +38,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest { @Test public void testLeftAlignment() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", + "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf --no_cmdline_in_header", 1, Arrays.asList("8e0991576518823b339a4e2f83299d4f")); executeTest("test left alignment", spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index 1308cb1e6..17bffe04f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -7,7 +7,7 @@ import java.util.Arrays; public class SelectVariantsIntegrationTest extends WalkerTest { public static String baseTestString(String args) { - return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s -NO_HEADER" + args; + return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s --no_cmdline_in_header" + args; } @Test @@ -30,7 +30,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -L 1:1-1000000 -o %s -NO_HEADER -xl_sn A -xl_sf " + samplesFile + " --variant " + testfile, + "-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("730f021fd6ecf1d195dabbee2e233bfd") ); @@ -56,7 +56,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("929bbb96381541c162dc7e5462e26ea2") ); @@ -69,7 +69,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + hg19Reference + " -L 20:1012700-1020000 --variant " + b37hapmapGenotypes + " -disc " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("5d7d899c0c4954ec59104aebfe4addd5") ); @@ -82,7 +82,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "NA12878.hg19.example1.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc " + b37hapmapGenotypes + " --variant " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a") ); @@ -95,7 +95,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "complexExample1.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + b36KGReference + " -restrictAllelesTo MULTIALLELIC -selectType MIXED --variant " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("e0b12c0b47a8a7a988b3587b47bfa8cf") ); @@ -108,7 +108,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "combine.3.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("167a1265df820978a74c267df44d5c43") ); @@ -121,7 +121,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "combine.3.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("0fd8e52bdcd1f4b921d8fb5c689f196a") ); @@ -134,7 +134,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "selectVariants.onePosition.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("ffa2524380d84a870d2e4a33d9f3d31a") ); @@ -147,7 +147,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testFile = validationDataLocation + "vcf4.1.example.vcf"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", 1, Arrays.asList("f17885e5cbd5387edb99112047ea43c1") ); @@ -182,7 +182,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String testfile = validationDataLocation + "multi-allelic.bi-allelicInGIH.vcf"; String samplesFile = validationDataLocation + "GIH.samples.list"; WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b37KGReference + " -o %s -NO_HEADER -sf " + samplesFile + " --excludeNonVariants --variant " + testfile, + "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile, 1, Arrays.asList("3fb50cc1c955491048108956d7087c35") ); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java index 3b45c5af3..b20240fd8 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -57,7 +57,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { "-T SelectVariants" + " -R " + b36KGReference + " --variant:vcf3,storage=STREAM " + tmpFifo.getAbsolutePath() + - " --NO_HEADER" + + " ---no_cmdline_in_header" + " -o %s", 1, Arrays.asList("658f580f7a294fd334bd897102616fed") @@ -81,7 +81,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { "-T SelectVariants" + " -R " + b36KGReference + " --variant:vcf3,storage=STREAM " + testFile + - " --NO_HEADER" + + " ---no_cmdline_in_header" + " -select 'QD > 2.0'" + " -o " + tmpFifo.getAbsolutePath(), 0, diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java index b56d4ef87..cf6d56cc7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -27,7 +27,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { " -T VariantsToVCF" + " -L 1:1-30,000,000" + " -o %s" + - " -NO_HEADER", + " --no_cmdline_in_header", 1, // just one output file md5); executeTest("testVariantsToVCFUsingDbsnpInput", spec).getFirst(); @@ -45,7 +45,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { " -L 1:10,000,000-11,000,000" + " -sample NA123AB" + " -o %s" + - " -NO_HEADER", + " --no_cmdline_in_header", 1, // just one output file md5); executeTest("testVariantsToVCFUsingGeliInput - calls", spec).getFirst(); @@ -63,7 +63,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { " -L 1:10,100,000-10,200,000" + " -sample NA123AB" + " -o %s" + - " -NO_HEADER", + " --no_cmdline_in_header", 1, // just one output file md5); executeTest("testVariantsToVCFUsingGeliInput - genotypes", spec).getFirst(); @@ -80,7 +80,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { " -T VariantsToVCF" + " -L 1:1-1,000,000" + " -o %s" + - " -NO_HEADER", + " --no_cmdline_in_header", 1, // just one output file md5); executeTest("testVariantsToVCFUsingHapMapInput", spec).getFirst(); @@ -96,7 +96,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { " --variant:VCF " + validationDataLocation + "complexExample.vcf4" + " -T VariantsToVCF" + " -o %s" + - " -NO_HEADER", + " --no_cmdline_in_header", 1, // just one output file md5); executeTest("testVariantsToVCFUsingVCFInput", spec).getFirst(); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index 30e86af34..84b88ea03 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -15,7 +15,7 @@ public class VCFIntegrationTest extends WalkerTest { String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447"; String testVCF = validationDataLocation + "vcf4.1.example.vcf"; - String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -L " + testVCF; WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF)); @@ -32,7 +32,7 @@ public class VCFIntegrationTest extends WalkerTest { String testVCF = testDir + "breakpoint-example.vcf"; //String testVCF = validationDataLocation + "multiallelic.vcf"; - String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + 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("acee3b6bdb4b759992f54065c675a249")); @@ -43,7 +43,7 @@ public class VCFIntegrationTest extends WalkerTest { public void testReadingAndWritingSamtools() { String testVCF = validationDataLocation + "samtools.vcf"; - String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; + 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("87d5b180ef5f9dc5aaee4b02601b43a2")); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index 196c32f19..40f66dba0 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -28,6 +28,7 @@ import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodecHeader; import org.broad.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec; import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.variantcontext.writer.Options; @@ -399,12 +400,18 @@ public class VariantContextTestProvider { writer.close(); final List actual = readAllVCs(tmpFile, tester.makeCodec()).getSecond(); - Assert.assertEquals(actual.size(), expected.size()); + assertEquals(actual, expected); - for ( int i = 0; i < expected.size(); i++ ) - VariantContextTestProvider.assertEquals(actual.get(i), expected.get(i)); } + /** + * Utility class to read all of the VC records from a file + * + * @param source + * @param codec + * @return + * @throws IOException + */ private final static Pair> readAllVCs( final File source, final FeatureCodec codec ) throws IOException { // read in the features PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source)); @@ -423,6 +430,25 @@ public class VariantContextTestProvider { return new Pair>((VCFHeader)header.getHeaderValue(), read); } + public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException { + final Pair> vcfData = readAllVCs(vcfFile, new VCFCodec()); + final Pair> bcfData = readAllVCs(bcfFile, new BCF2Codec()); + assertEquals(bcfData.getFirst(), vcfData.getFirst()); + assertEquals(bcfData.getSecond(), vcfData.getSecond()); + } + + public static void assertEquals(final List actual, final List expected) { + Assert.assertEquals(actual.size(), expected.size()); + + for ( int i = 0; i < expected.size(); i++ ) + assertEquals(actual.get(i), expected.get(i)); + } + + /** + * Assert that two variant contexts are actually equal + * @param actual + * @param expected + */ public static void assertEquals( final VariantContext actual, final VariantContext expected ) { Assert.assertNotNull(actual); Assert.assertEquals(actual.getChr(), expected.getChr()); @@ -430,4 +456,9 @@ public class VariantContextTestProvider { Assert.assertEquals(actual.getEnd(), expected.getEnd()); // TODO -- expand me } + + public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { + Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size()); + Assert.assertEquals(actual.getMetaData(), expected.getMetaData()); + } } \ No newline at end of file diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala index 8ac711f25..11a66a37b 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala @@ -50,7 +50,7 @@ class VcfGatherFunction extends CombineVariants with GatherFunction { // are added by the GATKExtensionsGenerator to the subclass of CommandLineGATK val noHeader = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.NO_HEADER_ARG_NAME) - this.NO_HEADER = originalGATK.getFieldValue(noHeader).asInstanceOf[Boolean] + this.no_cmdline_in_header = originalGATK.getFieldValue(noHeader).asInstanceOf[Boolean] val sitesOnly = QFunction.findField(originalFunction.getClass, VCFWriterArgumentTypeDescriptor.SITES_ONLY_ARG_NAME) this.sites_only = originalGATK.getFieldValue(sitesOnly).asInstanceOf[Boolean]