From b20c4d5286218ebccca790faa7a908235b3b9558 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 9 Aug 2011 12:04:55 -0400 Subject: [PATCH] Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two. --- .../walkers/annotator/VariantAnnotator.java | 3 +- .../beagle/ProduceBeagleInputWalker.java | 2 +- .../fasta/FastaAlternateReferenceWalker.java | 2 +- .../filters/VariantFiltrationWalker.java | 3 +- .../phasing/ReadBackedPhasingWalker.java | 2 +- .../walkers/variantutils/CombineVariants.java | 2 +- .../variantutils/LeftAlignVariants.java | 2 +- .../variantutils/LiftoverVariants.java | 2 +- .../walkers/variantutils/SelectVariants.java | 2 +- .../variantutils/ValidateVariants.java | 3 +- .../walkers/variantutils/VariantsToTable.java | 3 +- .../gatk/EngineFeaturesIntegrationTest.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 30 +++++++++---------- .../walkers/beagle/BeagleIntegrationTest.java | 8 ++--- .../VariantFiltrationIntegrationTest.java | 22 +++++++------- .../ReadBackedPhasingIntegrationTest.java | 2 +- .../DictionaryConsistencyIntegrationTest.java | 2 +- .../LeftAlignVariantsIntegrationTest.java | 2 +- .../LiftoverVariantsIntegrationTest.java | 6 ++-- .../SelectVariantsIntegrationTest.java | 8 ++--- .../VCFStreamingIntegrationTest.java | 4 +-- .../ValidateVariantsIntegrationTest.java | 2 +- .../VariantsToTableIntegrationTest.java | 2 +- .../utils/codecs/vcf/VCFIntegrationTest.java | 4 +-- 24 files changed, 62 insertions(+), 58 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index ef408fae3..ec7d51043 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -53,7 +53,8 @@ import java.util.*; @Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) public class VariantAnnotator extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 5bca61873..88b976e7e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -52,7 +52,7 @@ import java.util.*; */ @Requires(value={}) public class ProduceBeagleInputWalker extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index a509fec0f..93012ee10 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -48,7 +48,7 @@ import java.util.List; @Requires(value={DataSource.REFERENCE}) public class FastaAlternateReferenceWalker extends FastaReferenceWalker { - @Input(fullName = "variants", shortName = "V", doc="variants to model", required=false) + @Input(fullName = "variant", shortName = "V", doc="variants to model", required=false) public List> variants; @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 0daabfa45..e0bd58aea 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -52,7 +52,8 @@ import java.util.*; @Requires(value={}) @Reference(window=@Window(start=-50,stop=50)) public class VariantFiltrationWalker extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Input(fullName="mask", doc="Input ROD mask", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index 7df55b4cd..f81dec2ac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -67,7 +67,7 @@ public class ReadBackedPhasingWalker extends RodWalker variants; @Output(doc = "File to which variants should be written", required = true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 7905c2c32..f24d7a211 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -64,7 +64,7 @@ public class CombineVariants extends RodWalker { * are techincally order dependent. It is strongly recommended to provide explicit names when * a rod priority list is provided. */ - @Input(fullName = "variants", shortName = "V", doc="The VCF files to merge together", required=true) + @Input(fullName = "variant", shortName = "V", doc="The VCF files to merge together", required=true) public List> variantsToMerge; @Output(doc="File to which variants should be written",required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index d8bcb252d..52b633cdf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -50,7 +50,7 @@ import java.util.*; @Reference(window=@Window(start=-200,stop=200)) @Requires(value={}) public class LeftAlignVariants extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Output(doc="File to which variants should be written",required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index f3f0085f9..7edb4d52c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -52,7 +52,7 @@ import java.util.*; */ @Requires(value={}) public class LiftoverVariants extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Output(doc="File to which variants should be written",required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index ce885efc0..7179956c1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -61,7 +61,7 @@ public class SelectVariants extends RodWalker { * Variants from this file are sent through the filtering and modifying routines as directed * by the arguments to SelectVariants, and finally are emitted. */ - @Input(fullName="variants", shortName = "V", doc="Select variants from this VCF file", required=true) + @Input(fullName="variant", shortName = "V", doc="Select variants from this VCF file", required=true) public RodBinding variants; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index a0986143c..9f64e0ca4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -55,7 +55,8 @@ import java.util.Set; @Reference(window=@Window(start=0,stop=100)) @Requires(value={}) public class ValidateVariants extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; public enum ValidationType { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 8c1c33f1b..f999f25c0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -47,7 +47,8 @@ import java.util.*; */ @Requires(value={}) public class VariantsToTable extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + + @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @Output(doc="File to which results should be written",required=true) diff --git a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java index 80a8d2fa4..5b5083ef3 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java @@ -33,7 +33,7 @@ import org.testng.annotations.Test; */ public class EngineFeaturesIntegrationTest extends WalkerTest { private void testBadRODBindingInput(String type, String name, Class c) { - WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variants:variants," + type + " " + WalkerTestSpec spec = new WalkerTestSpec("-T SelectVariants -L 1:1 --variant:variant," + type + " " + b37dbSNP132 + " -R " + b37KGReference + " -o %s", 1, c); executeTest(name, spec); 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 cbfb3cd0b..492651635 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 @@ -14,7 +14,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " --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("8a105fa5eebdfffe7326bc5b3d8ffd1c")); 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() + " --variants:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " --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("964f1016ec9a3c55333f62dd834c14d6")); 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\" --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G \"Standard\" --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("8e7de435105499cd71ffc099e268a83e")); 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\" --variants:VCF3 " + 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\" --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("64b6804cb1e27826e3a47089349be581")); 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() + " --variants:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " --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("42ccee09fa9f8c58f4a0d4f1139c094f")); 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() + " --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " --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("f2ddfa8105c290b1f34b7a261a02a1ac")); 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\" --variants:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G \"Standard\" --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("fd1ffb669800c2e07df1e2719aa38e49")); 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\" --variants:VCF3 " + 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\" --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("09f8e840770a9411ff77508e0ed0837f")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -78,7 +78,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" --variants:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, + baseTestString() + " -G \"Standard\" --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, Arrays.asList("78d2c19f8107d865970dbaf3e12edd92")); executeTest("test overwriting header", spec); } @@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, Arrays.asList("16e3a1403fc376320d7c69492cad9345")); 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() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d")); 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\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688")); 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\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1, + baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1, Arrays.asList("e9c0d832dc6b4ed06c955060f830c140")); executeTest("using expression", spec); } @@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf"; 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 --variants:VCF " + validationDataLocation + "/" + file + " -BTI variants -NO_HEADER", 1, + baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variants -NO_HEADER", 1, Arrays.asList(MD5)); executeTest("Testing lookup vcf tabix vs. vcf tribble", spec); } @@ -129,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testSnpEffAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( - "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variants:VCF " + + "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant:VCF " + validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation + "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000", 1, 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 d6ff95539..5f759fdbf 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 @@ -37,7 +37,7 @@ public class BeagleIntegrationTest extends WalkerTest { public void testBeagleOutput() { WalkerTestSpec spec = new WalkerTestSpec( "-T BeagleOutputToVCF -R " + hg19Reference + " " + - "--variants:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + + "--variant:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + "--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " + "--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " + "--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 + " " + - "--variants:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + + "--variant:VCF3 " + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-o %s", 1, Arrays.asList("a01c704246f3dd1b9c65774007e51e69")); executeTest("test BeagleInput", spec); } @@ -57,7 +57,7 @@ public class BeagleIntegrationTest extends WalkerTest { @Test public void testBeagleInput2() { WalkerTestSpec spec = new WalkerTestSpec( - "-T ProduceBeagleInput --variants:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+ + "-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, Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166")); @@ -68,7 +68,7 @@ public class BeagleIntegrationTest extends WalkerTest { public void testBeagleOutput2() { WalkerTestSpec spec = new WalkerTestSpec( "-T BeagleOutputToVCF -R "+hg19Reference+" "+ - "--variants:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.vcf "+ + "--variant:VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.vcf "+ "--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 "+ 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 f613407e2..1cb43ceb1 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 @@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testNoAction() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c")); 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 --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -window 10 --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("27b13f179bb4920615dff3a32730d845")); executeTest("test clustered SNPs", spec); } @@ -31,17 +31,17 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testMasks() { WalkerTestSpec spec1 = new WalkerTestSpec( - baseTestString() + " -maskName foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo --mask:VCF3 " + validationDataLocation + "vcfexample2.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("578f9e774784c25871678e6464fd212b")); executeTest("test mask all", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - baseTestString() + " -maskName foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f")); executeTest("test mask some", spec2); WalkerTestSpec spec3 = new WalkerTestSpec( - baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -maskName foo -maskExtend 10 --mask:VCF " + validationDataLocation + "vcfMask.vcf --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("5939f80d14b32d88587373532d7b90e5")); executeTest("test mask extend", spec3); } @@ -49,7 +49,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368")); executeTest("test filter #1", spec); } @@ -57,7 +57,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("c95845e817da7352b9b72bc9794f18fb")); executeTest("test filter #2", spec); } @@ -65,7 +65,7 @@ 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' --variants:VCF3 " + 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' --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530")); executeTest("test filter with separate names #2", spec); } @@ -73,12 +73,12 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testGenotypeFilters() { WalkerTestSpec spec1 = new WalkerTestSpec( - baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("96b61e4543a73fe725e433f007260039")); executeTest("test genotype filter #1", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variants:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("6c8112ab17ce39c8022c891ae73bf38e")); executeTest("test genotype filter #2", spec2); } @@ -86,7 +86,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testDeletions() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variants:VCF " + validationDataLocation + "twoDeletions.vcf", 1, + baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo --variant:VCF " + validationDataLocation + "twoDeletions.vcf", 1, Arrays.asList("569546fd798afa0e65c5b61b440d07ac")); executeTest("test deletions", spec); } 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 3566ecd05..e1d22f107 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 @@ -11,7 +11,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { return "-T ReadBackedPhasing" + " -R " + reference + " -I " + validationDataLocation + reads + - " --variants " + validationDataLocation + VCF + + " --variant " + validationDataLocation + VCF + " --cacheWindowSize " + cacheWindowSize + " --maxPhaseSites " + maxPhaseSites + " --phaseQualityThresh " + phaseQualityThresh + diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java index 1392f136a..4be848164 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java @@ -56,7 +56,7 @@ public class DictionaryConsistencyIntegrationTest extends WalkerTest { } private WalkerTest.WalkerTestSpec testVCF(String ref, String vcf, Class c) { - return new WalkerTest.WalkerTestSpec("-T VariantsToTable -M 10 --variants:vcf " + return new WalkerTest.WalkerTestSpec("-T VariantsToTable -M 10 --variant:vcf " + vcf + " -F POS,CHROM -R " + ref + " -o %s", 1, c); 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 2f77a8f55..2139a53e7 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 + " --variants:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", + "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", 1, Arrays.asList("158b1d71b28c52e2789f164500b53732")); executeTest("test left alignment", spec); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index c3795f98e..d10bb4452 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/public/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 + " --variants: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", + "-T LiftoverVariants -o %s -R " + b36KGReference + " --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("70aeaca5b74cc7ba8e2da7b71ff0fbfd")); 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 + " --variants: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", + "-T LiftoverVariants -o %s -R " + b36KGReference + " --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("3fd7ec2dc4064ef410786276b0dc9d08")); executeTest("test b36 to hg19, unsorted samples", spec); @@ -56,7 +56,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testhg18Tohg19Unsorted() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + hg18Reference + " --variants:vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", + "-T LiftoverVariants -o %s -R " + hg18Reference + " --variant:vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", 1, Arrays.asList("ab2c6254225d7e2ecf52eee604d5673b")); executeTest("test hg18 to hg19, unsorted", 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 7332c40cb..b2ac3f4a6 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 @@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { String samplesFile = validationDataLocation + "SelectVariants.samples.txt"; WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variants:VCF3 " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' --variant:VCF3 " + testfile + " -NO_HEADER"), 1, Arrays.asList("d18516c1963802e92cb9e425c0b75fd6") ); @@ -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 --variants:VCF3 " + testfile + " -NO_HEADER"), + baseTestString(" -sn A -sn B -sn C --variant:VCF3 " + testfile + " -NO_HEADER"), 1, Arrays.asList("b74038779fe6485dbb8734ae48178356") ); @@ -42,7 +42,7 @@ 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 --variants:VCF " + b37hapmapGenotypes + " -disc:VCF " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant:VCF " + b37hapmapGenotypes + " -disc:VCF " + testFile + " -o %s -NO_HEADER", 1, Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e") ); @@ -55,7 +55,7 @@ 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:VCF " + b37hapmapGenotypes + " --variants:VCF " + testFile + " -o %s -NO_HEADER", + "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc:VCF " + b37hapmapGenotypes + " --variant:VCF " + testFile + " -o %s -NO_HEADER", 1, Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a") ); 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 458233b09..ec3d1f580 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 @@ -56,7 +56,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants" + " -R " + b36KGReference + - " --variants:vcf3,storage=STREAM " + tmpFifo.getAbsolutePath() + + " --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 + - " --variants:vcf3,storage=STREAM " + testFile + + " --variant:vcf3,storage=STREAM " + testFile + " --NO_HEADER" + " -select 'QD > 2.0'" + " -o " + tmpFifo.getAbsolutePath(), diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java index 73a389ba6..4d5f0359d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -34,7 +34,7 @@ import java.util.Arrays; public class ValidateVariantsIntegrationTest extends WalkerTest { public static String baseTestString(String file, String type) { - return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variants:vcf " + validationDataLocation + file + " --validationType " + type; + return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + validationDataLocation + file + " --validationType " + type; } @Test diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java index 96cece3ca..19021c1c2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -35,7 +35,7 @@ import java.io.File; public class VariantsToTableIntegrationTest extends WalkerTest { private String variantsToTableCmd(String moreArgs) { return "-R " + hg18Reference + - " --variants:vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" + + " --variant:vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" + " -T VariantsToTable" + " -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" + " -L chr1 -KMA -o %s" + moreArgs; 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 e758ce0a2..2ef116708 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 @@ -17,11 +17,11 @@ public class VCFIntegrationTest extends WalkerTest { String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s "; - String test1 = baseCommand + "-T VariantAnnotator --variants " + testVCF + " -BTI variants"; + String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -BTI variant"; WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF)); List result = executeTest("Test Variant Annotator with no changes", spec1).getFirst(); - String test2 = baseCommand + "-T VariantsToVCF --variants " + result.get(0).getAbsolutePath(); + String test2 = baseCommand + "-T VariantsToVCF --variant " + result.get(0).getAbsolutePath(); WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF)); executeTest("Test Variants To VCF from new output", spec2); }