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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.

This commit is contained in:
Eric Banks 2011-08-09 12:04:55 -04:00
parent 78aa6db076
commit b20c4d5286
24 changed files with 62 additions and 58 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -53,7 +53,8 @@ import java.util.*;
@Reference(window=@Window(start=-50,stop=50))
@By(DataSource.REFERENCE)
public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -52,7 +52,7 @@ import java.util.*;
*/
@Requires(value={})
public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -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<RodBinding<VariantContext>> variants;
@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)

3
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -52,7 +52,8 @@ import java.util.*;
@Requires(value={})
@Reference(window=@Window(start=-50,stop=50))
public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="mask", doc="Input ROD mask", required=false)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -67,7 +67,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
*
* All heterozygous variants found in this VCF file will be phased, where possible
*/
@Input(fullName="variants", shortName = "V", doc="Phase variants from this VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Phase variants from this VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc = "File to which variants should be written", required = true)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -64,7 +64,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
* 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<RodBinding<VariantContext>> variantsToMerge;
@Output(doc="File to which variants should be written",required=true)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
View File

@ -50,7 +50,7 @@ import java.util.*;
@Reference(window=@Window(start=-200,stop=200))
@Requires(value={})
public class LeftAlignVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc="File to which variants should be written",required=true)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -52,7 +52,7 @@ import java.util.*;
*/
@Requires(value={})
public class LiftoverVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc="File to which variants should be written",required=true)

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -61,7 +61,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* 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<VariantContext> variants;
/**

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
View File

@ -55,7 +55,8 @@ import java.util.Set;
@Reference(window=@Window(start=0,stop=100))
@Requires(value={})
public class ValidateVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
public enum ValidationType {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -47,7 +47,8 @@ import java.util.*;
*/
@Requires(value={})
public class VariantsToTable extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc="File to which results should be written",required=true)

2
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
View File

@ -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);

30
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -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,

8
public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -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 "+

22
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -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);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -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 +

2
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java
View File

@ -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);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java
View File

@ -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);

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
View File

@ -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);

8
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -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")
);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -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(),

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
View File

@ -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

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
View File

@ -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;

4
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -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<File> 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);
}