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Missed a few 'variants'

This commit is contained in:
Eric Banks 2011-08-09 14:29:15 -04:00
parent 5a3c99b7b9
commit 489e5cffc1
2 changed files with 6 additions and 6 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -54,7 +54,7 @@ import static java.lang.Math.log10;
*/
@Requires(value={})
public class BeagleOutputToVCFWalker 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="comp", shortName = "comp", doc="Comparison VCF file", required=false)

10
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 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\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 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\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 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\" --variant: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 variant", 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 --variant:VCF " + validationDataLocation + "/" + file + " -BTI variants -NO_HEADER", 1,
baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
Arrays.asList(MD5));
executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
}