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fix for PSPW with DbSNP mask. Added an integration test for this case. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3628 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-06-24 19:31:32 +00:00
parent 4840ef6d3e
commit 62bc7651a8
2 changed files with 14 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.sequenom; package org.broadinstitute.sting.gatk.walkers.sequenom;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broad.tribble.dbsnp.DbSNPFeature; import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -74,7 +75,7 @@ public class PickSequenomProbes extends RodWalker<String, String> {
ReferenceOrderedData snp_mask; ReferenceOrderedData snp_mask;
if ( SNP_MASK.contains(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)) { if ( SNP_MASK.contains(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)) {
TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder(); TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder();
CloseableIterator<GATKFeature> iter = builder.createInstanceOfTrack(DbSNPFeature.class,"snp_mask",new java.io.File(SNP_MASK)).getIterator(); CloseableIterator<GATKFeature> iter = builder.createInstanceOfTrack(DbSNPCodec.class,"snp_mask",new java.io.File(SNP_MASK)).getIterator();
snpMaskIterator = new SeekableRODIterator(iter); snpMaskIterator = new SeekableRODIterator(iter);
} else { } else {

12
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
View File

@ -14,4 +14,16 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
Arrays.asList("6b5409cc78960f1be855536ed89ea9dd")); Arrays.asList("6b5409cc78960f1be855536ed89ea9dd"));
executeTest("Test probes", spec); executeTest("Test probes", spec);
} }
@Test
public void testProbesUsingDbSNPMask() {
String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf";
String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
+ oneKGLocation + "reference/human_b36_both.fasta -omitWindow -nameConvention "
+ "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
"/pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("49bd6f53b93802576ed3dac8af4bcf8a"));
executeTest("Test probes", spec);
}
} }