diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index bb50329f0..4b92bf58b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.sequenom; import net.sf.samtools.util.CloseableIterator; +import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.dbsnp.DbSNPFeature; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -74,7 +75,7 @@ public class PickSequenomProbes extends RodWalker { ReferenceOrderedData snp_mask; if ( SNP_MASK.contains(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)) { TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder(); - CloseableIterator iter = builder.createInstanceOfTrack(DbSNPFeature.class,"snp_mask",new java.io.File(SNP_MASK)).getIterator(); + CloseableIterator iter = builder.createInstanceOfTrack(DbSNPCodec.class,"snp_mask",new java.io.File(SNP_MASK)).getIterator(); snpMaskIterator = new SeekableRODIterator(iter); } else { diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java index ae9462dd1..ad26d1f4c 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java @@ -14,4 +14,16 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { Arrays.asList("6b5409cc78960f1be855536ed89ea9dd")); 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); + } } \ No newline at end of file