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Bringing Indel Realigner up to speed with the new rod binding syntax; now use -known to specify the known indels track.

This commit is contained in:
Eric Banks 2011-08-09 23:21:17 -04:00
parent b8f572b571
commit bc2d4f554d
3 changed files with 11 additions and 11 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -30,10 +30,7 @@ import net.sf.samtools.*;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import net.sf.samtools.util.SequenceUtil; import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil; import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -86,6 +83,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
USE_SW USE_SW
} }
@Input(fullName="known", shortName = "known", doc="Input VCF file with known indels", required=false)
public RodBinding<VariantContext> known = RodBinding.makeUnbound(VariantContext.class);
@Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true) @Input(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
protected String intervalsFile = null; protected String intervalsFile = null;
@ -558,8 +558,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( indelRodsSeen.contains(rod) ) if ( indelRodsSeen.contains(rod) )
continue; continue;
indelRodsSeen.add(rod); indelRodsSeen.add(rod);
if ( VariantContextAdaptors.canBeConvertedToVariantContext(rod)) if ( rod instanceof VariantContext )
knownIndelsToTry.add(VariantContextAdaptors.toVariantContext("", rod, ref)); knownIndelsToTry.add((VariantContext)rod);
} }
} }
} }

6
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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@ -28,7 +28,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
executeTest("test realigner defaults", spec1); executeTest("test realigner defaults", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec( WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-B:indels,vcf " + knownIndels, baseCommand + "-known " + knownIndels,
1, 1,
Arrays.asList(base_md5_with_SW_or_VCF)); Arrays.asList(base_md5_with_SW_or_VCF));
executeTest("test realigner defaults with VCF", spec2); executeTest("test realigner defaults with VCF", spec2);
@ -37,7 +37,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test @Test
public void testKnownsOnly() { public void testKnownsOnly() {
WalkerTestSpec spec1 = new WalkerTestSpec( WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -B:indels,vcf " + knownIndels, baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
1, 1,
Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888")); Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
executeTest("realigner known indels only from VCF", spec1); executeTest("realigner known indels only from VCF", spec1);
@ -46,7 +46,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test @Test
public void testUseSW() { public void testUseSW() {
WalkerTestSpec spec1 = new WalkerTestSpec( WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel USE_SW -B:indels,vcf " + knownIndels, baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels,
1, 1,
Arrays.asList(base_md5_with_SW_or_VCF)); Arrays.asList(base_md5_with_SW_or_VCF));
executeTest("realigner use SW from VCF", spec1); executeTest("realigner use SW from VCF", spec1);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
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@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -LOD 5" + " -LOD 5" +
" -maxConsensuses 100" + " -maxConsensuses 100" +
" -greedy 100" + " -greedy 100" +
" -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -o /dev/null" + " -o /dev/null" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-5,650,000" + " -L chr1:1-5,650,000" +
@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -LOD 5" + " -LOD 5" +
" -maxConsensuses 100" + " -maxConsensuses 100" +
" -greedy 100" + " -greedy 100" +
" -dbsnp:vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -o /dev/null" + " -o /dev/null" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L chr1:1-150,000,000" + " -L chr1:1-150,000,000" +