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Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.

This commit is contained in:
Eric Banks 2011-08-02 10:34:46 -04:00
parent 5626199bb6
commit 2c5e526eb7
3 changed files with 6 additions and 6 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -64,7 +64,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
protected int windowSize = 10;
@Argument(fullName="mismatchFraction", shortName="mismatch", doc="fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1", required=false)
protected double mismatchThreshold = 0.15;
protected double mismatchThreshold = 0.0;
@Argument(fullName="minReadsAtLocus", shortName="minReads", doc="minimum reads at a locus to enable using the entropy calculation", required=false)
protected int minReadsAtLocus = 4;

6
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
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@ -11,16 +11,16 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
public void testIntervals() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
"-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("e7accfa58415d6da80383953b1a3a986"));
executeTest("test standard", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
"-T RealignerTargetCreator -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("f23ba17ee0f9573dd307708175d90cd2"));
executeTest("test dbsnp", spec2);
//executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",

4
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java
View File

@ -12,7 +12,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(
"-R " + hg18Reference +
" -T RealignerTargetCreator" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -o /dev/null",
@ -23,7 +23,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
WalkerTestSpec spec2 = new WalkerTestSpec(
"-R " + hg18Reference +
" -T RealignerTargetCreator" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -o /dev/null",