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More updates to be consistent with the new rod syntax.

This commit is contained in:
Eric Banks 2011-08-09 10:11:37 -04:00
parent 1e490e0dec
commit 7afb5c9f1c
5 changed files with 18 additions and 13 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -35,6 +35,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
/**
* Generates an alternative reference sequence over the specified interval. Given variant ROD tracks,
@ -45,6 +47,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
@Input(fullName = "variants", shortName = "V", doc="variants to model", required=false)
public List<RodBinding<VariantContext>> variants;
@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
public RodBinding<VariantContext> snpmask = RodBinding.makeUnbound(VariantContext.class);

13
public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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@ -24,16 +24,15 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
executeTest("testFastaReference", spec1b);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
1,
Arrays.asList("0567b32ebdc26604ddf2a390de4579ac"));
executeTest("testFastaAlternateReferenceIndels", spec2);
// TODO : Eric, update with new DBSNP
// WalkerTestSpec spec3 = new WalkerTestSpec(
// "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:snps,GeliText " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B:snpmask,dbsnp " + GATKDataLocation + "dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
// 1,
// Arrays.asList("82705a88f6fc25880dd2331183531d9a"));
// executeTest("testFastaAlternateReferenceSnps", spec3);
WalkerTestSpec spec3 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -V " + GATKDataLocation + "dbsnp_129_b36.vcf -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
1,
Arrays.asList("8b6cd2e20c381f9819aab2d270f5e641"));
executeTest("testFastaAlternateReferenceSnps", spec3);
}
}

6
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
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@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-50,000,000" +
" -dbsnp,VCF " + b36dbSNP129 +
" -dbsnp:VCF " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -30,7 +30,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
" -dbsnp,vcf " + b36dbSNP129 +
" -dbsnp:vcf " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));
@ -46,7 +46,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
" -glm BOTH" +
" -L chr1:1-50,000,000" +
" -nt 10" +
" -dbsnp,vcf " + b36dbSNP129 +
" -dbsnp:vcf " + b36dbSNP129 +
" -o /dev/null",
0,
new ArrayList<String>(0));

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

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

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
View File

@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --variant:dbsnp " + GATKDataLocation + "dbsnp_129_b36.rod" +
" --variant:dbsnp " + GATKDataLocation + "Comparisons/Validated/dbSNP/dbsnp_129_b36.rod" +
" -T VariantsToVCF" +
" -L 1:1-30,000,000" +
" -o %s" +