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Fixing broken walker as per GS; adding integration test to cover it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6040 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:54:04 +00:00
parent 0e057276ae
commit 4f7a64a798
3 changed files with 15 additions and 7 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -55,7 +55,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
return new Pair<GenomeLoc, String>(context.getLocation(), "");
}
String refBase = String.valueOf(ref.getBaseAsChar());
String refBase = String.valueOf((char)ref.getBase());
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref);

2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
View File

@ -56,7 +56,7 @@ public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, Gen
}
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf((char)ref.getBase()));
}
public GenomeLoc reduceInit() {

18
java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
View File

@ -9,11 +9,19 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
@Test
public void testIntervals() {
WalkerTestSpec spec1 = new WalkerTestSpec(
String md5_1 = "328d2d52cedfdc52da7d1abff487633d";
WalkerTestSpec spec1a = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
1,
Arrays.asList("328d2d52cedfdc52da7d1abff487633d"));
executeTest("testFastaReference", spec1);
Arrays.asList(md5_1));
executeTest("testFastaReference", spec1a);
WalkerTestSpec spec1b = new WalkerTestSpec(
"-T FastaReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
1,
Arrays.asList(md5_1));
executeTest("testFastaReference", spec1b);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
@ -21,10 +29,10 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
executeTest("testFastaAlternateReferenceIndels", spec2);
WalkerTestSpec spec4 = new WalkerTestSpec(
WalkerTestSpec spec3 = new WalkerTestSpec(
"-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:snps,GeliText " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B:snpmask,dbsnp /humgen/gsa-scr1/GATK_Data/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", spec4);
executeTest("testFastaAlternateReferenceSnps", spec3);
}
}