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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Guillermo del Angel 2011-06-29 13:58:04 -04:00
parent f736a1d61b 8586c86bc4
commit dee10140dd
3 changed files with 7 additions and 7 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -127,9 +127,9 @@ public class VariantContextAdaptors {
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
if ( DbSNPHelper.isDeletion(dbsnp) ) {
int index = ref.getLocus().getStart() - ref.getWindow().getStart() - 1;
int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
if ( index < 0 )
throw new ReviewedStingException("DbSNP conversion requested using a reference context with no window; we will fail to convert deletions");
return null; // we weren't given enough reference context to create the VariantContext
attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index]));
}
Collection<Genotype> genotypes = null;

8
public/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
View File

@ -19,12 +19,12 @@ public class VariantContextIntegrationTest extends WalkerTest {
static HashMap<String, String> expectations = new HashMap<String, String>();
static {
expectations.put("-L 1:1-10000 --printPerLocus", "493bf9bcde93c08c8c46f72c8e98cf2f");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "bd9e062b23c2c48fef8c299dc1d294d5");
expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "91c6a9489256d9ce77c8fedf7221a961");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc");
@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
// this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s",
1, // just one output file
Arrays.asList("d2a3f2fe329a0a64145cfd19fde45b99"));
Arrays.asList("529f936aa6c303658b23caf4e527782f"));
executeTest("testLargeScaleConversion", spec);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -52,7 +52,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList("78850024ac9ff3ba51b6f097c7041c1d"));
Arrays.asList("05a114623c126b0398fbc1703437461e"));
executeTest("realigner known indels only from dbsnp", spec2);
}