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

This commit is contained in:
Eric Banks 2011-07-28 13:57:22 -04:00
parent ff31fa7990 7a2a65155f
commit 33b32c4211
2 changed files with 15 additions and 12 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -112,26 +112,29 @@ public class VariantContextAdaptors {
alleles.add(refAllele); alleles.add(refAllele);
// add all of the alt alleles // add all of the alt alleles
boolean sawNullAllele = false;
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) { for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) { if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp); //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null; return null;
} }
alleles.add(Allele.create(alt, false)); Allele altAllele = Allele.create(alt, false);
alleles.add(altAllele);
if ( altAllele.isNull() )
sawNullAllele = true;
} }
Map<String, Object> attributes = new HashMap<String, Object>(); Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VariantContext.ID_KEY, dbsnp.getRsID()); attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
boolean vcIsDeletion = DbSNPHelper.isDeletion(dbsnp) || DbSNPHelper.isComplexIndel(dbsnp); if ( sawNullAllele ) {
if ( vcIsDeletion ) {
int index = dbsnp.getStart() - ref.getWindow().getStart() - 1; int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
if ( index < 0 ) if ( index < 0 )
return null; // we weren't given enough reference context to create the VariantContext 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])); attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index]));
} }
Collection<Genotype> genotypes = null; Collection<Genotype> genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (vcIsDeletion ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes); VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
return vc; return vc;
} else } else
return null; // can't handle anything else return null; // can't handle anything else

16
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -19,14 +19,14 @@ public class VariantContextIntegrationTest extends WalkerTest {
static HashMap<String, String> expectations = new HashMap<String, String>(); static HashMap<String, String> expectations = new HashMap<String, String>();
static { static {
expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a"); expectations.put("-L 1:1-10000 --printPerLocus", "e9d96677a57bc3a10fb6d9ba942c19f0");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f"); expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "8a1174d2b18b98e624abbe93e6af8fdd");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "3933f1fae5453c54c3f791a23de07599");
expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92"); expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "c9cf2f01bf045a58dcc7649fd6ea2396");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "a103d856e8bc558c949c6e3f184e8913");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5f2265ac6c6d80d64dc6e69a05c1250b");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "06a3ae4c0afa23b429a9491ab7707f3c");
expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc"); 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 // 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", WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s",
1, // just one output file 1, // just one output file
Arrays.asList("529f936aa6c303658b23caf4e527782f")); Arrays.asList("045a5b02c86aeb9301dc0b724da0c8f7"));
executeTest("testLargeScaleConversion", spec); executeTest("testLargeScaleConversion", spec);
} }
} }