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Final bugfix for CombineVariants 

-- Now handles multiple records at a site, so that you don't see records like set=dbsnp-dbsnp-dbsnp when combining something with dbsnp
-- Proper handling of ids.  If you are merging files with multiple ids for the same record, the ids are merged into a comma separated list
This commit is contained in:
Mark DePristo 2011-09-21 10:58:32 -04:00
parent a91ac0c5db
commit 7d11f93b82
2 changed files with 4 additions and 5 deletions
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3
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -550,8 +550,7 @@ public class VariantContextUtils {
if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY));
// TODO -- REVERT CHANGE
if (rsIDs.isEmpty() && vc.hasID()) rsIDs.add(vc.getID());
if ( vc.hasID() && ! vc.getID().equals(VCFConstants.EMPTY_ID_FIELD) ) rsIDs.add(vc.getID());
if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY);

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -90,14 +90,14 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f"); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9"); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a"); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "d76cd5b3ced7745d42fe0af39ce0b32e"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083"); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "e6a053129c5f7b13129beefed9282155"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "c6adeda751cb2a08690dd9202356629f"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "3a08fd5ee18993dfc8882156ccf5d2e9"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(