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Fixing problem reported on forum for VF: DP couldn't be filtered from the FORMAT field, only from the INFO field. Fixed and added integration test.

This commit is contained in:
Eric Banks 2012-10-26 00:57:40 -04:00
parent e93ff3ea6e
commit 91f2c847a3
2 changed files with 20 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
View File

@ -193,6 +193,8 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
infoMap.put("isHet", g.isHet() ? "1" : "0"); infoMap.put("isHet", g.isHet() ? "1" : "0");
infoMap.put("isHomVar", g.isHomVar() ? "1" : "0"); infoMap.put("isHomVar", g.isHomVar() ? "1" : "0");
infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getGQ()); infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getGQ());
if ( g.hasDP() )
infoMap.put(VCFConstants.DEPTH_KEY, g.getDP());
for ( Map.Entry<String, Object> e : g.getExtendedAttributes().entrySet() ) { for ( Map.Entry<String, Object> e : g.getExtendedAttributes().entrySet() ) {
if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) ) if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) )
infoMap.put(e.getKey(), e.getValue()); infoMap.put(e.getKey(), e.getValue());

18
public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -108,4 +108,22 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
Arrays.asList("8ed32a2272bab8043a255362335395ef")); Arrays.asList("8ed32a2272bab8043a255362335395ef"));
executeTest("testUnfilteredBecomesFilteredAndPass", spec); executeTest("testUnfilteredBecomesFilteredAndPass", spec);
} }
@Test
public void testFilteringDPfromINFO() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
Arrays.asList("a01f7cce53ea556c9741aa60b6124c41"));
executeTest("testFilteringDPfromINFO", spec);
}
@Test
public void testFilteringDPfromFORMAT() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+ " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
Arrays.asList("e10485c7c33d9211d0c1294fd7858476"));
executeTest("testFilteringDPfromFORMAT", spec);
}
} }