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Add the calculated lod value to the info field of each recalibrated VCF record. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4153 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-27 21:33:58 +00:00
parent fe19539188
commit 9c3f403307
2 changed files with 3 additions and 2 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -243,6 +243,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
attrs.put("OQ", String.format("%.2f", ((Double)vc.getPhredScaledQual())));
attrs.put("LOD", String.format("%.4f", lod));
Set<String> filters = new HashSet<String>();
filters.add(VCFConstants.PASSES_FILTERS_v4);
VariantContext newVC = new VariantContext(vc.getName(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), variantDatum.qual / 10.0, filters, attrs);

4
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -40,7 +40,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testVariantRecalibrator() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "446f0de46f59344ec5579d0c8b54ee66" );
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "f2790e2f4f3c23df800c18aaa39b3fde" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();
@ -75,7 +75,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testApplyVariantCuts() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "b25c2a563362897271bbee9db3f9c3af" );
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "d30eafb642a80a00bd82fb4140b5277e" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();