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The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-05-27 19:22:47 +00:00
parent ff4a0764df
commit e2674671e7
2 changed files with 7 additions and 21 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -132,11 +132,6 @@ public class VariantContextAdaptors {
}
private static class VCFRecordAdaptor extends VCAdaptor {
// // WARNING: do not use this method if you have anything other than point mutations in your VCF
// VariantContext convert(String name, Object input) {
// return vcfToVariantContext(name, (VCFRecord)input, null);
// }
VariantContext convert(String name, Object input, ReferenceContext ref) {
return vcfToVariantContext(name, (VCFRecord)input, ref);
}

23
java/src/org/broadinstitute/sting/gatk/walkers/vcf/FilterLiftedVCF.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.gatk.walkers.vcf;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -55,22 +54,14 @@ public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
char recordRef = record.getReference().charAt(0);
if ( recordRef != ref ) {
// is it reverse complemented?
if ( BaseUtils.simpleComplement(recordRef) == ref ) {
record.setFilterString(record.isFiltered() ? String.format("%s;LiftoverToReverseComplementRefBase", record.getFilterString()) : "LiftoverToNewBase");
failedLocs++;
} else {
record.setFilterString(record.isFiltered() ? String.format("%s;LiftoverToDifferentRefBase", record.getFilterString()) : "LiftoverToNewBase");
failedLocs++;
failedLocs++;
} else {
if ( writer == null ) {
writer = new VCFWriter(out);
writer.writeHeader(record.getHeader());
}
writer.addRecord(record);
}
if ( writer == null ) {
writer = new VCFWriter(out);
writer.writeHeader(record.getHeader());
}
writer.addRecord(record);
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@ -80,7 +71,7 @@ public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
List<Object> rods = tracker.getReferenceMetaData("vcf");
for ( Object rod : rods )
filterAndWrite(ref.getBaseAsChar(), (VCFRecord)rod);
filterAndWrite((char)ref.getBase(), (VCFRecord)rod);
return 0;
}