zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fix for mergeInfoWithMaxAC 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5978 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-06-12 20:10:16 +00:00
parent 1f4469976e
commit 6231bba288
1 changed files with 11 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -483,7 +483,8 @@ public class VariantContextUtils {
String rsID = null;
int depth = 0;
int maxAC = -1;
Map<String, Object> maxACAttributes = new TreeMap<String, Object>();
Map<String, Object> attributesWithMaxAC = new TreeMap<String, Object>();
VariantContext vcWithMaxAC = null;
// counting the number of filtered and variant VCs
int nFiltered = 0, nVariant = 0;
@ -532,14 +533,14 @@ public class VariantContextUtils {
final int ac = Integer.valueOf(alleleCount.trim());
if (ac > maxAC) {
maxAC = ac;
maxACAttributes = vc.getAttributes();
vcWithMaxAC = vc;
}
}
} else {
final int ac = Integer.valueOf(rawAlleleCounts);
if (ac > maxAC) {
maxAC = ac;
maxACAttributes = vc.getAttributes();
vcWithMaxAC = vc;
}
}
}
@ -565,6 +566,11 @@ public class VariantContextUtils {
}
}
// take the VC with the maxAC and pull the attributes into a modifiable map
if ( mergeInfoWithMaxAC && vcWithMaxAC != null ) {
attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes());
}
// if at least one record was unfiltered and we want a union, clear all of the filters
if ( filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size() )
filters.clear();
@ -588,7 +594,7 @@ public class VariantContextUtils {
if ( setKey != null ) {
attributes.put(setKey, setValue);
if( mergeInfoWithMaxAC ) { maxACAttributes.put(setKey, setValue); }
if( mergeInfoWithMaxAC && vcWithMaxAC != null ) { attributesWithMaxAC.put(setKey, vcWithMaxAC.getSource()); }
}
}
@ -597,7 +603,7 @@ public class VariantContextUtils {
if ( rsID != null )
attributes.put(VariantContext.ID_KEY, rsID);
VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? maxACAttributes : attributes) );
VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? attributesWithMaxAC : attributes) );
// Trim the padded bases of all alleles if necessary
merged = AbstractVCFCodec.createVariantContextWithTrimmedAlleles(merged);