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

Merge pull request #1548 from broadinstitute/rhl_synchonize_upstream_del_1188 

Make upstreamDeletionsLoc Thread Safe
This commit is contained in:
Ron Levine 2017-01-13 14:57:05 -05:00 committed by GitHub
parent bb87730ddc 1f6645539a
commit bfa633a90f
1 changed files with 3 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
View File

@ -106,7 +106,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
protected final GenomeLocParser genomeLocParser;
private final List<GenomeLoc> upstreamDeletionsLoc = new LinkedList<>();
private final ThreadLocal< List<GenomeLoc> > upstreamDeletionsLoc = ThreadLocal.withInitial(() -> new LinkedList<GenomeLoc>());
protected final AFCalculator newAFCalculator;
@ -411,7 +411,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
// Allele ia a deletion
if (deletionSize > 0) {
final GenomeLoc genomeLoc = genomeLocParser.createGenomeLocOnContig(vc.getContig(), vc.getStart(), vc.getStart() + deletionSize);
upstreamDeletionsLoc.add(genomeLoc);
upstreamDeletionsLoc.get().add(genomeLoc);
}
}
@ -422,7 +422,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
* @return true if the location is covered by an upstream deletion, false otherwise
*/
private boolean coveredByDeletion(final VariantContext vc) {
for (Iterator<GenomeLoc> it = upstreamDeletionsLoc.iterator(); it.hasNext(); ) {
for (Iterator<GenomeLoc> it = upstreamDeletionsLoc.get().iterator(); it.hasNext(); ) {
final GenomeLoc loc = it.next();
if (!loc.getContig().equals(vc.getContig())) { // past contig deletion.
it.remove();