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Bugfix for GetSatisfaction: ensure that the two statistics objects (the map, and the pair) are actually pointers to the very same object. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5156 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-02-01 06:40:42 +00:00
parent 34f5587f2c
commit e5e65ecfbe
1 changed files with 11 additions and 2 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -363,17 +363,22 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
}
private void printGeneStats(List<Pair<GenomeLoc, CoveragePartitioner>> statsByTarget) {
logger.debug("statsByTarget size is "+Integer.toString(statsByTarget.size()));
logger.debug("Initializing refseq...");
LocationAwareSeekableRODIterator refseqIterator = initializeRefSeq();
logger.debug("Refseq init done.");
List<Pair<String,DepthOfCoverageStats>> statsByGene = new ArrayList<Pair<String,DepthOfCoverageStats>>();// maintains order
Map<String,DepthOfCoverageStats> geneNamesToStats = new HashMap<String,DepthOfCoverageStats>(); // allows indirect updating of objects in list
for ( Pair<GenomeLoc, CoveragePartitioner> targetStats : statsByTarget ) {
String gene = getGeneName(targetStats.first,refseqIterator);
if ( geneNamesToStats.keySet().contains(gene) ) {
logger.debug("Merging "+geneNamesToStats.get(gene).toString()+" and "+targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample).toString());
geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample));
} else {
geneNamesToStats.put(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)));
statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample))));
DepthOfCoverageStats merger = new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample));
geneNamesToStats.put(gene,merger);
statsByGene.add(new Pair<String,DepthOfCoverageStats>(gene,merger));
}
}
@ -386,15 +391,19 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
//blatantly stolen from Andrew Kernytsky
private String getGeneName(GenomeLoc target, LocationAwareSeekableRODIterator refseqIterator) {
logger.debug("Examining "+target.toString());
if (refseqIterator == null) { return "UNKNOWN"; }
RODRecordList annotationList = refseqIterator.seekForward(target);
logger.debug("Annotation list is " + (annotationList == null ? "null" : annotationList.getName()));
if (annotationList == null) { return "UNKNOWN"; }
for(GATKFeature rec : annotationList) {
if ( ((RefSeqFeature)rec.getUnderlyingObject()).overlapsExonP(target) ) {
logger.debug("We do overlap "+ rec.getUnderlyingObject().toString());
return ((RefSeqFeature)rec.getUnderlyingObject()).getGeneName();
}
logger.debug("No overlap");
}
return "UNKNOWN";