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

Actually calculate base counts by read group when "both" is specified. Modified integration test to cement the now-correct "both" behavior. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2941 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-05 18:31:48 +00:00
parent 8738c544f1
commit 037ac9c9af
1 changed files with 16 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java
View File

@ -152,7 +152,7 @@ public class CoverageStatistics extends LocusWalker<Map<String,int[]>, CoverageA
public CoverageAggregator reduceInit() { public CoverageAggregator reduceInit() {
CoverageAggregator.AggregationType agType = useBoth ? CoverageAggregator.AggregationType.BOTH : CoverageAggregator.AggregationType agType = useBoth ? CoverageAggregator.AggregationType.BOTH :
( useReadGroup ? CoverageAggregator.AggregationType.READ : CoverageAggregator.AggregationType.SAMPLE) ; ( useReadGroup ? CoverageAggregator.AggregationType.READ : CoverageAggregator.AggregationType.SAMPLE ) ;
CoverageAggregator aggro = new CoverageAggregator(agType,start,stop,nBins); CoverageAggregator aggro = new CoverageAggregator(agType,start,stop,nBins);
@ -179,6 +179,14 @@ public class CoverageStatistics extends LocusWalker<Map<String,int[]>, CoverageA
Map<String,int[]> countsBySample = CoverageUtils.getBaseCountsBySample(context,minMappingQuality,minBaseQuality, Map<String,int[]> countsBySample = CoverageUtils.getBaseCountsBySample(context,minMappingQuality,minBaseQuality,
useReadGroup ? CoverageUtils.PartitionType.BY_READ_GROUP : CoverageUtils.PartitionType.BY_SAMPLE); useReadGroup ? CoverageUtils.PartitionType.BY_READ_GROUP : CoverageUtils.PartitionType.BY_SAMPLE);
if ( useBoth ) {
Map<String,int[]> countsByOther = CoverageUtils.getBaseCountsBySample(context,minMappingQuality,minBaseQuality,
!useReadGroup ? CoverageUtils.PartitionType.BY_READ_GROUP : CoverageUtils.PartitionType.BY_SAMPLE);
for ( String s : countsByOther.keySet()) {
countsBySample.put(s,countsByOther.get(s));
}
}
return countsBySample; return countsBySample;
} }
@ -217,7 +225,7 @@ public class CoverageStatistics extends LocusWalker<Map<String,int[]>, CoverageA
if ( useBoth || useReadGroup ) { if ( useBoth || useReadGroup ) {
File intervalStatisticsFile = deriveFromStream("read_group_interval_statistics"); File intervalStatisticsFile = deriveFromStream("read_group_interval_statistics");
File intervalSummaryFile = deriveFromStream("read_group_interval_summary"); File intervalSummaryFile = deriveFromStream("read_group_interval_summary");
printIntervalStats(statsByInterval,intervalSummaryFile, intervalStatisticsFile, true); printIntervalStats(statsByInterval,intervalSummaryFile, intervalStatisticsFile, false);
} }
onTraversalDone(mergeAll(statsByInterval)); onTraversalDone(mergeAll(statsByInterval));
@ -700,6 +708,7 @@ class CoverageAggregator {
} }
} }
public void initialize(boolean useDels, boolean omitLocusTable) { public void initialize(boolean useDels, boolean omitLocusTable) {
if ( agType == AggregationType.SAMPLE || agType == AggregationType.BOTH ) { if ( agType == AggregationType.SAMPLE || agType == AggregationType.BOTH ) {
if ( useDels ) { if ( useDels ) {
@ -731,14 +740,17 @@ class CoverageAggregator {
} }
} else { // have to separate samples and read groups } else { // have to separate samples and read groups
HashMap<String,int[]> countsBySample = new HashMap<String,int[]>(sampleNames.size()); HashMap<String,int[]> countsBySample = new HashMap<String,int[]>(sampleNames.size());
HashMap<String,int[]> countsByRG = new HashMap<String,int[]>(allSamples.size()-sampleNames.size());
for ( String s : countsByIdentifier.keySet() ) { for ( String s : countsByIdentifier.keySet() ) {
if ( sampleNames.contains(s) ) { if ( sampleNames.contains(s) ) {
countsBySample.put(s,countsByIdentifier.remove(s)); countsBySample.put(s,countsByIdentifier.get(s));
} else { // cannot use .remove() to save time due to concurrency issues
countsByRG.put(s,countsByIdentifier.get(s));
} }
} }
coverageBySample.update(countsBySample); coverageBySample.update(countsBySample);
coverageByRead.update(countsByIdentifier); coverageByRead.update(countsByRG);
} }
} }