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Bug fixes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-06-08 00:30:33 +00:00
parent 52ab9f2417
commit 199e4208cd
1 changed files with 17 additions and 6 deletions
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23
java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
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@ -284,7 +284,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames); readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames);
this.readInfo = readInformation; this.readInfo = readInformation;
this.filters = filters; this.filters = filters;
overflowTracker = new LocusOverflowTracker(readInformation.getMaxReadsAtLocus()); overflowTracker = new LocusOverflowTracker(readInformation.getMaxReadsAtLocus());
} }
public Iterator<AlignmentContext> iterator() { public Iterator<AlignmentContext> iterator() {
@ -534,11 +534,22 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, int maxReadsAtLocus, Collection<String> sampleNames) { public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, int maxReadsAtLocus, Collection<String> sampleNames) {
this.iterator = new PeekableIterator<SAMRecord>(source); this.iterator = new PeekableIterator<SAMRecord>(source);
this.downsamplingMethod = downsamplingMethod; this.downsamplingMethod = downsamplingMethod;
this.targetCoverage = downsamplingMethod.toCoverage != null ? downsamplingMethod.toCoverage : 1; switch(downsamplingMethod.type) {
case EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR:
this.targetCoverage = downsamplingMethod.toCoverage != null ? downsamplingMethod.toCoverage : 1;
break;
case EXPERIMENTAL_BY_SAMPLE:
if(downsamplingMethod.toCoverage == null)
throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample");
this.targetCoverage = downsamplingMethod.toCoverage;
break;
default:
this.targetCoverage = Integer.MAX_VALUE;
}
this.maxReadsAtLocus = maxReadsAtLocus; this.maxReadsAtLocus = maxReadsAtLocus;
if(downsamplingMethod.type == DownsampleType.NONE) if(downsamplingMethod.type == DownsampleType.NONE)
aggregatorsBySampleName.put(null,new ArrayList<SAMRecord>()); aggregatorsBySampleName.put(null,new ArrayList<SAMRecord>());
if(downsamplingMethod.type == DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR) else if(downsamplingMethod.type == DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR)
aggregatorsBySampleName.put(null,new ReservoirDownsampler<SAMRecord>(targetCoverage)); aggregatorsBySampleName.put(null,new ReservoirDownsampler<SAMRecord>(targetCoverage));
else { else {
for(String sampleName: sampleNames) for(String sampleName: sampleNames)
@ -705,10 +716,10 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
} }
private Collection<SAMRecord> getAggregator(String sampleName) { private Collection<SAMRecord> getAggregator(String sampleName) {
if(downsamplingMethod.type == DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR) if(downsamplingMethod.type == DownsampleType.EXPERIMENTAL_BY_SAMPLE)
return aggregatorsBySampleName.get(null);
else
return aggregatorsBySampleName.get(sampleName); return aggregatorsBySampleName.get(sampleName);
else
return aggregatorsBySampleName.get(null);
} }
private int countReadsInHanger(final String sampleName) { private int countReadsInHanger(final String sampleName) {