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If only dcov is specified, assume that selected downsample type is BY_SAMPLE. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4147 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-08-27 17:35:41 +00:00
parent 9584cbc05e
commit fb177c4fee
2 changed files with 4 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -143,6 +143,8 @@ public class GATKArgumentCollection {
public DownsamplingMethod getDownsamplingMethod() { public DownsamplingMethod getDownsamplingMethod() {
if(downsamplingType == null && downsampleFraction == null && downsampleCoverage == null) if(downsamplingType == null && downsampleFraction == null && downsampleCoverage == null)
return null; return null;
if(downsamplingType == null && downsampleCoverage != null)
return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE,downsampleCoverage,null);
return new DownsamplingMethod(downsamplingType,downsampleCoverage,downsampleFraction); return new DownsamplingMethod(downsamplingType,downsampleCoverage,downsampleFraction);
} }

4
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
View File

@ -541,8 +541,8 @@ public class LocusIteratorByState extends LocusIterator {
public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, Collection<String> sampleNames) { public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, Collection<String> sampleNames) {
this.iterator = new PeekableIterator<SAMRecord>(source); this.iterator = new PeekableIterator<SAMRecord>(source);
this.downsamplingMethod = downsamplingMethod; this.downsamplingMethod = downsamplingMethod.type != null ? downsamplingMethod : DownsamplingMethod.NONE;
switch(downsamplingMethod.type) { switch(this.downsamplingMethod.type) {
case BY_SAMPLE: case BY_SAMPLE:
if(downsamplingMethod.toCoverage == null) if(downsamplingMethod.toCoverage == null)
throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample"); throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample");