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If you have one sample in your BAM, getToolkit().getSamples().size() == 2 

Also deleted double initializationm, where a line of code was duplicated in creating the GATK engine.
This commit is contained in:
Mark DePristo 2011-08-18 11:51:53 -04:00
parent f5d7cabb20
commit c797616c65
2 changed files with 3 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -689,8 +689,6 @@ public class GenomeAnalysisEngine {
validateSuppliedReads(); validateSuppliedReads();
readsDataSource = createReadsDataSource(argCollection,genomeLocParser,referenceDataSource.getReference()); readsDataSource = createReadsDataSource(argCollection,genomeLocParser,referenceDataSource.getReference());
sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
for (ReadFilter filter : filters) for (ReadFilter filter : filters)
filter.initialize(this); filter.initialize(this);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
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@ -223,8 +223,10 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
@Override @Override
public void initialize() { public void initialize() {
if ( getToolkit().getSamples().size() > 1 ) if ( getToolkit().getSamples().size() != 2 ) {
// unbelievably there are actually two samples even when there's just one in the header. God I hate this Samples system
throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples()); throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
}
try { try {
PrintStream summaryOut = new PrintStream(summaryFile); PrintStream summaryOut = new PrintStream(summaryFile);