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Bug fix: reverted logic so that default behavior skips over sample lookup

This commit is contained in:
Guillermo del Angel 2011-07-20 10:23:10 -04:00
parent e8409c80fa
commit a2d90a3590
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -64,7 +64,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
public Set<String> sampleNames = new TreeSet<String>(); public Set<String> sampleNames = new TreeSet<String>();
private TreeSet<String> samplesToChoose = new TreeSet<String>(); private TreeSet<String> samplesToChoose = new TreeSet<String>();
private boolean NO_SAMPLES_SPECIFIED = false; private boolean SAMPLES_SPECIFIED = false;
/** /**
* The initialize function. * The initialize function.
@ -82,8 +82,8 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
if (!sampleNames.isEmpty()) if (!sampleNames.isEmpty())
samplesToChoose.addAll(sampleNames); samplesToChoose.addAll(sampleNames);
if(samplesToChoose.isEmpty()) { if(!samplesToChoose.isEmpty()) {
NO_SAMPLES_SPECIFIED = true; SAMPLES_SPECIFIED = true;
} }
} }
@ -112,7 +112,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
if ( readPlatformAttr == null || !readPlatformAttr.toString().toUpperCase().contains(platform)) if ( readPlatformAttr == null || !readPlatformAttr.toString().toUpperCase().contains(platform))
return false; return false;
} }
if (!NO_SAMPLES_SPECIFIED ) { if (SAMPLES_SPECIFIED ) {
// user specified samples to select // user specified samples to select
String readSample = read.getReadGroup().getSample(); String readSample = read.getReadGroup().getSample();
boolean found = false; boolean found = false;