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Protect PrintReads from strange state from TraverseReadsUnitTests

This commit is contained in:
Mark DePristo 2012-08-31 13:41:03 -04:00
parent e028901d54
commit 27ddebee53
1 changed files with 6 additions and 5 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
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@ -41,10 +41,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
import java.util.Collection;
import java.util.Random;
import java.util.Set;
import java.util.TreeSet;
import java.util.*;
/**
* Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
@ -141,6 +138,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
public boolean simplifyReads = false;
List<ReadTransformer> readTransformers = Collections.emptyList();
private TreeSet<String> samplesToChoose = new TreeSet<String>();
private boolean SAMPLES_SPECIFIED = false;
@ -153,6 +151,9 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
if ( platform != null )
platform = platform.toUpperCase();
if ( getToolkit() != null )
readTransformers = getToolkit().getReadTransformers();
Collection<String> samplesFromFile;
if (!sampleFile.isEmpty()) {
samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFile);
@ -226,7 +227,7 @@ public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> impleme
public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord readIn, RefMetaDataTracker metaDataTracker ) {
GATKSAMRecord workingRead = readIn;
for ( final ReadTransformer transformer : getToolkit().getReadTransformers() ) {
for ( final ReadTransformer transformer : readTransformers ) {
if ( logger.isDebugEnabled() ) logger.debug("Applying transformer " + transformer + " to read " + readIn.getReadName());
workingRead = transformer.apply(workingRead);
}