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Bug fix to prevent null pointer

This commit is contained in:
Guillermo del Angel 2011-07-19 20:13:56 -04:00
parent 6181d1e4cb
commit fb2d475c22
1 changed files with 7 additions and 4 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -59,7 +59,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false) @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
int nReadsToPrint = -1; int nReadsToPrint = -1;
@Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false) @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false)
public Set<File> sampleFiles; public Set<File> sampleFile;
@Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false) @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
public Set<String> sampleNames; public Set<String> sampleNames;
@ -73,10 +73,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
if ( platform != null ) if ( platform != null )
platform = platform.toUpperCase(); platform = platform.toUpperCase();
Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); Collection<String> samplesFromFile;
samplesToChoose.addAll(samplesFromFile); if (!sampleFile.isEmpty()) {
samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFile);
samplesToChoose.addAll(samplesFromFile);
}
if (sampleNames != null) if (!sampleNames.isEmpty())
samplesToChoose.addAll(sampleNames); samplesToChoose.addAll(sampleNames);
if(samplesToChoose.isEmpty()) { if(samplesToChoose.isEmpty()) {