diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java index 57ea5166a..78b6e7c04 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java @@ -59,7 +59,7 @@ public class PrintReadsWalker extends ReadWalker { @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false) 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) - public Set sampleFiles; + public Set sampleFile; @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false) public Set sampleNames; @@ -73,10 +73,13 @@ public class PrintReadsWalker extends ReadWalker { if ( platform != null ) platform = platform.toUpperCase(); - Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); - samplesToChoose.addAll(samplesFromFile); + Collection samplesFromFile; + if (!sampleFile.isEmpty()) { + samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFile); + samplesToChoose.addAll(samplesFromFile); + } - if (sampleNames != null) + if (!sampleNames.isEmpty()) samplesToChoose.addAll(sampleNames); if(samplesToChoose.isEmpty()) {