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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Roger Zurawicki 2011-07-20 11:17:36 -04:00
parent d3a8363491 b9c9e0e952
commit ea90af199c
1 changed files with 15 additions and 20 deletions
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35
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -59,12 +59,12 @@ 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 = new TreeSet<File>();
@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 = 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.
@ -73,14 +73,17 @@ 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()) {
NO_SAMPLES_SPECIFIED = true; SAMPLES_SPECIFIED = true;
} }
} }
@ -109,19 +112,11 @@ 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(); // todo - should be case-agnostic but for simplicity and speed this is ignored.
boolean found = false; // todo - can check at initialization intersection of requested samples and samples in BAM header to further speedup.
for (String sampleSelected : samplesToChoose) { if (!samplesToChoose.contains(read.getReadGroup().getSample()))
if (readSample.equalsIgnoreCase(sampleSelected)) {
found = true;
break;
}
}
if (!found)
return false; return false;
} }