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Better printing of multiple rods -- now produces a comma-separated set of values 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-21 21:58:27 +00:00
parent 8588f75eb6
commit 761d70faa1
1 changed files with 5 additions and 2 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -32,6 +32,8 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.ReadBackedPileup; import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import java.util.ArrayList;
/** /**
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment> * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
* *
@ -125,12 +127,13 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
* @return String representation of the reference-ordered data. * @return String representation of the reference-ordered data.
*/ */
private String getReferenceOrderedData( RefMetaDataTracker tracker ) { private String getReferenceOrderedData( RefMetaDataTracker tracker ) {
String rodString = ""; ArrayList<String> rodStrings = new ArrayList<String>();
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) { for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
if ( datum != null && ! (datum instanceof rodDbSNP)) { if ( datum != null && ! (datum instanceof rodDbSNP)) {
rodString += datum.toSimpleString(); rodStrings.add(datum.toSimpleString());
} }
} }
String rodString = Utils.join(", ", rodStrings);
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
if ( dbsnp != null ) if ( dbsnp != null )