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Augment PrintLocusContextWalker with extended event info. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5583 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-04-06 13:42:48 +00:00
parent ab5c4064ed
commit b231a40da5
1 changed files with 11 additions and 3 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
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@ -21,12 +21,15 @@ public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integ
private PrintStream out;
public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
out.printf( "In map: ref = %s, loc = %s, reads = %s%n", ref.getBaseAsChar(),
context.getLocation(),
Arrays.deepToString( getReadNames(context.getReads()) ) );
out.printf( "In map: ref = %s, loc = %s %s, reads = %s%n", ref.getBaseAsChar(),
context.getLocation(),
context.hasExtendedEventPileup() ? "[extended]" : "",
Arrays.deepToString( getReadNames(context.getReads()) ) );
return context;
}
public Integer reduceInit() { return 0; }
public Integer reduce(AlignmentContext context, Integer sum) {
@ -45,4 +48,9 @@ public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integ
//Arrays.sort(readNames);
return readNames;
}
@Override
public boolean generateExtendedEvents() {
return true;
}
}