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Make PrintLocusContextWalker less verbose. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-22 18:28:02 +00:00
parent ffcd672c1c
commit 3af66a462e
1 changed files with 4 additions and 7 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java
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@ -28,18 +28,15 @@ public class PrintLocusContextWalker extends LocusWalker<LocusContext, Integer>
public Integer reduceInit() { return 0; } public Integer reduceInit() { return 0; }
public Integer reduce(LocusContext context, Integer sum) { public Integer reduce(LocusContext context, Integer sum) {
out.printf( "In reduce: loc = %s, reads = %s, sum =%d%n", context.getLocation(),
Arrays.deepToString( getReadNames(context.getReads()) ),
sum );
return sum + 1; return sum + 1;
} }
private String[] getReadNames( List<SAMRecord> reads ) { private String[] getReadNames( List<SAMRecord> reads ) {
String[] readNames = new String[ reads.size() ]; String[] readNames = new String[ reads.size() ];
for( int i = 0; i < reads.size(); i++ ) for( int i = 0; i < reads.size(); i++ ) {
readNames[i] = reads.get(i).getReadName(); readNames[i] = String.format("%nname = %s, start = %d, end = %d", reads.get(i).getReadName(), reads.get(i).getAlignmentStart(), reads.get(i).getAlignmentEnd());
}
//Arrays.sort(readNames);
return readNames; return readNames;
} }
} }