diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java index 2aa556734..7c2033f7b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java @@ -28,18 +28,15 @@ public class PrintLocusContextWalker extends LocusWalker public Integer reduceInit() { return 0; } 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; } private String[] getReadNames( List reads ) { String[] readNames = new String[ reads.size() ]; - for( int i = 0; i < reads.size(); i++ ) - readNames[i] = reads.get(i).getReadName(); + for( int i = 0; i < reads.size(); i++ ) { + 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; } }