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Added a stub treeReduce function for debugging multi-threaded execution. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2146 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-11-24 18:51:19 +00:00
parent 277e6d6b32
commit 3fca23cd16
1 changed files with 6 additions and 2 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
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@ -25,7 +25,7 @@ import edu.mit.broad.picard.util.OverlapDetector;
import edu.mit.broad.picard.directed.IntervalList;
@By(DataSource.REFERENCE)
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> {
public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerformanceWalker.TargetInfo> implements TreeReducible<HybSelPerformanceWalker.TargetInfo> {
@Argument(fullName="min_mapq", shortName="mmq", required=false, doc="Minimum mapping quality of reads to consider")
public Integer MIN_MAPQ = 1;
@ -123,6 +123,10 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
return sum;
}
public TargetInfo treeReduce(TargetInfo lhs, TargetInfo rhs) {
return lhs; // dummy function to test if tree reduce by interval is working
}
public void onTraversalDone(TargetInfo result) {
}
@ -204,7 +208,7 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
Collection<Interval> bait_quant_hits = bait_quant.getOverlaps(targetInterval);
String bait_quant_string = (bait_quant_hits.size() == 1) ? bait_quant_hits.iterator().next().getName() : "0";
if (bait_quant_hits.size() <= 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L"); }
if (bait_quant_hits.size() > 1) { out.printf("Warning: multiple bait quantity intervals detected; perhaps bait quantity interval lengths don't match primary interval list specified with -L\n"); }
int adjacent_baits = adjacent_bait_detector.getOverlaps(targetInterval).size() - 1;
out.printf("%s:%d-%d\t%d\t%6.4f\t%6.4f\t%6.4f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%d\n",