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Give user ability to turn off max allowed interval size 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-20 03:20:22 +00:00
parent a5f75cbfd4
commit 566b556b50
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
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@ -70,7 +70,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
// ignore all intervals which we've passed // ignore all intervals which we've passed
while ( loc.isPast(currentInterval) ) { while ( loc.isPast(currentInterval) ) {
if ( currentIntervalIsUsed && currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize) { if ( currentIntervalIsUsed && (maxIntervalSize <= 0 || currentInterval.getStop() - currentInterval.getStart() <= maxIntervalSize) ) {
out.println(currentInterval); out.println(currentInterval);
currentIntervalIsUsed = false; currentIntervalIsUsed = false;
} }
@ -106,7 +106,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
@Override @Override
public void onTraversalDone( Integer value ) { public void onTraversalDone( Integer value ) {
if ( currentInterval != null && currentIntervalIsUsed && if ( currentInterval != null && currentIntervalIsUsed &&
currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize) (maxIntervalSize <= 0 || currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize) )
out.println(currentInterval); out.println(currentInterval);
} }
} }