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better filtering, plus deal with case where user doesn't input maxlength 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@939 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-08 18:44:29 +00:00
parent f6e985d97f
commit 58f7ae8628
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelIntervalWalker.java
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@ -25,7 +25,8 @@ public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval
public boolean filter(char[] ref, SAMRecord read) {
return ( !read.getReadUnmappedFlag() && // mapped
read.getReadLength() <= maxReadLength && // not too big
(maxReadLength < 0 || read.getReadLength() <= maxReadLength) && // not too big
read.getMappingQuality() != 0 && // positive mapping quality
read.getAlignmentBlocks().size() > 1); // indel
}