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Deal with randomly occurring unmapped reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@906 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-05 02:55:53 +00:00
parent fdfc3abf80
commit 45eeefbb80
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -120,8 +120,14 @@ public class TraverseByLocusWindows extends TraversalEngine {
TraversalStatistics.nRecords++;
SAMRecord read = readIter.next();
// if there are no locations or we're past the last one or it's unmapped, then act on the read separately
if ( currentInterval == null || read.getReadUnmappedFlag() ) {
// apparently, unmapped reads can occur anywhere in the file!
if ( read.getReadUnmappedFlag() ) {
walker.nonIntervalReadAction(read);
continue;
}
// if there are no locations or we're past the last one, then act on the read separately
if ( currentInterval == null ) {
if ( nextLociToCarry.size() > 0 ) {
sum = carryWalkerOverInterval(walker, sum, nextLociToCarry.get(0));
for (int i=1; i < nextLociToCarry.size(); i++)