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Temporary patch to filter out bad alignments that aren't quite fully reported as bad. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1176 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-06 18:41:55 +00:00
parent 6580211c2a
commit 31313481f6
1 changed files with 8 additions and 0 deletions
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8
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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@ -178,6 +178,14 @@ public abstract class LocusView extends LocusContextIterator implements View {
TraversalStatistics.nBadAlignments++;
result = true;
why = "No alignment start";
} else if (rec.getAlignmentEnd() != -1 && rec.getAlignmentEnd() < rec.getAlignmentStart() ) {
TraversalStatistics.nBadAlignments++;
result = true;
why = "Alignment ends before it starts";
} else if (rec.getAlignmentStart() != -1 && rec.getAlignmentBlocks().size() == 0) {
TraversalStatistics.nBadAlignments++;
result = true;
why = "Alignment cigar string is invalid";
} else if (rec.getDuplicateReadFlag()) {
TraversalStatistics.nDuplicates++;
result = true;