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resuse fasta file reader 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1446 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-08-20 16:01:58 +00:00
parent 0386e110cf
commit 6c0adc9145
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/HybSelPerformanceWalker.java
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@ -170,9 +170,13 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
return new Interval(target.getContig(), (int) target.getStart(), (int) target.getStop());
}
IndexedFastaSequenceFile seqFile = null;
private double calculateGC(GenomeLoc target) {
try {
IndexedFastaSequenceFile seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
if (seqFile == null) {
seqFile = new IndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
}
ReferenceSequence refSeq = seqFile.getSubsequenceAt(target.getContig(),target.getStart(), target.getStop());