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accidentally committed some debug code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1356 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-31 15:25:22 +00:00
parent 2f2c8576a5
commit 9a0761cd8f
1 changed files with 1 additions and 7 deletions
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8
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
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@ -92,12 +92,7 @@ public class GLFWriter implements GenotypeWriter {
int readDepth, int readDepth,
LikelihoodObject lhValues) { LikelihoodObject lhValues) {
getRidOfMe++; // check if we've jumped to a new contig
if (getRidOfMe == 500) {
this.close();
} else if (getRidOfMe < 500) {
System.err.println(contig.getSequenceName() + ":" + genomicLoc);
// check if we've jumped to a new contig
checkSequence(contig.getSequenceName(), contig.getSequenceLength()); checkSequence(contig.getSequenceName(), contig.getSequenceLength());
SinglePointCall call = new SinglePointCall(refBase, SinglePointCall call = new SinglePointCall(refBase,
@ -107,7 +102,6 @@ public class GLFWriter implements GenotypeWriter {
lhValues.toDoubleArray()); lhValues.toDoubleArray());
lastPos = genomicLoc; lastPos = genomicLoc;
call.write(this.outputBinaryCodec); call.write(this.outputBinaryCodec);
}
} }
/** /**