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Swap "." over to VCFConstants.MISSING_DEPTH_v3 

Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4421 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-10-04 13:41:41 +00:00
parent 74087c44ae
commit 0eb777612a
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFConstants;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
@ -255,7 +256,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
else if (g.isHomVar()) { alleleCount += 2; }
String dp = (String) g.getAttribute("DP");
if (dp != null && ! dp.equals(".")) {
if (dp != null && ! dp.equals(VCFConstants.MISSING_DEPTH_v3)) {
depth += Integer.valueOf(dp);
}
}