From 0eb777612a7102b6148945985099871b1139f1ac Mon Sep 17 00:00:00 2001 From: chartl Date: Mon, 4 Oct 2010 13:41:41 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/variantutils/SelectVariants.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index a15173725..c2dcf9553 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -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 { 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); } }