From 297f15a60ce11aba7ac7cfac30e38551faaf7e11 Mon Sep 17 00:00:00 2001 From: delangel Date: Mon, 12 Jul 2010 20:54:42 +0000 Subject: [PATCH] Protect ProduceBeagleInputWalker against evil users who feed to it VCF's with indels, no variation sites or other interesting markers: Write to Beagle input only in biallelic SNP sites since that's the only thing Beagle can do. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3772 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/ProduceBeagleInputWalker.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java index 041db79fc..6f8d0384c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java @@ -86,6 +86,12 @@ public class ProduceBeagleInputWalker extends RodWalker { if ( vc_eval == null || vc_eval.isFiltered() ) return 0; + if (vc_eval.getType() != VariantContext.Type.SNP) + return 0; + + if (vc_eval.getAlleles().size()!= 2) + return 0; + // output marker ID to Beagle input file beagleWriter.print(String.format("%s ", vc_eval.getLocation().toString()));