From 2fb45dbd736d39f8b84fb235529af574988d4dbc Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 3 Nov 2009 16:13:35 +0000 Subject: [PATCH] Make window size a command line argument git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index d57fcdebe..d6ebb81c4 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -64,8 +64,9 @@ public class IndelGenotyperV2Walker extends ReadWalker { "by this application, so they will not contribute indels to consider and will not be counted.", required=false) PlatformUnitFilterHelper dummy; @Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging",required=false) Boolean DEBUG = false; + @Argument(fullName="window_size", shortName="ws", doc="Size (bp) of the sliding window used for accumulating the coverage. "+ + "May need to be increased to accomodate longer reads or longer deletions.",required=false) int WINDOW_SIZE = 200; - private static int WINDOW_SIZE = 200; private WindowContext tumor_context; private WindowContext normal_context; private int currentContigIndex = -1;