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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
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asivache 2009-11-03 16:13:35 +00:00
parent 55f61b1f88
commit 2fb45dbd73
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -64,8 +64,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
"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;