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Forgot to deprecate the old args 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6009 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-06-16 17:54:44 +00:00
parent 4e85416af1
commit dd1d9cd76f
1 changed files with 6 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -164,6 +164,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false) @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
protected boolean DEPRECATED_REALIGN_MATES = false; protected boolean DEPRECATED_REALIGN_MATES = false;
@Deprecated
@Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false)
protected boolean DEPRECATED_KNOWNS_ONLY = false;
// DEBUGGING OPTIONS FOLLOW // DEBUGGING OPTIONS FOLLOW