From dd1d9cd76ff6b891b6938a349f9db7069e35fd9e Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 16 Jun 2011 17:54:44 +0000 Subject: [PATCH] Forgot to deprecate the old args git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6009 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 9cf55dee5..771468902 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -163,7 +163,11 @@ public class IndelRealigner extends ReadWalker { @Deprecated @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=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 @@ -1585,4 +1589,4 @@ public class IndelRealigner extends ReadWalker { } } -} \ No newline at end of file +}