From 600a6a43a64e63ba7de74210e35419fb82359c63 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 20 Jun 2011 16:30:19 +0000 Subject: [PATCH] Reverting previous commit, as promised. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6019 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 6 +----- 1 file changed, 1 insertion(+), 5 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 c181fd470..771468902 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -164,8 +164,7 @@ public class IndelRealigner extends ReadWalker { @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false) protected boolean DEPRECATED_REALIGN_MATES = false; - // @Deprecated - @Hidden + @Deprecated @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false) protected boolean DEPRECATED_KNOWNS_ONLY = false; @@ -230,9 +229,6 @@ public class IndelRealigner extends ReadWalker { public void initialize() { - if ( DEPRECATED_KNOWNS_ONLY ) - consensusModel = ConsensusDeterminationModel.KNOWNS_ONLY; - if ( LOD_THRESHOLD < 0.0 ) throw new RuntimeException("LOD threshold cannot be a negative number"); if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )