From ee18c9b0c250b250f8082f90539a953364e998c6 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 20 Jun 2011 16:28:58 +0000 Subject: [PATCH] Temporary commit to please those in 320: re-support the -knownsOnly argument (@Hidden). This will be reverted in a sec. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6018 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) 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 771468902..c181fd470 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -164,7 +164,8 @@ public class IndelRealigner extends ReadWalker { @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false) protected boolean DEPRECATED_REALIGN_MATES = false; - @Deprecated + // @Deprecated + @Hidden @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false) protected boolean DEPRECATED_KNOWNS_ONLY = false; @@ -229,6 +230,9 @@ 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 )