From 9e234cf5d6b8cf3439fc0703248c637c3119f1e2 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 30 Jun 2011 13:17:14 -0400 Subject: [PATCH] This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable. --- .../sting/gatk/walkers/indels/IndelRealigner.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 3cfa58c02..9816e17f7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -99,7 +99,7 @@ public class IndelRealigner extends ReadWalker { protected SAMFileWriter writerToUse = null; @Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses). The default is USE_READS", required = false) - public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_READS; + public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_SW; // ADVANCED OPTIONS FOLLOW @@ -167,7 +167,8 @@ 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; @@ -261,6 +262,9 @@ public class IndelRealigner extends ReadWalker { public void initialize() { + if ( DEPRECATED_KNOWNS_ONLY ) + consensusModel = ConsensusDeterminationModel.KNOWNS_ONLY; + if ( N_WAY_OUT == null && writer == null ) { throw new UserException.CommandLineException("Either -o or -nWayOut must be specified"); }