From 804d5f22d522516ea787e3873a7bfbaf3c2035a0 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 30 Jun 2011 13:18:30 -0400 Subject: [PATCH] Reverting previous change, as promised. --- .../sting/gatk/walkers/indels/IndelRealigner.java | 10 +++------- 1 file changed, 3 insertions(+), 7 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 9816e17f7..a53665d64 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_SW; + public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_READS; // ADVANCED OPTIONS FOLLOW @@ -167,8 +167,7 @@ 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; @@ -262,9 +261,6 @@ 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"); } @@ -1015,7 +1011,7 @@ public class IndelRealigner extends ReadWalker { sb.append((char)b); cigar.add(new CigarElement(indelStr.length, CigarOperator.I)); } else { - throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed"); + throw new IllegalStateException("Creating an alternate consensus from a complex indel is not allows"); } if ( reference.length - refIdx > 0 )