From 352c38fc0b48d8910ad3346eff0313b2f0890b06 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 30 Jun 2011 11:55:56 -0400 Subject: [PATCH 2/4] Updated to reflect dbsnp conversion fix --- .../walkers/indels/RealignerTargetCreatorIntegrationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java index acfcbab7b..4b225aaea 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -19,7 +19,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s", 1, - Arrays.asList("fd2d9dbf718f7a6d82ae1787ac1fe61e")); + Arrays.asList("f23ba17ee0f9573dd307708175d90cd2")); executeTest("test dbsnp", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( From 9e234cf5d6b8cf3439fc0703248c637c3119f1e2 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 30 Jun 2011 13:17:14 -0400 Subject: [PATCH 3/4] 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"); } From 804d5f22d522516ea787e3873a7bfbaf3c2035a0 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 30 Jun 2011 13:18:30 -0400 Subject: [PATCH 4/4] 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 )