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Reverting previous change, as promised.

This commit is contained in:
Eric Banks 2011-06-30 13:18:30 -04:00
parent 9e234cf5d6
commit 804d5f22d5
1 changed files with 3 additions and 7 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -99,7 +99,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
protected SAMFileWriter writerToUse = null; 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) @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 // ADVANCED OPTIONS FOLLOW
@ -167,8 +167,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false) @Argument(fullName="realignReadsWithBadMates", doc="This argument is no longer used.", required=false)
protected boolean DEPRECATED_REALIGN_MATES = 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) @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", doc="This argument is no longer used. See --consensusDeterminationModel instead.", required=false)
protected boolean DEPRECATED_KNOWNS_ONLY = false; protected boolean DEPRECATED_KNOWNS_ONLY = false;
@ -262,9 +261,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
public void initialize() { public void initialize() {
if ( DEPRECATED_KNOWNS_ONLY )
consensusModel = ConsensusDeterminationModel.KNOWNS_ONLY;
if ( N_WAY_OUT == null && writer == null ) { if ( N_WAY_OUT == null && writer == null ) {
throw new UserException.CommandLineException("Either -o or -nWayOut must be specified"); throw new UserException.CommandLineException("Either -o or -nWayOut must be specified");
} }
@ -1015,7 +1011,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
sb.append((char)b); sb.append((char)b);
cigar.add(new CigarElement(indelStr.length, CigarOperator.I)); cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
} else { } 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 ) if ( reference.length - refIdx > 0 )