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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
This commit is contained in:
ebanks 2011-06-20 16:28:58 +00:00
parent a37e9bdbd4
commit ee18c9b0c2
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -164,7 +164,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@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<Integer, Integer> {
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 )