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Minor change: make the --dontUseSoftClippedBases @Advanced instead of @Hidden

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Eric Banks 2014-02-27 13:29:10 -05:00
parent fa65716fe9
commit 4d69af189e
1 changed files with 1 additions and 1 deletions
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protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -459,7 +459,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
@Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler for only this graph size", required = false) @Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler for only this graph size", required = false)
protected boolean debugGraphTransformations = false; protected boolean debugGraphTransformations = false;
@Hidden @Advanced
@Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="If specified, we will not analyze soft clipped bases in the reads", required = false) @Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="If specified, we will not analyze soft clipped bases in the reads", required = false)
protected boolean dontUseSoftClippedBases = false; protected boolean dontUseSoftClippedBases = false;