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Re-adding --dont-use-softclipped-bases to the help output #8271

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Mar 29, 2023
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Re-adding --dont-use-softclipped-bases to the help output #8271

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4 changes: 1 addition & 3 deletions ...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
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Expand Up @@ -145,9 +145,7 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
@Hidden
@Argument(fullName = ALLELE_LIKELIHOOD_MATRIX_INTERVAL, doc="Interval for which to write the alleleLikelihoodMatrix", optional=true)
public String alleleLikelihoodMatrixInterval=null;

@Advanced
@Hidden

@Argument(fullName = DONT_USE_SOFT_CLIPPED_BASES_LONG_NAME, doc = "Do not analyze soft clipped bases in the reads", optional = true)
public boolean dontUseSoftClippedBases = false;

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