<BUG>@Hidden@Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)public String ASSUME_SINGLE_SAMPLE = null;</BUG><CONTEXT>public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;@Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false)public boolean COMPUTE_SLOD = false;@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)public RodBinding<VariantContext> alleles;<extra_id_0>@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)public int MIN_BASE_QUALTY_SCORE = 17;</CONTEXT>
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