Package org.broadinstitute.hellbender.tools.sv
package org.broadinstitute.hellbender.tools.sv
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ClassDescriptionAbstractEvidenceSortMerger<F extends SVFeature>A FeatureSink that buffers and resolves (by merging, or by checking for redundancy) features that occur on the same interval.Biallelic-frequency of a sample at some locus.Imposes additional ordering of same-locus BafEvidence by sample.Combines adjacent intervals in DepthEvidence files.Read counts for an indefinite number of samples on some interval.Merges records for the same interval into a single record, when possible, throws if not possible.Documents evidence of a too-close or too-far-apart read pair.Prints (and optionally subsets) an rd (DepthEvidence) file or a counts file as one or more (for multi-sample DepthEvidence files) counts files for CNV determination.Merges locus-sorted files of evidence for structural variation into a single output file.The read depth of each base call for a sample at some locus.Imposes additional ordering of same-locus SiteDepth records by sample.Merges locus-sorted SiteDepth evidence files, and calculates the bi-allelic frequency (baf) for each sample and site, and writes these values as a BafEvidence output file.Documents evidence of reads (of some sample at some locus) that align well to reference for some portion of the read, and fails to align for another portion of the read.Imposes additional ordering of same-locus SplitReadEvidence by sample and strand.Simple allele counter for SVs.Any class with loci that are potentially on different chromosomes should implement this interface.