Package org.broadinstitute.hellbender.tools.spark.sv.evidence
package org.broadinstitute.hellbender.tools.spark.sv.evidence
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ClassDescriptionAn assembly with its contigs aligned to reference, or a reason that there isn't an assembly.A class that acts as a filter for breakpoint evidence.Various types of read anomalies that provide evidence of genomic breakpoints.A class to examine a stream of BreakpointEvidence, and group it into Intervals.(Internal) Collects read metrics relevant to structural variant discoveryThis class holds information about pairs of intervals on the reference that are connected by one or more BreakpointEvidence objects that have distal targets.This class is responsible for iterating over a collection of BreakpointEvidence to find clusters of evidence with distal targets (discordant read pairs or split reads) that agree in their location and target intervals and strands.(Internal) Extracts evidence of structural variations from readsLocalAssemblyHandler that uses FermiLite.Identifies sequences that occur at high frequency in a reference(Internal) Produces local assemblies of genomic regions that may harbor structural variantsClass to find the coverage of the intervals.A <Kmer,IntervalId> pair.Eliminates dups, and removes over-represented kmers.Iterates over reads, kmerizing them, and counting up just the kmers that appear in a passed-in set.statistics of fragment length distributionsIt allows you to ask whether a given interval is near the beginning or end of the partition.A template name and an intervalId.Class to find the template names associated with reads in specified intervals.Iterates over reads, kmerizing them, and checking the kmers against a set of KmerAndIntervals to figure out which intervals (if any) a read belongs in.Class that acts as a mapper from a stream of reads to a stream of KmerAndIntervals.Class that acts as a mapper from a stream of reads to a stream of <kmer,qname> pairs for a set of interesting kmers.Figures out what kind of BreakpointEvidence, if any, a read represents.A bag of data about reads: contig name to id mapping, fragment length statistics by read group, mean length.A class to track the genomic location of the start of the first and last mapped reads in a partition.Find <intervalId,list
> pairs for interesting template names. Indicates the ordinal of a fragment in a paired sequenced template.