Package org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
package org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
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ClassDescriptionA helper struct for annotating complications that make the locations represented by its associated
NovelAdjacencyAndAltHaplotypea little ambiguous.For novel adjacency between reference locations that are on the same chromosome, and with a strand switch.For this specific complication, we support a what could be defined as incomplete picture, that involves inverted duplication: two overlapping alignments to reference first alignment: --------------------> second alignment: <--------------------- |--------||----------| Seg.1 Seg.2 At least Seg.1 is invert duplicated, and Seg.2 is inverted trans-inserted between the two copies (one of which is inverted).For simple deletion, insertion, and replacement (dep and ins at the same time).For duplications small enough that we seemingly have assembled across the whole event.This is for dealing with case when the duplicated range could NOT be inferred exactly, but only from a simple optimization scheme.Based on alignment signature of the input simple chimera, and evidence contig having the chimera, infers exact position of breakpoints following the left-aligning convention, alt haplotype sequence based on given contig sequence complications such as homology, inserted sequence and duplicated ref region, if any.This class scans the chimeric alignments of inputAlignedContig, filters out the alignments that offers weak evidence for a breakpoint and, makes interpretation based on theSimpleChimeraextracted.This struct contains two key pieces of information that provides interpretation of the event:One of the two fundamental classes (the other isCpxVariantCanonicalRepresentation) for complex variant interpretation and alt haplotype extraction.This deals with the special case where a contig has multiple (> 2) alignments and seemingly has the complete alt haplotype assembled.(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcfThis class represents a pair of inferred genomic locations on the reference whose novel adjacency is generated due to an SV event (in other words, a simple rearrangement between two genomic locations) that is suggested by the inputSimpleChimera, and complications as enclosed inBreakpointComplicationsin pinning down the locations to exact base pair resolution.For extracting simple variants from input GATK-SV complex variants.Conceptually, a simple chimera represents the junction onAssemblyContigWithFineTunedAlignmentsthat have exactly two good alignments.Struct to represent the (distance - 1) between boundaries of the two alignments represented by this CA, on reference, and on read.Simply a wrapper to link togetherNovelAdjacencyAndAltHaplotypeand evidenceSimpleChimera's.Utility structs for extraction information from the consensus NovelAdjacencyAndAltHaplotype out of multiple ChimericAlignments, to be later added to annotations of the VariantContext extracted.This deals with the special case where a contig has exactly two alignments and seemingly has the complete alt haplotype assembled.