Package org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
package org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
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ClassDescriptionHolding necessary information about a local assembly for use in SV discovery.Locally assembled contig: its name its sequence as produced by the assembler (no reverse complement like in the SAM record if it maps to '-' strand), and its stripped-down alignment information.After configuration scoring and picking, the original alignments can be classified as good and bad mappings: good: the ones used the picked configuration bad: unused alignments in the chosen configuration; these likely contain more noise than information they can be turned into string representation following the format as in
AlignmentInterval.toPackedString()Loads various upstream assembly and alignment formats and turn into customAlignedContigformat in the discovery stage.Each assembled contig should have at least one such accompanying structure, or 0 when it is unmapped.A simple heuristic optimizer based on extensive manual review of alignments produced by the aligner (currently "bwa mem -x intractg") with the aim for picking a configuration that provides "optimal coverage" for the input assembly contig.A wrapper aroundAlignedContigto represent mapped assembly contig whose alignments went throughAssemblyContigAlignmentsRDDProcessorand may represent SV breakpoints.For symbolizing the change of strand from one alignment to the next of an assembly contig.