Package org.broadinstitute.hellbender.tools.spark.pathseq
package org.broadinstitute.hellbender.tools.spark.pathseq
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ClassesClassDescriptionKeep reads that do NOT contain one or more kmers from a set of SVKmerShortsWrapper for ContainsKmerReadFilter to avoid serializing the kmer filter in SparkFilters out reads above a threshold identity (number of matches less deletions), given in bases.Produce a set of k-mers from the given host reference.Build an annotated taxonomy datafile for a given microbe reference.Align reads to a microbe reference using BWA-MEM and Spark.Filters low complexity, low quality, duplicate, and host reads.Combined tool that performs all PathSeq steps: read filtering, microbe reference alignment and abundance scoringClassify reads and estimate abundances of each taxon in the reference.Loads Bwa index and aligns reads.Wrapper class for using the PathSeq Bwa aligner class in Spark.Aligns using BWA and filters out reads above the minimum coverage and identity.Utility functions for PathSeq Bwa toolPerforms PathSeq filtering steps and manages associated resources.Kmer Bloom Filter class that encapsulates the filter, kmer size, and kmer maskClasses that provide a way to test kmers for set membership and keep track of the kmer size and maskKmer Hopscotch set class that encapsulates the filter, kmer size, and kmer maskPathSeq utilities for kmer librariesClass for separating paired and unpaired reads in an RDDStores taxonomic IDs that were hits of a read pair.Helper class for ClassifyReads that stores the name, taxonomic class and parent, reference length, and reference contig names of a given taxon in the pathogen reference.Pathogen abundance scores assigned to a taxonomic node and reported by the PathSeqScoreSpark tool.Important NCBI taxonomy database constantsHelper class for holding taxonomy data used by ClassifyReadsRepresents a taxonomic tree with nodes assigned a name and taxonomic rank (e.g.Node class for PSTreeCommon functions for PathSeq