Package org.broadinstitute.hellbender.utils.read.mergealignment
package org.broadinstitute.hellbender.utils.read.mergealignment
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ClassDescriptionAbstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.This strategy was designed for TopHat output, but could be of general utility.When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.Holds all the hits (alignments) for a read or read pair.For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.Iterate over queryname-sorted SAM, and return each group of reads with the same queryname.Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.