readTargetBam: Internal CrispRVariants function for reading and filtering a bam file

Description

Includes options for excluding reads either by name or range. The latter is useful if chimeras are excluded. Reads are excluded before chimeras are detected, thus a chimeric read consisting of two sections, one of which overlaps an excluded region, will not be considered chimeric. Chimeric reads can be ignored, excluded, which means that all sections of a chimeric read will be removed, or merged, which means that chimeras will be collapsed into a single read where possible. (Not implemented yet) If chimeras = "merge", chimeric reads are merged if all segments

Usage

readTargetBam(file, target, exclude.ranges = GRanges(), exclude.names = NA, chimera.to.target = 5, chimeras = c("count", "ignore", "exclude", "merge"), by.flag = TRUE, verbose = TRUE)

Arguments

file

The name of a bam file to read in

target

A GRanges object containing a single target range

exclude.ranges

A GRanges object of regions that should not be counted, e.g. primer or cloning vector sequences that have a match in the genome

exclude.names

A vector of read names to exclude.

chimera.to.target

Maximum distance between endpoints of chimeras and target.loc for assigning chimeras to targets (default: 5)

chimeras

Flag to determine how chimeric reads are treated. One of "ignore", "exclude", "count" and "merge". Default "ignore".

by.flag

Is the supplementary alignment flag set? Used for identifying chimeric alignments, function is much faster if TRUE. Not all aligners set this flag. If FALSE, chimeric alignments are identified using read names (Default: TRUE)

verbose

Print stats about number of alignments read and filtered. (Default: TRUE)

Value

A GenomicAlignments::GAlignment obj