collapsePairs

A GAlignments object.  We do not use GAlignmentPairs because amplicon-seq
can result in pairs in non-standard pairing orientation.
Must include BAM flag, must not include unmapped reads.

alns

Should the consensus sequence be used if pairs have a mismatch?
Setting this to be TRUE makes this function much slower (Default: TRUE)

use.consensus

Should unpaired and chimeric reads be included?  (Default: TRUE)

keep.unpaired

Report statistics on reads kept and excluded

verbose

Additional items with the same length as alns,
that should be filtered to match alns.


Given a set of alignments to a target region, finds read pairs.
Compares insertion/deletion locations within pairs using the cigar string.
Pairs with non-identical indels are excluded.  Pairs with identical indels are
collapsed to a single read, taking the consensus sequence of the pairs.


CrispRVariants provides tools for analysing the results of a
CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments
where variants within a given region are of interest. These tools allow users to
localize variant allele combinations with respect to any genomic location (e.g.
the Cas9 cut site), plot allele combinations and calculate mutation rates with
flexible filtering of unrelated variants.

collapsePairs: Internal CrispRVariants function for collapsing pairs with concordant indels

Description

Usage

Arguments

Value