seqsToAln: Creates a text alignment from a set of cigar strings

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Creates a one-to-one text alignment of a set of cigar strings with respect to the reference sequence by collapsing insertions and introducing gaps across deletions.

When genomic coordinates for the alignment start and the target region are provided, aligned sequences are cropped to the target region

Given a character vector of pairwise alignments and a region to display, trims alignments to the display regions, joined by a separator "join". Alignments should be equal length, e.g. created by seqsToAln

Usage

seqsToAln(cigar, dnaseq, target, del_char = "-", aln_start = NULL,
  reverse_complement = FALSE, allow_partial = FALSE)

selectAlnRegions(alns, reference, target, keep, join = "/ %s /",
  border.gaps = FALSE)

Arguments

cigar	A list of cigar strings to align
dnaseq	The set of sequences corresponding to the cigars, as Biostrings::DNAStrings
target	The target region to return, as GRanges. Sequences overlapping the target region are trimmed to exactly match it.
del_char	The character to represent deleted bases. Default "-"
aln_start	Genomic start locations of aligned sequences. Should be used in conjunction with target_start and target_end.
reverse_complement	(Default: FALSE)
allow_partial	Are alignments that do not span the target region allowed? (Default: FALSE)
alns	Character vector of pairwise alignments, with insertions removed
reference	Reference sequence
keep	Region to display, relative to the target region, i.e. not genomic coords (IRanges or GRanges)
join	character(1) String used for joining alignment segments. Can accept a placeholder to fill in the number of bases deleted with " deleted
border.gaps	(logical(1)) Should bases deleted from the borders be shown? (Default: FALSE)

Value

The sequences with insertions collapsed and deletions padded

A list of the truncated alignments (alns) and reference (ref)

Author(s)

Helen Lindsay

Helen Lindsay

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.