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

In markrobinsonuzh/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

Usage

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

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.

Value

The sequences with insertions collapsed and deletions padded

Author(s)

Helen Lindsay

markrobinsonuzh/CrispRVariants documentation built on May 21, 2019, 12:23 p.m.