seqsToAln {CrispRVariants} | R Documentation

## Creates a text alignment from a set of cigar strings

### 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

[Package CrispRVariants version 1.20.0 Index]