expandCigar {seqsetvis} | R Documentation

## Expand cigar codes to GRanges

### Description

see sam specs for cigar details

### Usage

    expandCigar(
      cigar_dt,
      op_2count = c("M", "D", "=", "X"),
      return_data.table = FALSE
    )

### Arguments

`cigar_dt` | data.table with 5 required named columns in any order. c("which_label", "seqnames", "strand", "start", "cigar")
`op_2count` | Cigar codes to count. Default is alignment (M), deletion (D), match (=), and mismatch (X). Other useful codes may be skipped regions for RNA splicing (N). The locations of any insterions (I) or clipping/padding (S, H, or P) will be a single bp immediately before the interval.
`return_data.table` | if TRUE, a data.table is returned, else a GRanges. Default is FALSE.

### Value

data.table with cigar entries expanded

### Examples

    qgr = CTCF_in_10a_overlaps_gr[1:5]
    bam_file = system.file("extdata/test.bam", package = "seqsetvis", mustWork = TRUE)
    raw_dt = ssvFetchBam(bam_file, qgr, return_unprocessed = TRUE)
    expandCigar(raw_dt)

[Package seqsetvis version 1.14.4 Index]