expandCigar: Expand cigar codes to GRanges

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

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

data(CTCF_in_10a_overlaps_gr)
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)

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.