dot-expand_cigar_dt: Expand intermediate bam fetch by cigar codes

.expand_cigar_dtR Documentation

Expand intermediate bam fetch by cigar codes

Description

see sam specs for cigar details

Usage

.expand_cigar_dt(cigar_dt, op_2count = c("M", "D", "=", "X"))

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.

Value

data.table with cigar entries expanded


jrboyd/seqsetvis documentation built on Oct. 15, 2024, 11:28 p.m.