expandCigar {seqsetvis} | R Documentation |
see sam specs for cigar details
expandCigar( cigar_dt, op_2count = c("M", "D", "=", "X"), return_data.table = FALSE )
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. |
data.table with cigar entries expanded
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)