cigarsToEvents {amplican} | R Documentation |
Transform extended CIGAR strings into GRanges
representation
with events of deletions, insertions and mismatches.
cigarsToEvents( cigars, aln_pos_start, query_seq, ref, read_id, mapq, seqnames, strands, counts )
cigars |
(character) Extended CIGARS. |
aln_pos_start |
(integer) Pos of CIGARS. |
query_seq |
(character) Aligned query sequences. |
ref |
(character) Reference sequences used for alignment. |
read_id |
(numeric) Read id for assignment for each of the CIGARS. |
mapq |
(numeric) Maping scores. |
seqnames |
(character) Names of the sequences, potentially ids of the reference sequences. |
strands |
(character) Strands to assign. |
counts |
(integer) Vector of cigar counts, if data collapsed. |
(GRanges
) Same as events.