cigarsToEvents {amplican} | R Documentation

## Transform extended CIGAR strings into GRanges.

### Description

Transform extended CIGAR strings into `GRanges` representation with events of deletions, insertions and mismatches.

### Usage

    cigarsToEvents(cigars, aln_pos_start, query_seq, ref, read_id, mapq,
      seqnames, strands, counts)

### Arguments

`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.

### Value

(`GRanges`) Same as events.

[Package amplican version 1.8.2 Index]