alumi

Detect CIGARs like `kSmN` and refer to `CG` tags.

#### input SAM ``` @SQ SN:ref LN:45 q001 0 ref 10 60 4I4M4D4M4I * 0 0 ATGCATGCATGCATGC ABCDEFGHIJKLMNOP ``` #### samtools output ``` ref 10 N 1 ^]A E ref...

Pileup reads with adjacent indels.

1

CIGAR code with adjacent indels (e.g. 1M2D3I, 1M2N3I) is allowed by [SAM file format specification](https://github.com/samtools/hts-specs/blob/a38e257ca855a9693737c85bc22c7689be49fdf4/SAMv1.tex#L358). Insertions and deletions are piled up at the base position just before them according to...

context: #260 Report an original position in a read for a base piled up