CIGAR alignment span decoder
Calculate query and reference bases consumed by an alignment operation string.
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The starting values are hypothetical. Use aggregate or synthetic inputs only.
Calculation results
- Query bases consumed
- 37
- Reference bases consumed
- 33
- Operation count
- 5
How to interpret the output
SAM operations M, I, S, = and X consume query bases. M, D, N, = and X consume reference bases. H and P consume neither. M can include mismatches. The decoder checks operation syntax and clipping placement, without checking alignment records, sequences or mapping quality.
Method reference