CIGAR Operation Summary
Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
Description
CIGAR distinguishes operations consuming read bases from those consuming reference bases.
CIGAR distinguishes operations consuming read bases from those consuming reference bases. Insertions, deletions and clipping affect these totals differently.1
Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
When to use CIGAR Operation Summary
Use this for the following task: Summarize CIGAR operations and distinguish query-consuming and reference-consuming bases.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use CIGAR Operation Summary and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter cigar using the field table, then run the tool.
- Read operations, operationBases, queryConsumed, referenceConsumed. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| cigar | Explicit CIGAR with positive lengths and terminal SAM clipping; * is unavailable, not an alignment. | string; minimum text length 2; maximum text length 1000000; pattern ^(?:[1-9][0-9]*[MIDNSHP=X])+(?![\s\S]) | Required |
Parse supported positive-length CIGAR tokens, accumulate bases by operation in first-occurrence order, and return independent safe query/reference totals.2
query consumes M,I,S,=,X; reference consumes M,D,N,=,X This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| operations | Operations | list of string |
| operationBases | Operation bases | list of integer |
| queryConsumed | Query consumed | integer |
| referenceConsumed | Reference consumed | integer |
{
"input": {
"cigar": "5S10M2I3D4N1H"
},
"output": {
"operations": [
"S",
"M",
"I",
"D",
"N",
"H"
],
"operationBases": [
5,
10,
2,
3,
4,
1
],
"queryConsumed": 17,
"referenceConsumed": 17
}
}Limitations and assumptions
M does not reveal mismatch count. No sequence comparison or alignment-quality evaluation is performed.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose CIGAR Junction Positions for this operation: Extract zero-based half-open reference skip junctions from CIGAR N operations. For a complementary task, use Soft Clip Breakpoints for this operation: Generate zero-based reference-boundary hints from terminal soft clips and aligned CIGAR span.
Further background: Background specification: CIGAR Operation Summary.
References
-
Background specification: CIGAR Operation Summary — GA4GH / HTS specifications
-
CIGAR Operation Summary — tool.io
Similar or alternative tools
- CIGAR Junction Positions
Extract zero-based half-open reference skip junctions from CIGAR N operations.
- Soft Clip Breakpoints
Generate zero-based reference-boundary hints from terminal soft clips and aligned CIGAR span.