Description
Locate zero-length CIGAR operation records.
Sequence alignments distinguish flag bits, query/reference coordinates, CIGAR operations and scoring conventions. A single flag or length contribution does not establish a complete valid alignment; consuming reference bases differs from consuming query bases or counting a gap penalty.
Locate zero-length CIGAR operation records.
When to use this tool
Use SAM CIGAR Zero Length Flag when checking the stated alignment flag, operation, span or gap-scoring convention.
How to use the tool and how it works
- Enter lengths, operations. Follow any array-alignment requirements below. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read hasZeroLength, zeroIndices. Inspect hasZeroLength before interpreting the associated values.
Locate zero-length CIGAR operation records. Require aligned nonempty arrays, nonnegative whole lengths and supported operation letters; zeroIndices lists exact zero lengths, hasZeroLength reports any.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| lengths | Nonnegative supplied whole operation lengths; zero values are reported diagnostically. | Required. Array of safe integer; maximum items 256. |
| operations | Operations | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| hasZeroLength | Has Zero Length | Required. Boolean. |
| zeroIndices | Zero Indices | Required. Array of safe integer; maximum items 256. |
{
"input": {
"lengths": [
10,
0,
5
],
"operations": [
"M",
"I",
"M"
]
},
"output": {
"hasZeroLength": true,
"zeroIndices": [
1
]
}
}Limitations and assumptions
- Lengths must be whole numbers; this zero-length diagnostic is not a complete valid CIGAR parser.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Alternative or Complementary methods
Use a complete SAM/BAM and reference-aware validator or alignment method with explicit clipping, coordinate and scoring policies for full processing.
References
Similar or alternative tools
- CIGAR Soft Clip Length
Sum soft-clipped CIGAR lengths.
- CIGAR Skipped Reference Length
Sum skipped-reference CIGAR lengths.