Description
Return one affine gap-run penalty.
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.
Return one affine gap-run penalty.
When to use this tool
Use Alignment Gap Open Extension One Run when checking the stated alignment flag, operation, span or gap-scoring convention.
How to use the tool and how it works
- Enter length, openPenalty, extendPenalty, extendFirst. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read penalty, extensionCount. Use the output convention below.
Return one affine gap-run penalty. Require positive whole length and nonnegative penalties; extensionCount = length when extendFirst, otherwise length-1; penalty = openPenalty+extensionCount*extendPenalty.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| length | Length | Required. Safe integer; minimum 1. |
| openPenalty | Open Penalty | Required. Finite number; minimum 0. |
| extendPenalty | Extend Penalty | Required. Finite number; minimum 0. |
| extendFirst | True charges length extension penalties; false charges length-1 in addition to the opening penalty. | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| penalty | Penalty | Required. Finite number. |
| extensionCount | Extension Count | Required. Safe integer. |
{
"input": {
"length": 3,
"openPenalty": 5,
"extendPenalty": 2,
"extendFirst": false
},
"output": {
"penalty": 9,
"extensionCount": 2
}
}Limitations and assumptions
- The extension convention must match the alignment method; no sequence alignment or suitable scoring model is selected.
- 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.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
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 Reference Consumption Gap
Return exact reference-consumed CIGAR span and discrepancy.