Description
Measure supplied research phase-block coordinates while preserving unknown-block status; no haplotype inference.
Pharmacogenomic records distinguish allele labels, copy counts, reference-sequence versions, coordinate systems, and evidence about chromosome phase. A balanced count or matching token can check a record without establishing the underlying genotype. Supplied activity values and interpretation rules remain separate from a current gene-specific clinical guideline.
Measure supplied research phase-block coordinates while preserving unknown-block status; no haplotype inference.
When to use this tool
Use Research Haplotype Phase Block Span when you need this specific allele-token, reference-coordinate, copy-budget, or source-support check.
How to use the tool and how it works
- Enter startPosition, endPosition, blockKnown, includeEnd. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read spanDefined, span. Inspect spanDefined before interpreting the associated values.
Return spanDefined=blockKnown and span=endPosition-startPosition plus one if includeEnd when known; require ordered endpoints only on that branch. An unknown block returns span=0.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| startPosition | Start Position | Required. Safe integer. |
| endPosition | End Position | Required. Safe integer. |
| blockKnown | Supplied assertion that a span is known; false yields a zero placeholder. | Required. Boolean. |
| includeEnd | Include End | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| spanDefined | Span Defined | Required. Boolean. |
| span | Coordinate span under the stated endpoint policy. | Required. Safe integer. |
{
"input": {
"startPosition": 100,
"endPosition": 150,
"blockKnown": true,
"includeEnd": true
},
"output": {
"spanDefined": true,
"span": 51
}
}Limitations and assumptions
- Coordinates must share a reference and origin. Unknown blocks bypass endpoint order checks, and zero span is a placeholder; no phase block is inferred from variants or reads.
- 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. Signed zero is exported as zero.
Alternative or Complementary methods
Use a current gene-specific nomenclature and a validated interpretation process when allele identity, phase, function, or clinical decisions matter. Verify source versions and reference coordinates before combining records.
References
Similar or alternative tools
- Reference Build Coordinate Offset
Apply a caller-verified local coordinate offset with explicit build labels; this is not a genome liftover algorithm.
- Phase Block Missing Site Count
Count explicitly listed missing research phase-block sites without phasing or clinical variant interpretation.