Description
Apply a caller-verified local coordinate offset with explicit build labels; this is not a genome liftover algorithm.
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.
Apply a caller-verified local coordinate offset with explicit build labels; this is not a genome liftover algorithm.
When to use this tool
Use Reference Build Coordinate Offset 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 coordinate, sourceOrigin, targetOrigin, sourceBuild, targetBuild, mappingVerified. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read mappedCoordinateDecimal, source, target. Use the output convention below.
Require mappingVerified=true and nonempty sourceBuild and targetBuild. Use exact integer arithmetic for mappedCoordinateDecimal=coordinate-sourceOrigin+targetOrigin, and return the two supplied build labels.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| coordinate | Safe-integer source coordinate, on the supplied origin convention. | Required. Safe integer. |
| sourceOrigin | Source Origin | Required. Safe integer. |
| targetOrigin | Target Origin | Required. Safe integer. |
| sourceBuild | Source Build | Required. Text; maximum UTF-16 length 8192. |
| targetBuild | Target Build | Required. Text; maximum UTF-16 length 8192. |
| mappingVerified | Must be true; a caller assertion rather than an independent mapping check. | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| mappedCoordinateDecimal | Exact signed integer text after applying the constant origin offset. | Required. Text; maximum UTF-16 length 8192. |
| source | Source | Required. Text; maximum UTF-16 length 8192. |
| target | Target | Required. Text; maximum UTF-16 length 8192. |
{
"input": {
"coordinate": 120,
"sourceOrigin": 100,
"targetOrigin": 200,
"sourceBuild": "A",
"targetBuild": "B",
"mappingVerified": true
},
"output": {
"mappedCoordinateDecimal": "220",
"source": "A",
"target": "B"
}
}Limitations and assumptions
- This applies an explicitly supplied constant offset, not a genome assembly liftover or alignment. The verification flag is trusted, negative coordinates may result, and reference sequence validity is not checked.
- 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
- Pharmacogenomic Assembly Coordinate Source Pair
Compare supplied coordinate/reference metadata without liftover or sequence interpretation.
- Hgvs Intron Offset Closure Flag
Inspect one explicitly signed nonzero intronic offset fragment; not a full HGVS expression or variant validator.