Description
Preserve the supplied phase-known flag without inferring haplotypes from labels.
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.
Preserve the supplied phase-known flag without inferring haplotypes from labels.
When to use this tool
Use Pharmacogene Phase Unknown Token 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 phaseKnown, firstAllele, secondAllele. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read phaseStatus, preservedAlleles. Use the output convention below.
Return phaseStatus=supplied-known when phaseKnown, otherwise unknown; preserve firstAllele and secondAllele in their original order.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| phaseKnown | Phase Known | Required. Boolean. |
| firstAllele | First Allele | Required. Text; maximum UTF-16 length 8192. |
| secondAllele | Second Allele | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| phaseStatus | Phase Status | Required. Text; maximum UTF-16 length 8192. |
| preservedAlleles | Preserved Alleles | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
{
"input": {
"phaseKnown": false,
"firstAllele": "*1",
"secondAllele": "*2"
},
"output": {
"phaseStatus": "unknown",
"preservedAlleles": [
"*1",
"*2"
]
}
}Limitations and assumptions
- PhaseKnown is a supplied assertion rather than read-level evidence. Allele syntax, cis/trans relationships, copy number, and phenotype are not inferred or verified.
- 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 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
- Pharmacogene Allele Frequency Sum Residual
For frequencies and expectedSum within zero through one and nonnegative tolerance return sum, residual=sum-expectedSum, and within=(abs(residual)<=tolerance).
- Pharmacogene Copy Number Token Field
Parse an explicit star-allele copy token; copies is zero when the copy number is unknown.