Pharmacogenomic Assembly Coordinate Source Pair Tool

Description

Compare supplied coordinate/reference metadata without liftover or sequence interpretation.

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.

Compare supplied coordinate/reference metadata without liftover or sequence interpretation.

When to use this tool

Use Pharmacogenomic Assembly Coordinate Source Pair 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 assembly, expectedAssembly, accession, expectedAccession, position, expectedPosition. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read assemblyMatches, accessionMatches, positionMatches. Inspect assemblyMatches, accessionMatches, positionMatches before interpreting the associated values.

For positive integer position and expectedPosition return exact equality flags for assembly, accession, and position against their expected values.^[1]

Input field	Meaning and units	Accepted input
assembly	Assembly	Required. Text; maximum UTF-16 length 8192.
expectedAssembly	Expected Assembly	Required. Text; maximum UTF-16 length 8192.
accession	Accession	Required. Text; maximum UTF-16 length 8192.
expectedAccession	Expected Accession	Required. Text; maximum UTF-16 length 8192.
position	Positive position coordinate under the explicitly supplied reference convention.	Required. Safe integer; minimum 1.
expectedPosition	Expected Position	Required. Safe integer; minimum 1.

Output field	Interpretation	Returned shape
assemblyMatches	Assembly Matches	Required. Boolean.
accessionMatches	Accession Matches	Required. Boolean.
positionMatches	Position Matches	Required. Boolean.

json

{
  "input": {
    "assembly": "A",
    "expectedAssembly": "A",
    "accession": "chr1",
    "expectedAccession": "chr1",
    "position": 100,
    "expectedPosition": 100
  },
  "output": {
    "assemblyMatches": true,
    "accessionMatches": true,
    "positionMatches": true
  }
}

Limitations and assumptions

Matching metadata does not authenticate a reference sequence, normalize assembly aliases, convert coordinate systems, or verify an actual variant mapping.
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

Calculation and input contract: pharmacogenomics/pharmacogenomic-assembly-coordinate-source-pair — tool.io

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