Hgvs Intron Offset Closure Flag Tool

Description

Inspect one explicitly signed nonzero intronic offset fragment; not a full HGVS expression or variant validator.

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.

Inspect one explicitly signed nonzero intronic offset fragment; not a full HGVS expression or variant validator.

When to use this tool

Use Hgvs Intron Offset Closure Flag 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 offsetToken, basePosition, lowerOffset, upperOffset, includeLower, includeUpper. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read offset, withinBounds, basePosition. Inspect withinBounds before interpreting the associated values.

Parse offsetToken as + or - followed by a positive safe integer. Require lowerOffset<=upperOffset and compare the signed offset using the chosen inclusive/exclusive endpoint flags; return offset, withinBounds, and the supplied basePosition.^[1]

Input field	Meaning and units	Accepted input
offsetToken	Offset Token	Required. Text; maximum UTF-16 length 8192.
basePosition	Base Position	Required. Safe integer.
lowerOffset	Lower Offset	Required. Safe integer.
upperOffset	Upper Offset	Required. Safe integer.
includeLower	Include Lower	Required. Boolean.
includeUpper	Include Upper	Required. Boolean.

Output field	Interpretation	Returned shape
offset	Signed coordinate or time offset under the stated formula.	Required. Safe integer.
withinBounds	Whether the supplied offset meets the selected endpoint comparisons.	Required. Boolean.
basePosition	Base Position	Required. Safe integer.

json

{
  "input": {
    "offsetToken": "+3",
    "basePosition": 20,
    "lowerOffset": 1,
    "upperOffset": 3,
    "includeLower": true,
    "includeUpper": false
  },
  "output": {
    "offset": 3,
    "withinBounds": false,
    "basePosition": 20
  }
}

Limitations and assumptions

The base is preserved rather than mapped. Bounds are caller-supplied and this local check does not establish a valid transcript intron or a full HGVS coordinate.
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/hgvs-intron-offset-closure-flag — tool.io

Similar or alternative tools

Pharmacogene Hgvs Intronic Offset Sign
Parse a positive coding-position/intronic-offset subset without mapping it to a reference sequence.
Pharmacogene Exon Intron Boundary Token
Parse an explicit exon/intron ordinal token without genomic boundary inference.