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Genomic Insertion Interbase Coordinate

Represent an insertion after the supplied one-based left base as a zero-based interbase boundary; zero denotes before the first base.

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Description

Crosswalk a supplied left-base insertion position to an interbase coordinate.

Sequence formats distinguish coordinate origins, included endpoints, allele separators and identifier grammars. A genomic interbase position differs from a base number, and a parsed optional-field value may still violate its declared type. Local token checks preserve representation without validating a complete file, sequence, reference assembly or biological interpretation.

Crosswalk a supplied left-base insertion position to an interbase coordinate.

When to use this tool

Use Genomic Insertion Interbase Coordinate when you already have leftBaseOneBased and need to crosswalk a supplied left-base insertion position to an interbase coordinate.

How to use the tool and how it works

  1. Enter leftBaseOneBased. Use the units and conventions below.
  2. Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
  3. Read interbaseZeroBased. Use the output convention below.

Require leftBaseOneBased a nonnegative safe integer; return the same number as interbaseZeroBased.1

Input fieldMeaning and unitsAccepted input
leftBaseOneBasedBase immediately left of the insertion, with zero accepted before the first base.Required. Safe integer; minimum 0.
Output fieldInterpretationReturned shape
interbaseZeroBasedSame integer as the supplied left-base position, representing the boundary after it.Required. Safe integer.
json
{
  "input": {
    "leftBaseOneBased": 100
  },
  "output": {
    "interbaseZeroBased": 100
  }
}

Limitations and assumptions

  • The insertion lies after that one-based base, so zero denotes before the first base. No reference sequence, contig length or insertion representation is 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. Numeric signed-zero results are exported as zero.

Alternative or Complementary methods

Use the complete applicable file specification and a full format validator for conformance. Verify reference assembly, sequence bounds, annotation and database context before interpreting local fields or coordinate transformations.

References

  1. Calculation and input contract: bioinformatics/genomic-insertion-interbase-coordinate — tool.io

Similar or alternative tools

  • BED Zero To Start

    Convert a nonempty zero-based half-open BED interval to one-based endpoints.

  • CDS Frame Offset

    Calculate a supplied coding-sequence offset modulo three.

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