BED Twelve Block Relative Start Term Tool

Description

Return one BED block's absolute half-open bounds.

Genome annotations depend on coordinate origin, endpoint inclusion, strand and reading-phase conventions. A local offset or phase token can be handled precisely while a complete transcript, reference identity and biological reading frame remain separate validation questions.

Return one BED block's absolute half-open bounds.

When to use this tool

Use BED Twelve Block Relative Start Term when checking the stated genomic coordinate, annotation phase or attribute-value convention.

How to use the tool and how it works

Enter chromStart, chromEnd, blockStart, blockSize. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read absoluteStart, absoluteEnd. Use the output convention below.

Return one BED block's absolute half-open bounds. Require nonnegative whole chromStart, blockStart, blockSize, chromEnd >= chromStart and block end <= chromEnd; add relative blockStart to chromStart.^[1]

BED uses a zero-based start and an excluded end; block starts are relative to the enclosing chromosome start. The complete record has additional constraints.^[2]

Input field	Meaning and units	Accepted input
chromStart	Chrom Start	Required. Safe integer; minimum 0.
chromEnd	Chrom End	Required. Safe integer.
blockStart	Zero-based start relative to chromStart, not an absolute chromosome position.	Required. Safe integer; minimum 0.
blockSize	Block Size	Required. Safe integer; minimum 0.

Output field	Interpretation	Returned shape
absoluteStart	Absolute Start	Required. Safe integer.
absoluteEnd	Absolute End	Required. Safe integer.

json

{
  "input": {
    "chromStart": 100,
    "chromEnd": 200,
    "blockStart": 20,
    "blockSize": 30
  },
  "output": {
    "absoluteStart": 120,
    "absoluteEnd": 150
  }
}

Limitations and assumptions

Zero-size blocks are accepted; this does not validate all twelve BED fields, block ordering, overlap or reference identity.
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 intended complete BED/GFF/GTF format, reference assembly and transcript model to validate full annotations and biological meaning.

References

Calculation and input contract: bioinformatics/bed-twelve-block-relative-start-term — tool.io
Genome Browser data file formats: BED — UCSC Genome Browser

Similar or alternative tools

Phasing Block Span
Return a phasing-block span under an endpoint convention.
Genomic Left Closed Right Open Length Term
Return length and last included position of a half-open interval.