seqlengthsobject

seqlengthsobject is a data structure used in bioinformatics to store the lengths of a set of sequences, typically identifiers such as chromosomes or contigs and their corresponding lengths from a genome assembly or sequencing dataset. It serves as a compact reference for coordinate arithmetic, range validation, and indexing, without storing the full sequences themselves.

Representation and implementations

In the Bioconductor ecosystem (R), the standard representation is a named integer vector called seqlengths, for example seqlengths <- c(chr1=248956422, chr2=242193529, chr3=198295559). For more complex contexts, the Seqinfo class (used by GenomicRanges and related packages) stores seqlengths along with genome name and per-sequence circularity flags; seqlengths can be accessed with seqlengths(object) and updated with seqlengths(object) <- value. Other programming languages commonly implement seqlengths as a dictionary or map, such as { 'chr1': 248956422, 'chr2': 242193529 }.

Creation and manipulation

Seqlengths can be created from assembly metadata, parsed from sequence headers, or derived from existing genomic objects. You can query a seqlengthsobject by sequence ID, assign new lengths, or subset to a subset of sequences. Validation routines check for missing identifiers, negative values, or conflicts between data sources.

Use cases

Seqlengthsobjects support coordinate-based operations, interval queries, and alignment workflows where coordinates must be validated against known sequence extents. They enable robust subsetting and error checking in pipelines that manipulate genomic coordinates and ensure consistency between sequence data and associated analyses.

See also

Seqinfo, seqlengths accessor, GenomicRanges.