CLOSEST-FEATURES(1)

📦
version 2.4.42 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 CLOSEST-FEATURES 💖

okay bestie, gather round, because today we're learning about closest-features — a User Command, manual section 1, and honestly? she's iconic. let's get into it 🫶

✨ NAME ✨

closest-features — the manual page for closest-features 2.4.42+dfsg, no cap 💅

🌸 DESCRIPTION 🌸

so like, closest-features is a whole program, and here's the receipts:

USAGE:

closest-features [Process-Flags] <input-file> <query-file>

okay so first things first, and this is non-negotiable: all input files must be sorted per sort-bed. like, that's the vibe check, and if you fail it, that's on you 😭

the program accepts BED and Starch file formats, and you may use - for a file to indicate reading from standard input (BED format only). so like, stdin works but only for BED, noted 📝

here's the actual tea: for every element in <input-file>, the program determines the two elements from <query-file> falling nearest to its left and right edges (See NOTES below, bestie, don't skip them 👀). and by default? it echoes the <input-file> element, followed by those left and right elements found in <query-file>. cute, right? 🎀

🚩 Process Flags 🚩

  • --chrom <chromosome> — jump to and process data for the given <chromosome> only. like, one chromosome, main character energy, everyone else stay home ✨
  • --closest — choose the closest element for output only. and listen, ties go the left element, periodt.
  • --delim <delim> — change the output delimiter from '|' to <delim> between columns (e.g. '\t'). customize her 💅
  • --dist — print the signed distances to the <input-file> element as additional columns of output. and an overlapping element has a distance of 0. yes, zero, that's the whole point 🫶
  • --ec — error check all input files. it's slower, but she's thorough, and honestly? we respect the hustle.
  • --header — accept headers (VCF, GFF, SAM, BED, WIG) in any input file. let the headers live 🌈
  • --help — print this message and exit successfully. the classic. she never misses.
  • --no-overlaps — overlapping elements from <query-file> will not be reported. bye bestie 👋
  • --no-ref — do not echo elements from <input-file>. shy behavior, lowkey valid.
  • --no-query — do not echo elements from <query-file>. also shy, also valid.
  • --version — print program information. know your queen's stats 💖

📌 NOTES 📌

okay this is the part where you actually pay attention, bestie, because it's giving important semantics:

  • if an element from <query-file> overlaps the <input-file> element, its distance is zero.
  • an overlapping element takes precedence over all non-overlapping elements. and this is true even when the overlapping element's edge-to-edge distance to the <input-file>'s element is greater than the edge-to-edge distance from a non-overlapping element. like yeah, overlap just wins, no matter how the numbers look. that's the rule, that's the law 👑
overlapping elements may be ignored completely (no precedence) with --no-overlaps. so if you want overlap to stop being the main character, that's your flag.
  • elements reported as closest to the left and right edges are never the same. fr fr, never.
  • when no qualifying element from <query-file> exists as a closest feature, 'NA' is reported. not a vibe, but at least it's honest 😭

🦋 SEE ALSO 🦋

the full documentation for closest-features is maintained as a Texinfo manual. and if the info and closest-features programs are properly installed at your site, the command

info closest-features

should give you access to the complete manual. slay ✨

and that's the whole page, bestie 🎀 this was closest-features 2.4.42+dfsg, dated August 2025, living her best life under CLOSEST-FEATURES(1). go sort your files and stay hydrated 💖🌸

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