CHROMOSTITCH(1)

✨ CHROMOSTITCH(1) ✨

okay so bestie, we're doing chromostitch.pl today and it's genuinely a whole vibe 💖 She lives in the User Contributed Perl Documentation corner of the manual, and she's here to make stitch files. Periodt.

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🌸 NAME 🌸

chromostitch.pl — makes stitch files for feeding to geneparse.pl so you can feed multiple chromosomes to programs like murasaki 🧬✨

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🎀 SYNOPSIS 🎀

chromostitch.pl [options] <stitch file> <chromosome1 chromosome2 ... >

Options:
--sort           sorts everything
--output=<file>  altnerate way of specifying an output file

(yes the spelling is altnerate in the original, not me, I would never 😭 we keep it verbatim bestie, character for character, that's the rule)

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🦋 PARAMETERS 🦋

• stitch file — your output file. And heads up: she overwrites it. No asking, no backup, no "are you sure", just gone 💀
• chromosome1 chromosome2 ... — the list of chromosome input files. All of them. Bring the whole squad 🫶
• B--output=<file> — alternate way of specifying an output file. (the B is literally just sitting there in the original page, iconic behaviour honestly 🎀)
• --sort — always sort EVERYTHING. All of it. This is what lets you get nicely sorted lists out of sloppy input — like when your filenames come from multiple directories of *.gbk or something 🙈

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💅 DESCRIPTION 💅

Makes stitch files for feeding to geneparse.pl, so you can feed multiple chromosomes to programs like murasaki. It's giving glue, it's giving middleware, it's giving main character energy between your raw chromosomes and whatever fancy tool needs them stitched together 👑

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ngl bestie, --sort sorting EVERYTHING is not a drill. If you want order in your life, that's the flag. If you don't, well, it's giving chaos, and honestly? Also valid 🌈

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that's the whole page, you ate it, go stitch some chromosomes 💜

take care of her, she's running on perl v5.40.1 and shipped on 2026-08-12 mwah 💋 CHROMOSTITCH(1) forever ✨