CHAIN2DIM(1)

💖 CHAIN2DIM 💖

okay bestie, welcome to chain2dim — that's section 1 of the manual, we're in the Unix manuals, we're doing two-dimensional match chaining and honestly? it eats. this is a tool from the Vmatch package and it is lowkey the moment. let's get into it 🦋

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✨ NAME ✨

chain2dim — two-dimensional match chaining. that's the whole vibe. chaining, but in 2D. 💅

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🌸 SYNOPSIS 🌸

chain2dim [options] <matchfile>

you give it a <matchfile>, you sprinkle in [options], and it gives you chains. main character behaviour fr fr 👑

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🎀 OPTIONS 🎀

• -global <param> — global chaining, periodt. the <param> is optional, and there are two of them you can pass: "gc" switches on gap costs (following the L1-model), and "ov" means overlaps between matches are allowed. 🌈
• -local <param> — computes local chains (also according to the L1-model). if you give it no parameter at all, it computes local chains with the maximum score, simple as that. if you do give a parameter, it has to be a positive number, and it can optionally be followed by the character b or p. here's the breakdown, bestie, don't skip it:
  • just the number — say k — means: that's the minimum score of the chains that get output.
  • number followed by b — output all chains with the largest k scores.
  • number followed by p — output all chains with scores at most k percent away from the best score.
• -wf <factor> — specify a weight factor, and it has to be > 0.0, to obtain the score of a fragment. ⚠️ this one requires one of -local, -global gc, or -global ov. no cap.
• -maxgap <width> — maximal width of gap in a chain. that's it, that's the whole thing. 🫶
• -outprefix <prefix> — specify the prefix of the files to output chains into. name your babies 💖
• -withinborders — only compute chains which do not cross sequence borders. heads up though: this is not possible for matches in open format. 😭
• -thread <keywords...> — thread the chains, i.e. close the gaps. 🧵 it accepts an optional list of keywords: "minlen1 minlen2 maxerror1 maxerror2", each followed by a number. that number specifies the minimum length and the maximum error rate of the thread. and the numbering, because it matters: 1 refers to the match instance in the indexed sequence, 2 refers to the matching instance in the query. iykyk ✨
• -silent — do not output the chains, and only report their lengths and scores. quiet queen behaviour 🙈
• -v — be verbose. tell me everything, i'm listening 💜
• -version — show the version of the Vmatch package. ⭐
• -help — show help. we love a helper 🎀

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👀 SEE ALSO 👀

• vmatch(1)

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and that's the page, bestie!! 🦋 this one lives in the CHAIN2DIM(1) section of the manuals and it ships with the Vmatch package — so when you run -version you're literally getting the Vmatch package version, iconic. the footer of the original page just signs it off as CHAIN2DIM(1) again, no date, no nothing, and honestly? mysterious. we respect it. go chain some matches, you've got this 💅💖🌸