GT-CHAIN2DIM(1)

🦋 GT-CHAIN2DIM — the chaining glow-up 💅

okay bestie, so this is a page from the GenomeTools Manual, and the star of the show is gt-chain2dim, which does exactly one iconic thing: it chains pairwise matches. that's the whole vibe. let's get into it 🫶

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✨ NAME ✨

gt-chain2dim — Chain pairwise matches. yes queen, that's the job. 💖

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🌸 SYNOPSIS 🌸

gt chain2dim [options] -m matchfile

like, that's the shape of every invocation. -m matchfile is non-negotiable, the rest is seasoning 🧚

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👑 DESCRIPTION 👑

heads up bestie: yes, all the options live right here in DESCRIPTION. that's just how this page is built. no cap.

• -m [filename] — point this at the file containing the matches. it is a mandatory option. default: undefined (which is a fancy way of saying "you literally have to give it, bestie"). 🌈
• -global — do a global chaining. and it takes optional parameters, because of course it does:
  • optional parameter gc switches on gap costs (according to L1-model)
  • optional parameter ov means that overlaps between matches are allowed
  • optional parameter all means that all optimal chains are processed
• -local — do a local chaining; compute local chains (according to L1-model). the parameter rules are a whole saga, so stay with me:
  • if no parameter is given, compute local chains with maximum score.
  • if a parameter is given, it must be a positive number optionally followed by the character b or p.
  • if only the number, say k, is given, this is the minimum score of the chains output.
  • if a number is followed by the character b, then output all chains with the largest k scores.
  • if a number is followed by the character p, then output all chains with scores at most k percent away from the best score.
• -wf [value] — specify the weight factor > 0.0 to obtain score of a fragment. ⚠️ requires one of the options -local const -global gc -global ov. default: 1.000000. 💀 (yes it really has to be greater than 0.0, don't try it)
• -maxgap [value] — specify the maximal width of gap in chain. default: 0.
• -silent [yes|no] — do not output the chains but only report their lengths and scores. default: no.
• -v [yes|no] — be verbose. default: no. (turn it on if you want the tea ☕)
• -help — display help and exit. the classic escape hatch 🎀
• -version — display version information and exit. 💜

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😭 REPORTING BUGS 😭

found a bug? don't suffer in silence, bestie — report bugs to <kurtz@zbh.uni-hamburg.de>. they want to know, fr fr. 📬

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and that's the whole page, periodt. this was GenomeTools 1.6.6, dated 11/09/2025 — so if you're reading this later, hi from the past, the vibes were immaculate, slay 💅✨🦋