GT-MATSTAT(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 GT-MATSTAT(1) 💖

okay bestie, welcome to gt-matstat — it lives in the GenomeTools Manual and it's literally here to compute matching statistics. that's the whole vibe. no cap. ✨

🌸 NAME 🌸

gt-matstat — compute matching statistics. yeah that's it, that's the job, and she does it gorgeously 💅

🎀 SYNOPSIS 🎀

gt matstat [options ...] -query queryfile [...]

see how the -query is sitting there with a queryfile and then a lil [...]? that means you can pile on more than one. main character energy fr fr 🦋

✨ DESCRIPTION ✨

okay so here's every single flag, and yes we're doing all of them, no skipping, we don't do that here 🫶

  • -fmi [string] — specify fmindex (default: undefined). it's undefined by default so like, you gotta tell her, she's not a mind reader 😭
  • -esa [string] — specify suffix array (default: undefined). same situation, also undefined, also waiting on you 🙈
  • -pck [string] — specify packed index (default: undefined). yeah, undefined again. three whole index options just vibing there with no default 🌈
  • -query — specify queryfiles. plural! as many as you want, go off 👑
  • -min [value] — only output length if >= given minimum length (default: 0). so like, tiny lengths get filtered out unless you say otherwise ⭐
  • -max [value] — only output length if ⇐ given maximum length (default: 0). the upper bound bestie, also defaulting to 0 🍓
  • -output — set output flags (sequence, querypos, subjectpos). pick your faves, those are the three choices 💜
  • -help — display help and exit. the classic escape hatch, iconic, we love her 🧚
  • -version — display version information and exit. for when you just wanna know who you're dealing with 💖

💌 ADDITIONAL INFORMATION 💌

for detailed information, please refer to the manual of matstat. like, go read the big one, this is the appetizer not the meal 🎀

🐛 REPORTING BUGS 🐛

found a bug? don't be shy, report it to <kurtz@zbh.uni-hamburg.de>. be nice, be specific, be brave 🫶

lowkey that's the whole page bestie, you're so ready, go compute some matching statistics 💅✨

GenomeTools 1.6.6 · 11/09/2025 — mwah, bye, slay 🌸🦋💖

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