GT-TALLYMER-OCCRAT(1)

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

💖 GT-TALLYMER-OCCRAT(1) 💖

okay so bestie, welcome to the GenomeTools Manual page for gt-tallymer-occratio — she's a little tool that computes the occurrence ratio for a set of sequences, and those sequences are represented by an enhanced suffix array. iconic behaviour, honestly. 🎀

✨ NAME ✨

gt-tallymer-occratio — compute occurrence ratio for a set of sequences represented by an enhanced suffix array. that's the whole job. she does it. slay. 💅

🌸 SYNOPSIS 🌸

gt tallymer occratio [options] -esa suffixerator-index [options]

like… you pass your -esa suffixerator-index and then whatever options your heart desires. the vibes are: options, then index, then more options. no cap. ✨

🦋 DESCRIPTION 🦋

okay so here's the whole menu of options, and no I am NOT skipping any of them, every single one is getting her moment. 🫶

  • -esa [string] — specify the suffixerator-index. this one is mandatory, bestie, like it is not optional, it is the main character. (default: undefined — aka literally nothing, so pls actually pass it 😭)
  • -minmersize [value] — specify minimum mer size for which to compute the occurrence distribution. (default: 0)
  • -maxmersize [value] — specify maximum mer size for which to compute the occurrence distribution. (default: 0)
  • -step [value] — specify step size when specifying mer sizes. (default: 1)
  • -mersizes — specify mer sizes as a non-empty sequence of non decreasing positive integers. so like, they go up, they do not go down, and there are no zeroes or negatives in this house. 💀
  • -output — use a combination of the following keywords: unique nonunique nonuniquemulti relative total — to specify the kind of output you want. mix and match, it's giving build-your-own-output. 🌈
  • -scan [yes|no] — read the suffixerator-index sequentially instead of mapping it to memory. (default: no)
  • -v [yes|no] — be verbose. say more. spill the tea. (default: no)
  • -help — display help and exit. she's got your back. 🫶
  • -version — display version information and exit. 📌
lowkey reminder: -esa is the only mandatory one, everything else has a default and will just chill unless you ask for something specific. ✨

🎀 REPORTING BUGS 🎀

found a bug? first of all, relatable. second of all, report it to <kurtz@zbh.uni-hamburg.de>. they want to know. tell them everything. 💌

and that's the page!! 🌟 this was GenomeTools 1.6.6, dated 11/09/2025 — thank you for coming to my ted talk, ily, go compute some occurrence ratios bestie 💜🦋✨

📦 where this page comes from