FAHASH(1)

📦 version 2.3.12-1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 FAHASH(1) — the fahash girlie's guide 💖

okay so bestie, you found the manual for fahash — that's a User Commands page, section 1, and it's genuinely one of the most underrated little tools in the whole e-PCR suite. pull up a chair, grab a boba, we're doing this together 💅

✨ NAME ✨

fahash — sequence hash builder for reverse e-PCR 🧬✨

🦋 SYNOPSIS 🦋

like, here's the whole vibe in one glance:

fahash [-hV] -b hash-file [-w wdsize] [-f period] [-F fragment_min,fragment_max] [-k] [-c cachesize] [-v 1|2] famap-file ...

fahash [-hV] -T hash-file [-o outfile]

🌸 DESCRIPTION 🌸

so fahash is part of the e-PCR suite (iykyk), and its whole main character job is building hash-files. it also prints out word usage statistics for reverse e-PCR searches. that's it, that's the gig, and it ate. 👑

🎀 OPTIONS 🎀

the main-girl options 💖

  • -b hash-file — build hash tables (hash-file) out of your sequence files. this is the one you'll use 99% of the time fr fr.
  • -T hash-file — print word usage statistics for hash-file. stats girlies rise 🫶
  • -o outfile — write the output to the file outfile, not to your terminal.

build-options: the little extras ✨

⭐ build-options

  • -w wordsize — set the word size for when you're building hash tables.
  • -f period — set the discontiguity when building hash tables.
  • -k — skip repeats while building the hash-file. no repeats, we don't know them 💀
  • -F min,max — set watermarks for fragment size (in Mb). > heads up bestie: this is version 1 only 🙈
  • -c cachesize — set the cache size. > and this one? version 2 only ✨
  • -v ver — pick the format version (1|2, and 2 is the default, no cap).

also, both synopsis forms take -h and -V — you know the drill, help and version 🎀

🌈 EXAMPLE 🌈

here's the whole pipeline in action, and honestly? iconic:

 famap -tN -b genome.famap org/chr_*.fa

 fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

 re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

and if you wanna go deeper, go read famap(1) and re-pcr(1) — they're the besties of this page 🦋

👀 SEE ALSO 👀

💜 AUTHORS 💜

this manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

and on Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. 📜

and that's the whole page bestie!! 💖 this one's from the Reverse e-PCR: sequence hash bu... source, version-dated April 2008, and it lives in section FAHASH(1). go build some hashes, you're doing amazing, mwah 🫶✨🎀

📦 where this page comes from