SAWRITER(1)

📦 version 5.3.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 SAWRITER 💖

okay so bestie, welcome to sawriter(1) — a User Commands girlie whose whole entire personality is generating suffix arrays for nucleotide sequences. No cap, that's the job. It eats FASTA and hands you a suffix array. Periodt. 🧬✨

✨ NAME ✨

sawriter — generate suffix arrays for nucleotide sequences 🦋

🌸 SYNOPSIS 🌸

sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-larsson]
[-4bit] [-manmy] [-kar]

sawriter fastaIn  (writes to fastIn.sa).

the way that second form just quietly does the thing for you and drops the result into fastIn.sa — lowkey the laziest, comfiest way to use this tool 💅

🫶 heads up bestie: the synopsis up there spells two flags as -manmy and -kar, and the options list down below spells them -mamy and -kark. That is exactly what the page says. Not me fixing it. Not my business. I'm just the messenger. 💀

🎀 OPTIONS 🎀

  • -blt p — builds a lookup table on prefixes of length p. This makes lookups considerably faster (like, more than the LCP table does, fr fr), but it will miss matches that are shorter than p when you're searching. So it's giving speed with a lil side of "oops, didn't see that one." ⚡🙈
  • -4bit — reads in (one) fasta file as a compressed sequence file. One. Singular. Just the one. 💀
  • -larsson — (this is the default, bestie) uses the method of Larsson and Sadakane to build the array. The main character. The go-to. 👑
  • -mamy — uses the method of MAnber and MYers to build the array. It's slower than larsson and it produces the same result — so honestly it's mainly there for double checking the correctness of larsson. It's the friend who re-reads your essay. 😭
  • -kark — use the Karkkainen DS3 method for building the suffix array. This will probably be more slow than larsson, but it only takes an extra N/(sqrt 3) extra space. Trades time for room. 🌈
  • -mafe — (disabled for now!) uses the lightweight construction algorithm from Manzini and Ferragina. She's not available right now, babe. 💀
  • -welter — use lightweight (sort of light) suffix array construction. This is a bit more slow than normal larsson. "Sort of light" is doing a lot of heavy lifting in that sentence and I respect it. ✨
  • -welterweight N — use a difference cover of size N for building the suffix array. Valid values are 7, 32, 64, 111, and 2281. Those are the numbers, no others, don't try it. 🎯

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶 shoutout Andreas, icon behaviour, ate and left no crumbs.

and that's the whole page, bestie — go build some suffix arrays, you absolute legend 🌸🎀🦋

sawriter 5.3.2 — January 2019 — mwah, take care of her 💖

📦 where this page comes from