REPEATOIRE(1)

📦 version 1.2.0+4713, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 REPEATOIRE(1) 💖

ok so bestie, you found a User Commands page, section 1, and the vibe is very much "I'm a little helper program that lives inside a bigger friend group." Let's get into it 🫶

✨ NAME ✨

repeatoire — literally just part of the mauveAligner package, no big deal, she's one of the girlies in the squad 💅

🌸 DESCRIPTION 🌸

She does her thing. That's it. That's the description. But listen — the real tea is down in the options, and there are a lot of them, so grab a strawberry drink and let's go 🍓

🎀 Allowed options 🎀

  • --allow-redundant arg (=1) — should we let redundant alignments happen? default says yes, we're permissive like that ✨
  • --chain arg (=1) — chain the seeds? yes bestie, chain them 👑
  • --extend arg (=1) — do the gapped extension on the chains? yep, by default we do 🔥
  • --window arg (=-1) — how big is the window we use during that gapped extension 🪟
  • --gapopen arg (=0) — gap open penalty, that's the price of opening a gap 💀
  • --gapextend arg (=0) — gap extension penalty, the price of making it longer 😭
  • --h arg (=0.00800000038) — Transition to Homologous, that's the threshold, no cap
  • --help — get the help message, bestie's hand reaching out to you 🫶
  • --highest arg (=procrast.highest) — file containing the highest scoring alignment for each multiplicity 📁
  • --l arg (=1) — minimum repeat length, keep it at least this long
  • --large-repeats arg (=0) — optimize for large repeats? this is the switch for that 🦋
  • --load-sml arg (=0) — try to load an existing SML file? maybe 👀
  • --onlydirect arg (=0) — only process seed matches on the same strand? same-strand only, we're exclusive 💅
  • --onlyextended arg (=0) — only output extended matches?
  • --output arg — the procrastAligner output, that's where it goes ✨
  • --percentid arg (=0) — min repeat family % id, the identity floor
  • --novel-subsets arg (=0) — find novel subset matches? go off 🔍
  • --novel-matches arg (=1) — use the novel matches we found during gapped extension? default is yes
  • --rmax arg (=500) — maximum repeat multiplicity, aka max copy number 📈
  • --rmin arg (=2) — minimum repeat multiplicity, aka min copy number 📉
  • --seeds arg — seed output file 🌱
  • --sequence arg — FastA sequence file, the main character of the whole operation 🧬
  • --small-repeats arg (=0) — optimize for small repeats? tiny but mighty 🧚
  • --score-out arg — output with corresponding score and alignment info 📝
  • --solid arg (=0) — use solid/exact seeds? solid as a rock, periodt 🪨
  • --sp arg (=0) — minimum Sum-of-Pairs alignment score
  • --tandem arg (=1) — allow tandem repeats? default says yes 🌈
  • --two-hits arg (=0) — require two hits within w to trigger gapped extension? two hits, that's the rule ✌️
  • --u arg (=0.00100000005) — Transition to Unrelated
  • --unalign arg (=1) — unalign non-homologous sequence? by default yes
  • --w arg (=0) — max gap width, keep it wide or keep it narrow, your call
  • --xmfa arg — XMFA format output 💾
  • --xml arg — XML format output 💾
  • --z arg (=0) — seed weight, it's giving important tbh ⭐
🌟 lowkey reminder: all those arg values are defaults, so if you don't pass the flag, that's what you get. don't come for me if you didn't read, iykyk 💀

💜 that's the whole page bestie 💜

ngl she's a short one, but she's iconic. this was repeatoire version 1.2.0+4713, dated April 2015 — yes, 2015, she's a vintage queen 👑 and she still ate. mwah, go forth and align 🎀✨🦋

📦 where this page comes from