REAPR-SEQRENAME(1)

💅 REAPR-SEQRENAME 💅

okay so bestie, welcome to reapr-seqrename, section 1 of the manual — the little glow-up station for your BAM file's sequence names ✨

---

🌸 NAME 🌸

reapr-seqrename — it renames all sequences in a BAM file. that's it. that's the whole job. and she does it flawlessly 💖

---

🎀 SYNOPSIS 🎀

reapr seqrename <renamefile> <in.bam> <out.bam>

so you call her as a reapr subcommand, and she takes three things, in this exact order, no wiggle room:

• <renamefile> — the glow-up instructions 💅
• <in.bam> — the BAM you're walking in with
• <out.bam> — the BAM that walks out 🦋

---

✨ DESCRIPTION ✨

okay so the tea ☕ — <renamefile> is the .info file made by facheck, and inside it lives the mapping of old name ➡️ new name. that's the whole point of it. every old name gets its new name, and she applies them across all the sequences in the BAM. no cap, that's the vibe. 👑

🫶 friendly reminder: the file you hand her is specifically the .info one that facheck produces — that's where the old-name-to-new-name mapping comes from. don't come at her with some random file and expect main character results, okay?

---

🌈 SEE ALSO 🌈

• reapr(1) — go say hi to the parent command, she's iconic too 👑

---

and that's the whole page, bestie 💜 the footer down there is just REAPR-SEQRENAME(1) sitting by itself — no source line, no version, no date, she's mysterious like that 🙈 so no version drama to report, just the page name and nothing else. slay, go rename some sequences. periodt. 🎀✨