BAMHEADRG.PY(1)

💖 bamheadrg.py — like, the readgroup injector bestie 💖

okay so welcome to bamheadrg.py, a User Commands girly living in section 1 of the manual. she's little, she's focused, she has ONE job and she does it flawlessly. no cap. 🎀

✨ NAME ✨

bamheadrg.py — Inject readgroup info 🧬

🌸 SYNOPSIS 🌸

bamheadrg.py [-h] [-r READGROUP] -d DONOR [-S] [recipient]

🦋 DESCRIPTION 🦋

Inject readgroup info.

that's it. that's the whole vibe. she takes readgroup info from somewhere and puts it into somewhere else. main character energy, honestly. 💅

🔥 OPTIONS 🔥

🍓 positional arguments:

• recipient — the SAM file you want the header lines injected into. and if you pass - or just... don't pass anything at all? she defaults to stdin, periodt. she's flexible like that. 😌

💜 optional arguments:

• -h, --help — shows this help message and exits. the classic. the icon. every manpage's emotional support flag. 🫶
• -r READGROUP, --readgroup READGROUP — the read group(s) you want to extract, comma separated. yes bestie, you can do more than one, just sprinkle those commas in there. 🌈
• -d DONOR, --donor DONOR — the donor BAM/SAM file to extract read group info from. this one is where the info is coming from. she's the source, the origin story, the blueprint. 🔍
• -S, --donor_is_sam — tells her the donor file is SAM. just a lil heads up so she doesn't get confused. 🙈

lowkey important: -d DONOR is required. it's not optional-optional, it's in the synopsis without brackets for a reason. don't come for her with no donor. she will simply not know what to do. 😭

👑 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, absolute legend, we love a Debian moment 💖)

so yeah, that's the whole page. run her, love her, inject those readgroups. this was bamheadrg.py, version 0.0.1+git20170413...., dated June 2020 — a true vintage queen from the git era, and she still ate. 💅✨🦋 slay, bye bestie! 🎀