BAMGROUPREADS.PY(1)

📦 version 0.0.1+git20170413.ccd079d, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

🌸 BAMGROUPREADS.PY 💅

okay bestie, so this is the manual for bamgroupreads.py, a lil user command that lives in section 1 of the manual. it's giving "niche but iconic" and honestly? we're obsessed.

✨ NAME ✨

bamgroupreads.py — group a BAM file by read IDs, without sorting. no sorting. none. zero. that's the whole vibe. 🦋

✨ SYNOPSIS ✨

bamgroupreads.py [-h] [-i BAM] [-r STR] [-d] [-f] [-S] [-b] [-u] [-M]

like, that's it. that's the whole command. short king behavior. 👑

✨ DESCRIPTION ✨

group BAM file by read IDs without sorting. periodt. 💖

✨ OPTIONS ✨

optional arguments: 🌈

  • -h, --help — show this help message and exit. the classic. the moment you're lost, she's there. 🫶
  • -i BAM, --input BAM — input BAM file. like, the file you're feeding in. the main character of the input situation. 📥
  • -r STR, --readgroup STR — read group(s) to extract, comma separated. so if you want more than one, separate them with commas, bestie, don't be shy. 🎀
  • -d, --reset_dups — reset duplicate flags. clearing the drama, wiping the slate. ✨
  • -f, --fix_flags — fix mate flags for secondary reads. she's a little repair tech, fixing what's broken. 🔧
  • -S — input is SAM format. not BAM. SAM. important distinction, iykyk. ⭐
  • -b — output BAM format. 📦
  • -u — output uncompressed BAM format (and yes, this implies -b, so you don't gotta say both). 💀
  • -M — split reads are flagged as secondary, not supplementary. this one exists for compatibility with the legacy BWA-MEM "-M" flag, so if you're running old-school stuff, this is your girl. 🔥

✨ AUTHOR ✨

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. shoutout to him, honestly. 👑

lowkey important reminder: every flag up there is exactly what it says, no cap. don't go freestyling with flags that aren't listed, bestie, the program did not consent to that. 😭

okay so the source/version vibe is bamgroupreads.py 0.0.1+git20170... and the date on this whole thing is June 2020 — and that's the BAMGROUPREADS.PY(1) page, slay, bye bestie 💅✨

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