BAMFIXFLAGS.PY(1)

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

💖 BAMFIXFLAGS.PY(1) 💖

okay bestie, welcome to the User Commands corner of the manual 💅 this is bamfixflags.py, and she's here to filter readgroup(s) out of your BAM file. let's get into it 🧚

✨ NAME ✨

bamfixflags.py — filter readgroup(s) from a BAM file 🎀

🌸 SYNOPSIS 🌸

bamfixflags.py [-h] [-i BAM] -l FILE [-n INT] [-S] [-b] [-u]

that's the whole vibe. short, sweet, slays ✨

🦋 DESCRIPTION 🦋

filter readgroup(s) from a BAM file. that's it, that's the whole job, and she does it gorgeously 👑

💅 OPTIONS 💅

optional arguments:

  • -h, --help — show this help message and exit. the classic escape hatch, she's always there for you 🫶
  • -i BAM, --input BAM — Input BAM file. this is the file you're feeding in, bestie 🍓
  • -l FILE, --lib_info FILE — SVTyper JSON file of library information. yes, a JSON, yes, from SVTyper, yes, it's library info, no you can't skip it (it's required, see that synopsis) 📚
  • -n INT — Output first n alignments and quit. like, just dip out after n alignments, no big deal 💀
  • -S — Input is SAM format. heads up, it's not BAM this time, it's SAM ✨
  • -b — Output BAM format. she's giving BAM on the way out 🌈
  • -u — Output uncompressed BAM format (implies -b). uncompressed BAM, and yeah, it brings -b along with it automatically 💖

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

and that's the whole page, babe. no cap. go filter those readgroups 💜

this has been bamfixflags.py version 0.0.1+git2017041..., dated June 2020, coming at you from the BAMFIXFLAGS.PY(1) manual page — mwah, ily, bye 💋

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