BAMTOFASTQ.PY(1)

💖 BAMTOFASTQ.PY 💖

okay bestie, welcome to the bamtofastq.py page of the manual — section 1, user commands, she's iconic ✨

🌸 NAME 🌸

bamtofastq.py — convert a coordinate sorted BAM file to FASTQ

🦋 SYNOPSIS 🦋

bamtofastq.py [-h] [-r STR] [-n] [-S] [-H FILE] [BAM [BAM ...]]

✨ DESCRIPTION ✨

Convert a coordinate sorted BAM file to FASTQ. That's the whole vibe. 💅

🚨 tiny but important: this one ignores unpaired reads. like, they're not invited to the party. periodt.

🎀 OPTIONS 🎀

💜 positional arguments:

• BAM — your input BAM file(s). and if you don't pass any? no stress, it just defaults to stdin. main character energy fr fr 🫶

💅 optional arguments:

• -h, --help — show this help message and exit. the classic. the beloved. ✨
• -r STR, --readgroup STR — read group(s) to extract, and yes they're comma separated 🍓
• -n, --rename — rename reads 👑
• -S, --is_sam — input is SAM format, not BAM. plot twist 🌈
• -H FILE, --header FILE — write the BAM header to FILE 📝

👑 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, bestie!! go convert some reads, you absolute legend 🧚💖

bamtofastq.py version 0.0.1+git20170413..., June 2020 — shoutout to the BAMTOFASTQ.PY(1) manual page, she ate and left no crumbs 💅✨