BAMCLEANHEADER.PY(1)

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

✨ BAMCLEANHEADER.PY(1) ✨

User Commands 🎀 bamcleanheader.py

okay bestie, sit down, hydrate, and let me tell you about bamcleanheader.py 💅 it lives in section 1 of the manual, and it is literally the little cleanup fairy of the BAM world 🧚

🌸 NAME 🌸

bamcleanheader.py — remove illegal and malformed fields from a BAM file's header 🧹✨

like… it takes your BAM header and goes "ma'am, this field is illegal, this one is malformed, we're not doing this today" and yeets them out 🫶

🦋 SYNOPSIS 🦋

bamcleanheader.py [-h] [-S] [input [input ...]]

that's the whole vibe check right there 👑

💜 DESCRIPTION 💜

remove illegal and malformed fields from a BAM file's header 🌈

that's it. that's the job. no cap. it goes through the header, finds the fields that are illegal or malformed, and removes them, so the rest of your pipeline doesn't have a meltdown 😭🔥

🎀 OPTIONS 🎀

✨ positional arguments ✨

  • input — SAM/BAM file to inject header lines into. If it's '-' or it's just… not there at all, then it defaults to stdin 💖 (yes bestie, it's giving "I'll just read from your keyboard, no pressure")

✨ optional arguments ✨

  • -h, --help — show this help message and exit 👋 the classic "help me I'm lost" button, iconic
  • -S, --is_sam — input is SAM 🫶 (lowkey important, highkey slay, tell it what it's actually looking at)

👑 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!! 🦋

this gorgeous thing is bamcleanheader.py 0.0.1+git2017... and it dropped in June 2020 — a whole era, fr fr ⭐

kisses, go clean those headers, mwah 💖🎀✨

📦 where this page comes from