QUALITY_CHECK(1)

📦 version 0.0.r19, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 QUALITY_CHECK(1) 💖

okay so bestie, welcome to the User Commands section of the manual, and today's main character is quality_check — she's here to vibe check your SAM file and tell you if your mapping results are actually serving or just giving chaos. 🦋

✨ NAME ✨

quality_check — perform a sanity check on the mapping results (SAM file) 💅

🌸 SYNOPSIS 🌸

quality_check [Options] SAMFILE

🧚 DESCRIPTION 🧚

Perform a sanity check on the mapping results (SAM file). periodt.

This tool analyzes the output of the read mapper and hands you back useful information, so you — yes you, the user — can decide whether the set of reference sequences and the mapper settings are feasible for the given dataset. it's literally giving "let me check if this is even going to work before you commit, queen" energy. 🎀

💖 OPTIONS 💖

  • SAMFILE — name of the SAM file to analyze. this is the whole reason we're here, no cap. 🔥
  • -h, --help — show this help message and exit. the classic "wait what do I do" button, and she ate. 👑
  • -o OUT, --outpath=OUT — path to the directory for the analysis output. [default: ./] — so if you don't say anything, she just drops it right in the current directory like it's her own bedroom floor. 🫶
ngl bestie, always double check your SAMFILE actually exists before you run this, because she will simply not be able to analyze vibes that aren't there. 😭

that's the whole page, you're so welcome, go forth and sanity check your mappings, i'm obsessed with you 🌈⭐💜

this iconic little manual page is from version SVNr18, dated February 2014, and it lives under QUALITY_CHECK(1) — mwah, bye! 💅✨🍓

📦 where this page comes from