GT-COMPREADS-DECOM(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

🦋 GT-COMPREADS-DECOM — it's the GenomeTools manual, bestie ✨

okay so real quick, this is the manual page for gt-compreads-decompress, which lives in section 1 of the GenomeTools manual. yes it's a mouthful, no you don't have to say it out loud 💅

🌸 NAME 🌸

gt-compreads-decompress — decodes a file of compressed reads. that's it. that's the whole job. unzipping but make it genetics 🧬✨

🎀 SYNOPSIS 🎀

gt compreads decompress [option ...] (-file file)
heads up bestie: -file is not optional. like, at all. it's in parentheses in the synopsis which is manpage-speak for "you literally cannot run this without it." no -file, no decompression, no nothing 😭

💖 DESCRIPTION 💖

so here's every single knob you can turn. don't skip any, i know they look like a lot, but we're getting through this together 🫶

  • -v [yes|no] — turn on verbose mode. basically your terminal starts yapping about what it's doing. default: no (she's quiet, she's mysterious, she's default 🎀)
  • -descs [yes|no] — enable description decoding. default: no 🙈
  • -file [string] — specify the base name of the files containing HCR. this is required, no cap. default: undefined
  • -name [string] — specify the base name for the decoded hcr (the suffix will be ".fastq", okay, that gets tacked on for you). default: undefined
  • -smap [string] — specify a file containing alphabetdescription (and that file has to be an .al1 file, don't try to be cute with it). if "-smap" is not set, the dna alphabet is used. default: undefined ✨
  • -range [start end] — decode multiple consecutive reads. if range is not specified, the entire file will be decoded — like, all of it, the whole thing. default: undefined
  • -width [value] — set the width of the output. 0 disables formatting. default: 0
⚠️ lowkey important: line breaks in quality strings can cause problems with parsers. use with care. i'm not being dramatic, the manpage said "use with care" and i am simply relaying that energy to you 💀
  • -help — display help and exit 🫶
  • -version — display version information and exit ⭐

🐛 REPORTING BUGS 🐛

found a bug? not me manifesting bugs for you but if you did, report it here:

https://github.com/genometools/genometools/issues

🌈 SEE ALSO 🌈

okay so there's genuinely no SEE ALSO section in this one, bestie. she stands alone. main character energy 👑

and that's the whole page!! you ate that, fr fr. go decompress some reads, i believe in you 🧚💜

this page is from GenomeTools 1.6.6, dated 11/09/2025 — and yeah, GT-COMPREADS-DECOM(1) is the name on the tin 💖✨

📦 where this page comes from