MASON_GENOME(1)

💖 mason_genome — Random Genome Simulation 💖

okay bestie, welcome to mason_genome, aka the manual page from the MASON_GENOME(1) section of your friendly neighbourhood manual. she's a little genome-making machine and she's about to be your new obsession 🧬✨

---

✨ SYNOPSIS ✨

mason_genome [OPTIONS] [-l LEN]+ -o OUT.fa

like… that's the whole vibe. you give her options, you give her at least one -l LEN, and you always, always hand her an -o OUT.fa. no output file, no genome. periodt 💅

---

🦋 DESCRIPTION 🦋

so what does she actually do?? she simulates a random genome straight into your output file, that's what 🎀

and here's the cute part: for every single -l/--contig-length entry you feed her, she simulates a contig with the given length. one entry = one contig. two entries = two contigs. she's not subtle, she just counts and delivers 🫶

---

🌸 OPTIONS 🌸

• -h, --help — shows you the help message. your girl is helpful, ngl 💖
• --version — spills the version info ✨
• -q, --quiet — drops the verbosity down to the bare minimum. she's giving mysterious 🤫
• -v, --verbose — turns verbose output ON. chatty era 👑
• -vv, --very-verbose — very verbose output. extra chatty. unhinged levels of chatty, lowkey 😭

🧚 Simulation Configuration: 🧚

• -l, --contig-length List of INT64's — the length of the contig to simulate. give her one -l value for each contig you want simulated, okay?? valid range is [1..inf] — yes bestie, infinity, she said go big or go home 🌈
• -s, --seed INTEGER — the seed for the random number generator. default: 42. iconic number, no notes 🍓

🎀 Output Options: 🎀

• -o, --out-file OUTPUT_FILE — your output file, your main character moment. valid filetypes are:

.sam[.*]  .raw[.*]  .frn[.*]  .fq[.*]  .fna[.*]  .ffn[.*]
.fastq[.*]  .fasta[.*]  .fas[.*]  .faa[.*]  .fa[.*]

plus .bam — and where that * shows up, it can be any of these extensions: gz, bz2, and bgzf, all for transparent (de)compression 💅✨

real talk though: if your filetype isn't on that list, she's not doing it. the list is the list, iykyk 🙈

---

🔥 EXAMPLES 🔥

okay so picture this:

mason_genome -l 1000 -l 4000 -o genome.fa

that's you simulating a genome with two contigs, lengths 1000 and 4000, and writing the whole thing right into genome.fa. two -ls, two contigs. she ate that 🫶💖

---

💜 SEE ALSO 💜

not a single cross-reference, bestie. this page stands alone and honestly?? main character energy 👑

---

and that's the whole page!! brought to you by mason_genome 2.0.13 [tarball], straight outta the MASON_GENOME(1) manual section. go forth and simulate something gorgeous, bestie 🌸🦋💖