MAF-CONVERT(1)

✨ MAF-CONVERT ✨

okay bestie, sit DOWN, because maf-convert is about to become your new favorite little tool 💅 it's the manual page for maf-convert, a User Command, and it is genuinely so good. here's the whole thing, no skips, no cap 🫶

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💖 NAME 💖

maf-convert — convert MAF-format alignments to tabular format ✨

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🌸 DESCRIPTION 🌸

🎀 Usage:

maf-convert --help
maf-convert axt mafFile(s)
maf-convert bed mafFile(s)
maf-convert blast mafFile(s)
maf-convert blasttab mafFile(s)
maf-convert blasttab+ mafFile(s)
maf-convert chain mafFile(s)
maf-convert gff mafFile(s)
maf-convert html mafFile(s)
maf-convert psl mafFile(s)
maf-convert sam mafFile(s)
maf-convert tab mafFile(s)

so like. what does it DO. it reads MAF-format alignments 📖 and writes them back out in another format. that's it. that's the whole vibe. read in MAF, write out literally anything else 🦋 iconic behavior honestly.

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✨ OPTIONS ✨

• -h, --help — show this help message and exit 👋 that's your little escape hatch, bestie.
• -s N, --subject=N — which sequence to use as subject/reference 👑 you're picking the main character of the alignment, fr.
• -p, --protein — assume protein alignments, for psl match counts 🧬 yes, it changes how the psl match counts come out. don't come for me, it's just what it says.
• -j N, --join=N — join consecutive co-linear alignments separated by <= N letters 🔗 like, if there's a lil gap of N or fewer letters between them, they get glued together.
• -J N, --Join=N — join nearest co-linear alignments separated by <= N letters 🔥 same energy as -j but capitalized, and it goes for the nearest ones. the uppercase really said "I'm different."
• -n, --noheader — omit any header lines from the output 🙈 no headers, no thoughts, just vibes.
• -d, --dictionary — include dictionary of sequence lengths in sam format 📚 sam output gets the receipts on how long everything is.
• -f DICTFILE, --dictfile=DICTFILE — get sequence dictionary from DICTFILE 🗂️ you bring the dictionary file, it brings the sequence dictionary. teamwork makes the dream work.
• -r READGROUP, --readgroup=READGROUP — read group info for sam format 🏷️ read group info, sam format only, iykyk.
• -l LINESIZE, --linesize=LINESIZE — line length for blast and html formats (default: 60) 📏 blast and html only, and the default is 60 in case you were wondering (you were).

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💀 heads up bestie: this page doesn't list any warnings, side effects, or exit statuses, so I'm not gonna invent any. everything above is everything that's there. periodt.

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and that's the whole page, no crumbs left 🙌 stay slay, convert your alignments, and remember — this was page maf-convert 1654, from August 2026. love you, bye!! 💖✨🎀🦋🌸💅🫶👑