REAPR-SCORE(1)

💖 REAPR-SCORE(1) 💖

okay bestie, welcome to reapr-score — the section 1 manual page that's about to be your new hyperfixation. she does scores, she does assembly errors, she does it all. let's get into it 🦋

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✨ NAME ✨

reapr-score — calculate scores and assembly errors 💅

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🌸 SYNOPSIS 🌸

reapr score [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix>
<FCDcutoff> <outprefix>

so yes, that's reapr score (not reapr-score, the command is doing the two-word thing, we don't make the rules) and then it wants SIX things from you: your gaps file, your BAM, a stats prefix, the FCD cutoff, and an out prefix. main character demands, honestly 👑

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🎀 OPTIONS 🎀

every flag, every default, no gatekeeping. the number in the square brackets? that's the default if you say nothing, so don't come for me 🫶

• -f <int> — minimum inner fragment coverage, bestie. defaults to [1]
• -g <int> — the max gap length we're willing to call over. default is [0.5 * outer_mean_insert_size], so she scales herself, iconic behavior ✨
• -l <int> — length of the window 💫 default [100]
• -p <int> — use perfect mapping reads score with the given min coverage. incompatible with -P, pick a lane please 😭
• -P <int> — same as -p but with a lil plot twist: it forces the score to be zero at any position that has at least the given coverage of perfect mapping reads and which has an OK insert plot. i.e. perfect mapping reads + insert distribution override all other tests when calculating the score. incompatible with -p — yes, really, choose one 🙈
• -q <float> — max bad read ratio. default [0.33]
• -r <int> — min read coverage. the default is literally [max(1, mean_read_cov - 4 * read_cov_stddev)] — she computes her own vibe check, no cap 🔥
• -R <int> — repeat calling cutoff. -R N means call a repeat if the fragment coverage is >= N times (expected coverage). and use -R 0 to not call repeats. default [2]
• -s <int> — min score to report in the errors file. default [0.4]
• -u <int> — FCD error window length for error calling. default [insert_size / 2]
• -w <float> — min percentage of bases in a window needed to call it bad. default [0.8]

pro tip from your girl: -p and -P are mutual enemies. do not try to run both, the manpage literally says incompatible twice and I'm not about to argue with her 💀

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🌈 SEE ALSO 🌈

• reapr(1) — go read the mothership, she's got the lore 🧚

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and that's the whole page, bestie!! take care of her, use your defaults, and remember: choosing between -p and -P is a personality test 💜

signing off from the REAPR-SCORE(1) manual page — section 1, footer and all — so whenever you're reading this, that's the page you're on 🎀💖 slay responsibly ✨