DAMAPPER(1)

💖 damapper — long read to reference genome mapping tool 💖

okay so. bestie. gather round. this is the manual page for damapper(1), which lives in the User Commands corner of the manual. she's a long read to reference genome mapping tool and honestly? she ate. let's get into it. 🦋

✨ NAME ✨

damapper — long read to reference genome mapping tool. that's it, that's the name. short, sweet, does exactly what it says on the tin. 💅

🌸 DESCRIPTION 🌸

So basically, this whole thing is Recognised as the Damapper Library, and what that means for you, bestie, is that it's a long read to reference genome mapping command line tool. long reads go in, mapping to a reference genome comes out. no cap. 🧚

🎀 SYNOPSIS 🎀

damapper [-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-T<int(4)>]
[-P<dir(/tmp)>] [-e<double(.85)] [-s<int(100)>] [-n<double(1.00)>]
[-m<track>]+ <reference:dam> <reads:db> ...

like, look at her. flags in the front, <reference:dam> and then one or more <reads:db> at the end, because yes you can feed her multiple read databases, she's got range. 👑

🔥 OPTIONS 🔥

one bullet per flag, zero skips, we do not gatekeep here. 💜

• -k — the k-mer size, and heads up: it must be <= 32. (default is <int(20)>.) so if you were feeling spicy with a big number, don't. ✨
• -t — ignore k-mers that occur >= -t times in a block. frequent little guys get benched. 💀
• -M — use only -M GB of memory by ignoring most frequent k-mers. it's giving budgeting, and honestly? responsible. 🫶
• -e — look for alignments with -e percent similarity. (default <double(.85)>.) so like, how close do you want the match to be, bestie. 🌸
• -s — use -s as the trace point spacing for encoding alignments. (default <int(100)>.) yes she's encoding, yes it's on purpose. 🎀
• -n — output all matches within this % of the best. (default <double(1.00)>.) the best match is the main character, but the close runners-up are invited to the party too. ✨
• -T — use -T threads. (default <int(4)>.) parallelism slay. 🔥
• -P — do sorts and merges in directory -P. (default <dir(/tmp)>.) so she needs somewhere to crash while she works. 🍓
• -m — soft mask the blocks with the specified mask. note the + in the synopsis: you can stack these, so -m<track> more than once is fully allowed. 💅
• -v — verbose mode, output statistics as proceed. she will narrate. enjoy. 👑
• -z — sort .las by A,B-read pairs (overlap piles).
  • off => sort .las by A-read,A-position pairs (this is the default for mapping). so if you don't pass -z, that's the vibe you're getting. 🌈
• -p — output repeat profile track. 🙈
• -C — output reference vs reads .las. 🦋
• -N — do not output reads vs reference .las. (yes this is the opposite of -C. they're not enemies, they're just different flags, periodt.) 💀

heads up bestie: remember -k must be <= 32. that's not me being dramatic, that's just the rule. 💖

that's the whole page, fr fr. every flag accounted for, nothing dropped, nothing invented. 🫶

this page is damapper, from August 2020, and it lives in the User Commands section of the manual — mwah, iconic, no notes. ✨💅🎀