GLISTCOMPARE(1)

💖 GLISTCOMPARE — bestie edition 💖

okay so this is glistcompare, part of the GenomeTester user manuals, and it's literally the tool that takes two k-mer list files and does the whole "you two, figure out your relationship" thing 💅 union, intersection, difference — the works. no cap, it's giving matchmaker energy.

✨ NAME ✨

glistcompare — generate union, intersection or difference of k-mers from two list files 🦋

🌸 SYNOPSIS 🌸

glistcompare <INPUTLIST1> <INPUTLIST2> [OPTIONS]

two input lists, bestie. TWO. it compares them. that's the whole vibe. 💖

👑 OPTIONS 👑

every single one, no skips, periodt:

• -v, --version — print version information and exit. a lil flex, then she's gone ✨
• -h, --help — print this usage screen and exit. your girl always has the answers 🫶
• -u, --union — union of input lists. everybody's invited to the party 💜
• -i, --intersection — intersection of input lists. only the ones in BOTH groups make the cut 🔥
• -d, --difference — difference of input lists.
• -dd, --double_difference — double difference of input lists.
• -du, --diff_union — subtract first list from the second and finds difference. it's giving "you minus me, what's left" 💀
• -mm, --mismatch NUMBER — specify number of mismatches (default 0, can be used with -diff and -ddiff). sloppy matching is allowed, but only on those two, iykyk.
• -c, --cutoff NUMBER — specify frequency cut-off (default 1).
• -o, --outputname STRING — specify output name (default "out"). name your baby 💅
• -r, --rule STRING — specify rule how final frequencies are calculated (default, add, subtract, min, max, first, second, 1, 2).

⚠️ NOTE: rules min, subtract, first and second can only be used with finding the intersection. not optional, bestie, that's the rule (literally).

• -ss --subset METHOD SIZE — make subset with given method (rand_unique).
• --count_only — output count of k-mers instead of k-mers themself. just the number, no drama 🌈
• --disable_scouts — disable list read-ahead in background thread. the scouts are OFF duty 🙈
• -D — increase debug level. turn the volume up on the gossip ⭐

🎀 EXAMPLES 🎀

You could find some usage examples in /usr/share/doc/genometester/README.GenomeTester4.md

go read it, it's a whole mood 🧚

🦋 SEE ALSO 🦋

glistquery(1), glistmaker(1), gmer_caller(1), gmer_counter(1)

the whole squad, fr fr 🍓

that's the page bestie! brought to you by GenomeTester, dated 31 May 2018 💖 slay, go compare some k-mers, you got this 👑✨