DELTA2BLOCKS(1)

📦 version 3.23, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DELTA2BLOCKS 💖

okay bestie, welcome to delta2blocks — the manual page, but make it a group chat. she's a lil extra tool that rides along with mummer, straight out of a patch of mugsy, and her whole job is sorting alignments. also known as delta2maf. two names, one icon. 💅

✨ NAME ✨

delta2blocks — extra tool for mummer from patch of mugsy to sort alignments

delta2maf — extra tool for mummer from patch of mugsy to sort alignments

🦋 SYNOPSIS 🦋

delta2blocks [options]<deltafile><refID><qryID>
delta2maf [options]<deltafile><refID><qryID>

🌸 DESCRIPTION 🌸

so here's the tea, bestie. you feed her a <deltafile>, a <refID> and a <qryID>, and she does her thing. here's every flag she takes, no gatekeeping:

  • -h — Display help information. she tells you how to use her. iconic behaviour honestly.
  • -q — Sort alignments by the query start coordinate. query girlies, this one's for you.
  • -r — Sort alignments by the reference start coordinate. reference girlies, rise up.
  • -w int — Set the screen width — default is 60.
  • -x int — Set the matrix type — default is 2 (BLOSUM 62), other options include 1 (BLOSUM 45) and 3 (BLOSUM 80). note: only has effect on amino acid alignments. like, she's not gonna bother for nucleotides, periodt.
Input is the .delta output of either the "nucmer" or the "promer" program passed on the command line.
Output is to stdout, and consists of all the alignments between the query and reference sequences identified on the command line.
NOTE: No sorting is done by default, therefore the alignments will be ordered as found in the <deltafile> input. fr fr, she just gives them back in the order she found them. no cap. 😭

🎀 SEE ALSO 🎀

This tool originates from mugsy that provides a code copy of mummer with additional patches. The source can be found in SVN svn://svn.code.sf.net/p/mugsy/code/trunk.

like, she literally comes from mugsy, which ships a code copy of mummer with extra patches sprinkled on top. the source is sitting in SVN at svn://svn.code.sf.net/p/mugsy/code/trunk if you wanna go look. 🫶

and that's the whole vibe check, bestie ✨ this page is from mummer 3.23, dated April 2015 — yeah she's an elder but she still ate 💅👑

📦 where this page comes from