SHOW-DIFF(1)

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

💅 SHOW-DIFF(1) — user commands, but make it cute

okay bestie, so show-diff is the little tool that spills the tea on structural differences — it's part of the mummer package, and yes it's iconic for that 💖

✨ NAME ✨

show-diff — show diff information (part of mummer package) 🦋

🌸 SYNOPSIS 🌸

show-diff [options]<deltafile>

💜 DESCRIPTION 💜

  • -f — output diff information as AMOS features ✨
  • -h — display help information 🙋‍♀️
  • -H — do not show header 🚫
  • -q — show diff information for queries 🔍
  • -r — show diff information for references (this is the default, no cap) 👑

It outputs a list of structural differences for each sequence in the reference and the query, sorted by position. So for a reference sequence R and its matching query sequence Q, the differences get sorted into these lil categories:

  • GAP — a gap between two mutually consistent alignments 🕳️
  • DUP — an inserted duplication 👯
  • BRK — other inserted sequence 🧩
  • JMP — a rearrangement 🦘
  • INV — a rearrangement with inversion 🙃
  • SEQ — a rearrangement with another sequence 🌀

The first five columns of the output are: seq ID, feature type, feature start, feature end, and feature length. Extra columns get added depending on the feature type, because of course they do 💅

heads up! Negative feature lengths mean there are overlapping adjacent alignment blocks. Not a glitch, just math 😭

Here's what the output looks like for each type:

IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff

IDR DUP dup-start dup-end dup-length

IDR BRK gap-start gap-end gap-length

IDR JMP gap-start gap-end gap-length

IDR INV gap-start gap-end gap-length

IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence

Positions always reference the sequence with the given ID, fr fr.

The sum of the fifth column (ignoring negative values) is the total amount of inserted sequence 🧮✨ Summing the fifth column after removing DUP features gives you the total unique inserted sequence 🫶

important bestie!! Note that unaligned sequence is not counted, and could represent additional "unique" sequences 👀 See the documentation for tips on how to interpret these alignment break features, iykyk 📖

and that's the whole vibe, bestie 🎀 this page is from mummer 3.23, dated April 2015 — go off, you got this 💖✨👑

📦 where this page comes from