Skip to content

v0.1.3
Compare
Choose a tag to compare
@bluenote-1577 bluenote-1577 released this 11 May 00:15
· 45 commits to main since this release
v0.1.3
7724041
This commit was created on github.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

v0.1.3 released - 2023-05-09

Major

  • Fixed a bug where memory was blowing up in dist and triangle when the marker-index was activated. For big datasets, there could be > 100 GBs of wasted memory.
  • skani now outputs intermediate results after processing each batch of 5000 queries. This will mean that outputs may no longer be deterministically ordered if there are > 5000 genomes, but you can sort the output file to get deterministic outputs, i.e skani triangle *.fa | sort -k 3 -n > sorted_skani_result.txt will guarantee deterministic output order.

Minor

  • Changed the marker index hash table population method. Used to overestimate memory usage slightly.
  • New help message for marker parameters. Turns out that for small genomes, having more markers may make filtering significantly better.
  • Added -i option to sketch so you can sketch individual records in multifastas -- does not work for search yet though, only for sketching.
Assets 2
Loading