Skip to content

v1.3.0
Compare
Choose a tag to compare
@GuillaumeHolley GuillaumeHolley released this 10 Oct 14:01
· 34 commits to master since this release
v1.3.0
b1a2fa6
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Bifrost memory usage and running time has improved by up to 30% (depending on the input dataset)

  • The minimizer index and kmer hash-table use now robin-hood hashing instead of linear probing. They default to 95% maximum bucket occupancy instead of 80% in previous versions. Furthermore, hash table resizing uses now a 20% memory increase instead of doubling the size.
  • Blocked Bloom Filter uses a default 24 bits per key to enable a much faster joining step.
  • Extracting the exact unitigs from the Blocked Bloom Filter is done in 3 steps instead of 2: approximate unitigs are extracted to disk, read from disk and indexed in memory before annotating k-mers with their respective counts. Reader-writer locks can be avoided this way. However, Bifrost now uses a bit of disk space.
  • Code refactoring

New options for querying

  • -p, --nb-found-km: Output the number of found k-mers for each query (disable parameter -e)
  • -P, --ratio-found-km: Output the ratio of found k-mers for each query (disable parameter -e)
  • Fix rounding issue in #67

This version breaks Bifrost Index File (.bfi) compatibility with previous Bifrost versions, i.e. v1.3.0 cannot read .bfi files generated by v1.2.1 and older versions.

Assets 2
Loading