v2.2.5: Time improvements

Changes since last release:

2.2.5 (02.11.2024)

• Improved logging.

2.2.4 (31.10.2024)

• Improved support of patterns shared by large number of samples ('bubbles').

v2.2.3: Added `-version` switch

Added `-version` switch

v2.2.2: Added unified filtering and sampling

• Added rows sampling (-sample-rows option) in all2all-sp and all2all-parts modes.
• Added unified filtering based on any specified measure (parameters -above, -above_eq, -below, and -below_eq replaced with -min and -max options).
• Changed interface in distance mode: only one measure allowed, output file has to be specified.

NOTE: In this release an Kmer-db interface has changed slightly: -above/-above_eq/-below/-below_eq options have been replaced with -min/ -max and distance mode requires additional argument. Please update your pipelines accordingly.

v2.0.5: Updates in tests and automatic building scripts

Updates in tests and automatic building scripts

v2.0.4: Update in `all2all-sp` mode: `above` and `below` options supported.

Automatic release deployment

v2.0.3: Bugfix release

Bugfix for wrong input (non-DNA).

v2.0.2: Second version

• Added new modes: all2all_sparse, all2all_parts,
• Serious time and memory optimizations,
• Support of MacOS (Apple M and x86 CPUs) and ARM platforms.

v1.11.1

Changes from the previous release:

• Removed deadlock in -multisample-fasta mode,
• Added support of sparse inputs in distance mode,
• Added support of sparse outputs in all2all, new2all, and distance modes (-sparse switch) with optional filtering (-above/-below),
• Extended help information.

v1.9.4

GitHub Actions badge fixed

v1.9.2

Changes from the last release:

• Output matrices can be stored in sparse format (-sparse switch).
• Better workload balancing.
• Improved parallelization scheme in new2all mode (few-fold speed improvement).
• Reduced memory footprint of -multisample-fasta mode.
• More than one input FASTA files supported in -multisample-fasta mode.
• Added -extend switch which allows extending existing kmer database.
• Serialization/deserialization works much faster now.
• Fixed serious bug in -multisample-fasta mode which caused incorrect kmers counting.