v0.1.2

Added

• Add gap-compressed ANI to output.

v0.1.1

Added

• Add options to control EM early stop.

Changed

• Use scipy.sparse to reduce peak memory usage and computational time.
• Change default terminal condition of EM (max_iteration: 100 -> 1000; epsilon: 1e-5 -> 1e-10).

Fixed

• Fix a bug causing chimeric reads not being aggregated.

v0.1.0

Added

• Output a json file to indicate the lineage of processed reads.

Changed

• Make databases indexed by default.
• Use only kraken's prediction for removal of non-prokaryotic reads.
• Change --db_kraken to --db-kraken for consistency.
• Change sp[0-9]+ to sp[0-9]+ for consistency.
• Change copies to copy in output files for consistency.

Fixed

• Prevent numpy from using all logical cores.

v0.0.1

Added

• First release.