v0.2.0

Changed

• [breaking] Simplify command line interface (-I -> -i, -S -> -s), options related genome copy estimation are removed.

Added

• Add --skip-melon for skipping genome copy estimation.

v0.1.3

Changed

• Change default mode (without --plasmid) to classifying all reads that carry ARGs.

v0.1.2

Changed

• Use total bitscores per cluster for determining final HSPs. This help reduce false positives in certain cases.
• Switch from dok_matrix to coo_matrix for speed.

Fixed

• Make database size checking more flexible.
• Reduce peak memory usage.

v0.1.1

Fixed

• Fix a bug causing all reads not being classified when --plasmid is not given.

v0.1.0

Added

• Add option --plasmid for controlling whether plasmid reads should be classified.
• Reduce plasmid detection cutoff from 0.9 to 0.5.
• Increase max overlap identity filtering cutoff from 0.01 to 0.05.

v0.0.1

Added

• First release.