v0.2.5

Fixed

• Fix a bug that causes one-column rows to be reduced to scalars (e07636d). This bug occurs with pure isolates when all reads can be unambiguously assigned to a single species (#5).

v0.2.4

Added

• Add -g to control the minimum number of unique marker genes (default: 1) required for a species to report its genome copies. Increase -g (1 -> 2) lowers recall (detection limit: 0.125 -> 0.25) but improves precision.

v0.2.3

Fixed

• Fix a bug introduced in v0.2.2 causing ties not resolved properly. Results should be identical to v0.2.1.

v0.2.2

Changed

• Avoid direct float comparison (315b795).

v0.2.1

Changed

• Revert filtering criteria back to v0.1.6. The old criteria turn out to be helpful in rescuing certain chimeric reads in very rare settings.

Fixed

• Reduce peak memory usage.

v0.2.0

Added

• [breaking] Add decoy protein sequences (RefSeq fungi, protozoa, viral, plant, and human GRCh38/hg38) which effectively trap non-prokaryotic reads and prevent them from inflating total prokaryotic genome copy estimates if the pre-filtering module (default with Kraken2) is not enabled. Pre-filtering is no longer necessary even if samples are contaminated with human DNA or other common eukaryotes/viruses, unless the mean genome size of prokaryotes needs to be estimated. See 8918168 for more details. This function requires a database released on or after 2024-06-28.

Changed

• Simplify filtering criteria for alignments.

v0.1.6

Changed

• Prevent extract_sequence from loading all marker-containing reads into memory.
• Change -F to --frameshift and max_iteration to max_iterations for consistency.
• Switch from figshare to zenodo for better database versioning.

v0.1.5

Fixed

• Fix a bug causing tqdm being disabled (3bbd087).

v0.1.4

Changed

• Use tqdm for logging.
• Reduce peak memory usage by parsing PAF files on the fly.

v0.1.3

Changed

• Change alignment filtering criteria: make AS cutoff more stringent, drop MS. See 7cc6dbd for details.

Fixed

• Fix a bug causing total genome copies not being properly calculated with diamond>=2.1.9.

Added

• Output both gap-compressed and gap-uncompressed (BLAST-like) identity.
• Refine output format.