Releases: Danderson123/Amira
Releases · Danderson123/Amira
v0.11.0
0.11.0 (2025-08-02)
Miscellaneous Chores
- version bump (5dccac8)
Documentation
- fix ESKAPEES link (d590eaf)
- update Amira docs to detail assembly and metagenome mode (6878ced)
- update README with latest citation (cfb585b)
Features
- add metagenome-specific files (33c1c13)
- add metagenome-specific files (93cb582)
- report NA for copy numbers if this step skipped (92e96e9)
Bug Fixes
- accounts for an empty core gene set (e097a63)
- add value for sourmash n (c7671ba)
- do not assume tandem repeat dead end is of length 1 (712eb70)
- do not trim dead ends that are actually tandem repeats (bb0fd15)
- fix path similarity estimates (4f807e1)
- reduce dead end depth threshold (c1022a0)
- remove redundant output graphs (1d308b3)
- rename to ESKAPEES (5cb2112)
- skip ccn estimation if running from assemblies or in metagenome mode (cc9bc1f)
- skip pandora gene filtering in some circumstances (187ef87)
Styles
v0.10.0
0.10.0 (2025-07-18)
Miscellaneous Chores
- output mid correction gene calls for debugging (7c57776)
- output unitigs after each correction stage (2c48be1)
- output unitigs after each correction stage (73976f4)
- output unitigs after each correction stage (ed2cd22)
- output unitigs after each correction stage (3b2e652)
Features
- allows running of Amira from assemblies and the option --assemble-paths can be used to try to assemble the reads in each cluster of genes, to aid epidemiological studies (0d04b5e)
Bug Fixes
- filter out longer paths instead of shorter ones in iterative correction (82b297d)
- remove mid correction graph output (aa0ec1e)
- undo reverse sort (87b26aa)
- update E. coli-specific files (227c15f)
Styles
Tests
- add lcs test (0dedb82)
v0.9.3
0.9.3 (2025-05-29)
Miscellaneous Chores
- version bump (f4e38d8)
Documentation
Bug Fixes
- add KP plasmid gene files (4ca3672)
- add SA and SP plasmid gene files (0b8683e)
- fix for underestimation of relative read depth in some cases (347e5d4)
- improper filtering of low identity genes (4a3ddf5)
- pre-commit formatting (2c2950a)
- properly report coverage across genes with no fully covering reads (2585180)
- remove debug line (c67ec67)
- undo coverage check change (74e85ba)
- update setuptools version (716b405)
v0.9.2
0.9.2 (2025-05-16)
Bug Fixes
- correct shortest paths first (eeb77b5)
- missing arguements when genotyping promoters (f47e5e8)
- reduce sourmash k to marginally improve precision (94fc4ef)
- remove overwriting of JSON annotations (6e71c13)
- update unittests for new sourmash params (b0d951e)
- use a single core to build the graph in the graph correction stage (06cf34d)
v0.9.1
v0.9.0
0.9.0 (2025-05-07)
Continuous Integration
- do not test on python 3.9 (ae1de18)
- do not test on python 3.9 (d33391e)
- test on python 3.12 (a6dc2c1)
Miscellaneous Chores
- support S. pneumoniae and S. aureus (31e0b0a)
- support S. pneumoniae and S. aureus (44eebb8)
- version bump (93418c5)
- version bump (d9ffa24)
Documentation
- fix README (03d6f40)
- specify pandora version (9fd68ab)
- update download links in README (20f278a)
- update README (46a2058)
- update README (17c555b)
- update README (27a6c37)
- update README (f630555)
- update README (84af8be)
Features
- add SA and SP files (fe041ef)
- increase subsample size (0f0e353)
- refactor graph correction to massively improve runtime (70a8d66)
Bug Fixes
- allow reads with .fq extension (38cf4db)
- allow reads with .fq extension (8c3ac75)
- allow underscores in read identifiers (d2a3826)
- allow underscores in read identifiers (d135d96)
- attempt optimisation (61cae8f)
- bring up to speed with dev (d50bb5f)
- do not delete uncompressed fastq (ea151b6)
- do not write a modified fastq file (59c013c)
- extend bubble popping path length (6978c20)
- file path fix (0a94737)
- fix bug in modifying read identifiers (d309f47)
- fix parsing of non-gzipped fastq (4760b2c)
- fix unittests (6610dc9)
- further attempts to optimise bubble popping (e43b0b5)
- missing output dir (b3d62d1)
- missing output dir (ffa58c0)
- new fastq path (2de66e7)
- new fastq path (c3c4574)
- optimise path correction filtering (be6dd67)
- optimise path filtering with suffix trees (dd2a08a)
- optimise path filtering, leads to 10x speedup in some cases (fb2e871)
- prevent unnecessary path comparisons (4af472c)
- progress reporting fix (2781493)
- reduce bubble popping path length slightly (18caf38)
- reduce sourmash version (2199d35)
- remove bounds from k-mer cutoff estimation (128c8f2)
- remove debug line (d0b3c04)
- remove debug message (85c6713)
- remove unnecessary progress report (18c28d2)
- revert optimisation attempt (22b5ec5)
Styles
- pre-commit reformatting (3db9704)
- pre-commit reformatting (eab1299)
- pre-commit reformatting (9283732)
- pre-commit reformatting (01cc43c)
- pre-commit reformatting (78bc7fc)
- pre-commit reformatting (cf0e509)
- pre-commit reformattng (e1d7bf0)
- refactor main function (e592795)
- remove redundant reporting (d1ad5a0)
- rename cellular copy number column (01adc54)
v0.8.0
0.8.0 (2025-03-25)
Miscellaneous Chores
- version bump (487c6b0)
Documentation
- improve arguement documentation (431dcab)
Features
- allow parsing of species files from command line (a0dc317)
- estimate copy numbers of paths and apply to covered AMR genes (870f5e3)
- use jellyfish to estimate cellular copy numbers (5198fe2)
- use kmer counts to estimate cellular copy number (1ac9040)
Bug Fixes
- add jellyfish to singularity recipe (00b24d4)
- add test files (cee63ba)
- bug fix for non-redundant path filtering (f5cfa38)
- bug in gene positions when path does not need correcting (a9a9652)
- build container from main (b65cc54)
- correctly modify gene positions (5925772)
- divide depth estimate by genomic copy number (943577f)
- do not filter out whole paths (adfa1eb)
- don't specify jellyfish version in recipe (818437d)
- estimate peak coverage from filtered histogram (5c2ef2c)
- file extension bug (429bfe6)
- filter alleles solely based on relative read depth (f645a20)
- filter gene positions too (a05b1ff)
- filter genes based on relative frequency (f559141)
- fix bug where path finding is blind to paths that start within an internal block (0b0012d)
- fix bug where path finding is blind to paths that start within an internal block (03f1020)
- fix bug where path finding is blind to paths that start within an internal block (f8dc458)
- gene coverage default val (756870f)
- gunzip reads before giving to jellyfish (c865567)
- increase debugging information (78e9408)
- increase debugging information (87737e2)
- increase gene_min_coverage default (ac38d91)
- increase k-mer size and filter by mean relative depth instead of copy number (f879ce7)
- minor bug fix for read ids (09b5d47)
- ouput node coverage (557f84a)
- reduce kmer size (f78ab56)
- remove print statement (9fc6349)
- remove redundant tests (b5da866)
- remove redundant variables (08230cd)
- removes contamination filtering and replaces with filtering by depth (428d01a)
- resolve conflicts (ac6c46f)
- revert back to short reads (f39e422)
- skip relative depth based filtering if read coverage is low (eb83fad)
- skip supplementary reads (6115e40)
- stop pandora from filtering based on coverage (f77d228)
- unittest fix (6f006a6)
- unittest fix (05bd1ec)
- use estimated read depth when kmer depth estimate is too high (d4a411f)
- use initial reads to supplement AMR genes (e128d57)
- use kmer depth to get copy number estimate (bfeddba)
- use main branch for Singularity container (899311f)
- use scipy find peaks to estimate mean k-mer depth (a85faf4)
Styles
- more consistent stderr messages (b4a72b4)
- pre-commit reformatting (2ca3bc1)
- pre-commit reformatting (697e0e3)
- pre-commit reformatting (4fd4030)
- pre-commit reformatting (01de505)
- pre-commit reformatting (86bab63)
- pre-commit reformatting (e06c36d)
- pre-commit reformatting (8084235)
- pre-commit reformatting (7270d99)
- pre-commit reformatting (7182e75)