Releases: Danderson123/Amira
Releases · Danderson123/Amira
v0.3.1
v0.3.0
0.3.0 (2024-11-18)
Miscellaneous Chores
- version bump (04b1bef)
Documentation
- add citation placeholder (0e1168e)
Features
- use suffix trees to obtain all paths that span from the start of a block of AMR genes to the end (db6eb3c)
Bug Fixes
- supplement full paths with singleton nodes (7f6e028)
Code Refactoring
- import modularity of graph operations (a2ebde5)
- improve modularity of read operations (425370a)
- improve modularity of result operations (747276f)
Styles
- pre-commit reformatting (580064a)
Tests
- add missing test files (aa552a1)
v0.2.0
v0.1.0
0.1.0 (2024-11-06)
Continuous Integration
- add .isort.cfg (47a69b5)
- add pre-commit to dependencies (608333e)
- adds ci.yaml to run makefile (ad91b87)
- adds poetry.lock, .pre-commit-config.yaml and Makefile (73810a3)
- change release-please repo name (f6126ef)
- comment out redundant tests (f0ad490)
- comment out redundant tests (1b41b3c)
- create release-pypi.yaml (3b9ae5c)
- Creates release-please.yaml (53abf05)
- install dependencies before test (7fc194a)
- install dependencies before test (2d13af7)
- install dependencies in actions (be2a163)
- install pytest before running tests (79e8011)
- Merge branch 'CI_integration' of https://github.com/Danderson123/amira_prototype into CI_integration (44506b2)
- remove python3.8 support (01d6a0e)
- remove unused test script (c8947f5)
- remove Windows support (466cbcf)
- removes redundant .github/workflows/run_tests.yml (869fd5d)
- set up python installation (278a4a5)
- update main.py (2cdeebb)
- update ci.yaml (028b3c3)
- update ci.yaml (bda10f6)
- update ci.yaml (f74ee4f)
- update ci.yaml (95a4c46)
- update poetry.locl (1ab43b4)
- update pre-commit tools using poetry (40e7adc)
- update release-please.yaml (30e89e4)
- use pip to install pypi dependencies (392864f)
Documentation
- update README (82e282b)
- update README (00d8263)
- update README (056c60c)
- update README (a178cab)
- update README (2e427d6)
- update README and add ref files (a6f85ae)
Features
- add closest reference allele header to read clustering keys for evaluation (5967028)
- add dynamic determination of node threshold (307744c)
- add partial untittests for new functions (4eb534b)
- add source direction to gml (63d3b38)
- applies a fixed path threshold for correction then uses minimizer containment of paths to correct high coverage paths in the final round. (824bec0)
- correct bubbles until a maximum of 10 iterations (7d4c87e)
- dynamic determination of post-bubble popping node filtering thresholds (e84bc97)
- dynamically choose a value for k (dfee11a)
- filters alleles that are not >=90% similar to a reference allele and polishes reference alleles to obtain Amira allele (9d3e0e4)
- initial attempts to correct all bubbles at once (cd5fbae)
- initial attempts to correct all bubbles at once (15c40cd)
- kind of working correction method (e79d6cf)
- mulit-processed DFS of paths and adds minimizer comparison of paths for accurate correction (9718b80)
- multiprocessed graph building using joblib (c6af7ac)
- new approach to cluster reads based on paths through the graph (0c36248)
- output approximate copy numbers and reference allele depths (fbe147b)
- output tsv of amira results (cbe3c96)
- output txt file of depths across reference alleles (5128c5c)
- recover reads from paths that have been filtered out (ef58223)
- report all equally close variants (d373b7e)
- take fasta reference file as input and polish closest AMR gene to get nucleotide sequence (3255f28)
- ten iterations of racon polishing (a81ddce)
- tracks the position of each gene through each correction step to allow extraction of its sequence. Also removes redundant code and tests and improves code modularity. (5a21e91)
- use allele sequences to polish pandora consensus instead of entire read (cd07418)
- use as many adjacent nodes as possible to resolve complex AMR gene paths (ca677c5)
- use overall mean node coverage for specific k to estimate copy number (ece0037)
Bug Fixes
- accounts for racon runtime errors, prevents AMR gene bubbles being popped (d0be7f4)
- add dependencies to pyproject.toml (9ebc9f3)
- add minimal instructions to README (570e8af)
- add pandas as dependency (5569a2e)
- add sourmash as a dependency (edc19a0)
- add sourmash as a dependency (11a4b4d)
- apply allele filters to genes from short reads (e3fdc4f)
- avoids undercalling genes due to collapsed paths (02787dd)
- bug fix for getting the genes from a list of nodes ([6114f75](https://github.c...