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)
- bug fix for missing gene due to improper sorting (3b79f5a)
- bug in bubble popping that was missing bubbles (7b1de79)
- correct relative import of scripts (9986fc8)
- de novo check gene coverages with minimap2 and do not allow racon to trim AMR alleles (709e0b0)
- edge case fix for assigning reads to paths and adds a component ID column to the amira tsv (83cc331)
- edge case in AMR path finding (95889a8)
- find genes missing from the graph (108d1df)
- find genes missing from the graph (6713e4d)
- fix a bunch of bugs that messed with evaluation in real data (a4e76c9)
- fix for known bug where two different AMR paths overlap, tweaks params to filer out AMR genes and prevents k from being increased when the coverage is too low (70506d1)
- fixes bug where AMR blocks are missed if they start or end at a junction (c5c0d46)
- improper handling of edge cases where duplicate genes occur on a read we are trying to correct and/or in a path that we are trying to correct to. (6973ecb)
- improves modularity of main function and allows JSON inputs (2ed1347)
- improves modularity of main function and allows JSON inputs (02d15b0)
- increase coverage threshold for filtering and allow replacement of AMR genes in low coverage paths (a80d980)
- limit allele coverage to 100 (06ae3e2)
- minor memory optimisation for minimizer extraction (3dde066)
- missing AMR path (8e94b44)
- missing AMR path (b0d64fd)
- output empty dataframe when no AMR genes are present (6fef804)
- prevent removal of full components and AMR nodes in dead ends (deea859)
- reduce AMR allele coverage threshold to 85% (92cca4f)
- relative import location of fastq functions (4e74456)
- remove legacy script (3094671)
- remove redundant print (d9908df)
- remove threshold for initial AMR path finding (551e090)
- return empty result when no AMR genes found (659fceb)
- sort ref alleles first by length then by similarity (e056b56)
- tweaks parameters to filter AMR genes and ensures subsampling reads does not remove AMR genes completely (e2ff182)
- undefined variable fix and pre-commit reformatting (9e9c8e0)
- update to latest pysam (beebe6d)
- use reads to define start and stop points of paths through AMR blocks (88dcf51)
Styles
- black reformatting (c2c2ed0)
- black reformatting (3502cfc)
- black refotmatting recommendations (b41c635)
- fix all flake8 style recommendations (13f66f1)
- flake8 formatting (bd28289)
- flake8 formatting (0d477de)
- flake8 formatting (436d5d9)
- flake8 formatting recommendations (d7d37b8)
- flake8 formatting recommendations (b02baec)
- flake8 reformatting (0f9333c)
- flake8 reformatting (06a72f2)
- flake8 reformatting (c93b288)
- flake8 reformatting (da83389)
- isort and black recommended formatting (51853a6)
- isort and black recommended formatting (92efeff)
- partial typing (4abdcd4)
- pre-commit formatting (c4f18d7)
- pre-commit recommended formatting (8a097d9)
- pre-commit reformat (0d6a1f2)
- pre-commit reformatting (e188bb9)
- pre-commit reformatting (3ae42d7)
- reformatting recommendations (e8f2b57)
- reformatting recommendations (e523293)
- reformatting using black (451a5b4)
- remove redundant commented code (cec5de5)
- rename to Amira (3f4da1c)
- rename to Amira (7a4a6f5)