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Release/1.0.0 #35

Merged
merged 79 commits into from
Jan 21, 2024
Merged

Release/1.0.0 #35

merged 79 commits into from
Jan 21, 2024

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christianfares
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  • Updated all modules of mity to improve the code quality and remove deprecated packages
  • Updated the consistency of the code and behaviour of mity across all modules

trentzz and others added 30 commits June 13, 2023 04:04
@trentzz
added azure-pipeline skeleton yaml file
d3fe847
@trentzz
Renamed folders, moved reference and annot folders to res, reorganise…
408280f 
…d test files
@trentzz
updated dependencies for dockerfile
d7613b2
@trentzz
added azurepipeline files
cf7cfaa
@trentzz
added build and tests back, edited gitignore
15aa09d
@trentzz
added config file
9aaf4a8
@trentzz
finished azure pipelines for dev
b572f92
@trentzz
removed requirements.txt
c9fcd82
@trentzz
removed cram file
16e1890
@trentzz
edited dockerfile, gitignore, made build-test.sh for pushing to test.…
69660e1 
…pypi
@trentzz
ver bumped to 0.4.7, reverted a lot of changes, currently works
d6060da
@trentzz
ver bumped to 0.4.23, debug flag works, config file setup, pyvcf remo…
2047320 
…ved, python version bumped to 3.10.6
@trentzz
argparse not working properly
775ffb4
@trentzz
added debug flag
b0cd964
@trentzz
removed unused function: create_genome_file
ed28634
@trentzz
Merge pull request #23 from KCCG/other/MITY-29-cleanup-and-update-dep…
d107ac5 
…endencies

Merge cleanup and updated dependencies to development
@trentzz
merged cleanup changes into development-env
6c702c7
@trentzz
updated pipeline file to use dynamic version links based on tag name
66e6dcb
@trentzz
fixed syntax
c6c6cdb
@trentzz
changed name in pipeline
8292521
@trentzz
added VERSION to docker build in pipelines
a5a58f7
@trentzz
added VERSION to dockerfile
9e87d32
@trentzz
removed _version.py, added script to pipline stages to create _versio…
5faf247 
…n file (untested)
@trentzz
removed bcftools and htslib from dockerfiles, removed bcftools_sort_v…
3090a51 
…cf and removed --custom_reference flag from mity call and merge
@trentzz
added initial new normalise, only replicates filter
dccac57
@trentzz
removed VERSION ENV stuff
19b2ef5
@trentzz
removed env line 29 in pipeline-stages
5210496
@trentzz
changed prod pipeline tag to *.*.*
fbfb426
@trentzz
added gsort to mity normalise replacement, changed file naming in mit…
bdc51c4 
…y call and normalise, changed mity commands to match new normalise
@trentzz
Merge branch 'other/MITY-29-cleanup-and-update-dependencies' of githu…
072e6d4 
…b.com:KCCG/mity into other/MITY-17-replace-mity-normalise
trentzz and others added 29 commits September 13, 2023 16:07
@trentzz
added code to make table for non-annotated vcf
76a86c6
@trentzz
changed mity normalise filter behaviour and removed tests
2ad91f6
@trentzz
Merge pull request #29 from KCCG/other/MITY-17-replace-mity-normalise
b58b78c 
Changed mity normalise filter behaviour and removed tests
@trentzz
mity report now calls vcfanno and replicates most of old-report (exce…
61c1ff8 
…pt cohort count, vepped vcfs)
@trentzz
added yaml file with excel headers and dictionary, refactored report …
583e663 
…to use classes
@trentzz
finished rewriting new mity report
d7302d1
@trentzz
resolved merge conflicts
bf44a79
@trentzz
removed testing code
36c3452
@trentzz
removed vscode settings
c474249
@trentzz
removed vscode settings
f4dfb51
@trentzz
fixed cohort count
fd5d063
@trentzz
rewriting in progress
4a5b235
@trentzz
added module description and fixed allele frequency mitomap constant
0f35aee
@trentzz
removed unzipped annotation files and added documentation for adding …
4a69298 
…new annotations
@trentzz
Merge branch 'other/MITY-18-replace-mity-report' of github.com:KCCG/m…
485e8cd 
…ity into feature/MITY-32-rewrite-commands-and-add-classes
@trentzz
Merge pull request #30 from KCCG/other/MITY-18-replace-mity-report
aef542c 
Merge mity report rewrite into development
@trentzz
added keep, refactored mity call, normalise, util to use classes
5f88a3a
@trentzz
added and edited files
a169d38
@trentzz
Merge branch 'development' of github.com:KCCG/mity into other/MITY-33…
0c26fa1 
…-replace-mity-merge
@trentzz
Merge pull request #31 from KCCG/feature/MITY-32-rewrite-commands-and…
e3a5e3d 
…-add-classes

Merge feature/mity 32 rewrite commands and add classes into development
@trentzz
added implementation of mity merge, works but needs more testing
c93b2eb
@trentzz
finished up mity merge, moved gsort to util and made some other small…
31b2cfd 
… cleanup changes
@trentzz
removed unused files and commented out code
c811c82
@trentzz
added check for Description in header line
4ac2cc5
@trentzz
Merge pull request #33 from KCCG/other/MITY-33-replace-mity-merge
9b590a3 
Merge mity merge rewrite into development
@christianfares
- Fixed last remaining bugs
0475461 
- Tested new mity workflow
- Update documentation
@christianfares
Merge pull request #34 from KCCG/MITY-34-prepare-release
03ad174 
Mity 34 prepare release
@christianfares
- Updated dev dockerfile to have the correct mity test package name
0a1a4a5
@christianfares
Merge pull request #36 from KCCG/MITY-34-prepare-release
dbd4bab 
Mity release prep
@christianfares christianfares merged commit 6dc3dba into master Jan 21, 2024
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2 participants
@christianfares @trentzz