Ecosyste.ms: Issues

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GitHub / bcgsc/mavis issues and pull requests

#359 - How to run mavis annotate directly?

Issue - State: open - Opened by Weiyifan 8 months ago - 1 comment
Labels: bug

#358 - backmerge releases to develop_v3

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment

#357 - Release/v3.1.2

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment

#356 - #355 fix chromosome comparison check

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment

#354 - fix errors on empty columns

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment

#353 - Release/v2.2.12

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment

#352 - #350 fix overlapping imprecise breakpoints in mavis v2

Pull Request - State: closed - Opened by calchoo over 1 year ago - 2 comments

#351 - Bump Snakefile version to release 3.1.1

Pull Request - State: closed - Opened by zhemingfan over 1 year ago - 1 comment

#350 - error:('error: expected one of', {'duplication'}, 'but found', 'deletion'

Issue - State: closed - Opened by Nitin123-4 over 1 year ago - 10 comments
Labels: bug

#349 - Release/v3.1.1

Pull Request - State: closed - Opened by calchoo over 1 year ago - 1 comment
Labels: release

#348 - adding gridss vcf support to mavis

Pull Request - State: closed - Opened by calchoo almost 2 years ago - 1 comment

#347 - filtering unmapped, duplicate, qcfailed reads from ref/alt calculation

Pull Request - State: closed - Opened by calchoo almost 2 years ago - 2 comments

#346 - Improvement/add arriba test

Pull Request - State: closed - Opened by calchoo almost 2 years ago - 3 comments

#344 - Update mini.md

Pull Request - State: open - Opened by creisle about 2 years ago - 1 comment

#343 - master back to dev

Pull Request - State: closed - Opened by creisle about 2 years ago

#342 - Refactor/enforce isort

Pull Request - State: closed - Opened by creisle about 2 years ago - 1 comment
Labels: devops, code-style

#341 - Feature/enforce isort

Pull Request - State: closed - Opened by creisle about 2 years ago

#340 - Ignore type-checking only lines in coverage report

Pull Request - State: closed - Opened by creisle about 2 years ago - 1 comment
Labels: devops

#339 - Release/v3.1.0

Pull Request - State: closed - Opened by creisle about 2 years ago - 1 comment
Labels: SV caller, code-style, release

#338 - Require mavis config 1.2.2+

Pull Request - State: closed - Opened by creisle about 2 years ago - 1 comment

#337 - Bugfix to Summary module clustering output

Pull Request - State: closed - Opened by zhemingfan about 2 years ago - 1 comment
Labels: bug

#336 - Change support for MAVIS input in summary module

Pull Request - State: closed - Opened by zhemingfan about 2 years ago - 4 comments
Labels: enhancement

#335 - snakemake.exceptions.WorkflowError: Config file is not valid JSON or YAML

Issue - State: open - Opened by mattdoug604 about 2 years ago - 12 comments
Labels: bug, question, documentation

#334 - Unused variables in validation module

Issue - State: open - Opened by zhemingfan over 2 years ago - 2 comments
Labels: enhancement

#333 - Refactor/simplify tests

Pull Request - State: closed - Opened by creisle over 2 years ago - 1 comment
Labels: bug, refactor

#332 - Docker Validation Error - tutorial full

Issue - State: open - Opened by husamia over 2 years ago - 3 comments
Labels: bug

#331 - Move class method off of class definition

Pull Request - State: closed - Opened by creisle over 2 years ago - 1 comment
Labels: refactor

#330 - Feature/simplify split algn

Pull Request - State: closed - Opened by creisle over 2 years ago - 1 comment
Labels: refactor, code-style

#329 - Feature/add arriba support

Pull Request - State: closed - Opened by calchoo over 2 years ago - 1 comment

#328 - Split read gathering methods into a separate module

Pull Request - State: closed - Opened by creisle over 2 years ago - 1 comment
Labels: refactor, code-style

#327 - Change support for MAVIS input

Pull Request - State: closed - Opened by zhemingfan over 2 years ago - 1 comment

#326 - #325 Adding arriba support

Pull Request - State: closed - Opened by calchoo over 2 years ago - 2 comments

#325 - Add support for Arriba

Issue - State: closed - Opened by calchoo over 2 years ago
Labels: enhancement, SV caller

#324 - Integrate CHM13-T2T support

Issue - State: open - Opened by zhemingfan over 2 years ago
Labels: enhancement

#323 - Add compression step to MAVIS snakemake v3

Issue - State: open - Opened by creisle over 2 years ago
Labels: enhancement, performance

#322 - Integration information from fusion calls with transcriptomic data

Issue - State: open - Opened by zhemingfan over 2 years ago
Labels: enhancement

#321 - Convention Deletion Bug

Issue - State: closed - Opened by zhemingfan over 2 years ago
Labels: bug

#320 - Adopt cutesv error handling

Pull Request - State: closed - Opened by zhemingfan over 2 years ago - 1 comment

#319 - Summary module swaps LR to RL orientation

Issue - State: closed - Opened by zhemingfan over 2 years ago - 1 comment
Labels: bug

#318 - Feature/straglr

Pull Request - State: closed - Opened by creisle over 2 years ago - 1 comment
Labels: SV caller

#317 - Straglr conversion support to json for MAVIS annotation

Issue - State: open - Opened by sarahdada almost 3 years ago - 5 comments
Labels: enhancement, long read support, SV caller

#316 - Update README.md

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago - 3 comments

#315 - master back to dev

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment

#314 - Release/v3.0.0

Pull Request - State: closed - Opened by creisle almost 3 years ago - 2 comments
Labels: release

#313 - Bugfix/enforce unique tid

Pull Request - State: closed - Opened by creisle almost 3 years ago - 2 comments
Labels: bug

#312 - Add wheel upgrade recommendations for users

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago - 1 comment

#311 - Make template metadata file optional

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: bug

#310 - Optional parameters are required

Issue - State: closed - Opened by zhemingfan almost 3 years ago
Labels: bug, reference files

#309 - Feature/fix rtd typo

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: documentation

#308 - Feature/reorganize tests

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: bug, refactor

#307 - Modify DGV annotations to more general tab format to support complex SVs

Issue - State: open - Opened by zhemingfan almost 3 years ago
Labels: enhancement, long read support, reference files

#306 - Feature/gff support

Pull Request - State: closed - Opened by creisle almost 3 years ago - 2 comments
Labels: enhancement

#305 - Add local assembly support for breakpoint validation in Nanopore inputs

Issue - State: open - Opened by zhemingfan almost 3 years ago - 1 comment
Labels: enhancement, long read support

#304 - Add support for converting gtf/gff3 files

Pull Request - State: closed - Opened by creisle almost 3 years ago - 2 comments
Labels: enhancement

#303 - Feature/more type annotations

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: documentation, code-style

#302 - Offer support for conversion of gtf and gff files to MAVIS json format

Issue - State: closed - Opened by zhemingfan almost 3 years ago - 7 comments
Labels: enhancement

#301 - Feature/type annotations

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: documentation, code-style

#300 - Feature/sniffle convert handling

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago - 1 comment
Labels: long read support, SV caller

#299 - Feature/stdz logging

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: code-style

#298 - Feature/annotations cleanup

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: enhancement, documentation

#297 - Performance/pyfaidx

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: enhancement, performance

#296 - Bugfix/support validation skip

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: bug, documentation

#295 - Test using pyfaidx instead of Biopython for loading reference FASTA files

Issue - State: open - Opened by creisle almost 3 years ago - 4 comments
Labels: enhancement, performance

#294 - Long reads support for Sniffles files

Issue - State: closed - Opened by zhemingfan almost 3 years ago - 2 comments
Labels: enhancement, long read support, SV caller

#270 - Edited docker container needed for long reads support and added to documentation

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago - 1 comment

#269 - Cleaned up vcf.py and added unit tests for sniffles and cuteSV

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago - 1 comment

#268 - Release/2.2.11

Pull Request - State: closed - Opened by calchoo almost 3 years ago - 1 comment

#267 - Feature/python3.9 10

Pull Request - State: closed - Opened by creisle almost 3 years ago - 2 comments

#266 - Feature/v3 pysam upgrade

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment

#265 - Upgrade Pysam

Issue - State: closed - Opened by creisle almost 3 years ago - 3 comments
Labels: enhancement, devops

#264 - Bugfix/debug dependency install

Pull Request - State: closed - Opened by creisle almost 3 years ago - 1 comment
Labels: devops

#263 - Limit setuptools version

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago

#262 - Add pyproject toml features

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago

#261 - Swap to pyproject.toml and setup.cfg instead of setup.cfg

Issue - State: closed - Opened by creisle almost 3 years ago - 3 comments
Labels: enhancement, devops

#260 - Update setup to include correct mistune version

Pull Request - State: closed - Opened by zhemingfan almost 3 years ago

#259 - Viral integration

Issue - State: open - Opened by oghzzang about 3 years ago - 1 comment
Labels: question, awaiting reply

#258 - TypeError: __init__() missing 1 required positional argument: 'args'

Issue - State: open - Opened by imsarath about 3 years ago - 1 comment
Labels: bug, awaiting reply

#257 - Release/2.2.10

Pull Request - State: closed - Opened by calchoo over 3 years ago - 1 comment

#256 - #253 adding qos priority to slurm

Pull Request - State: closed - Opened by calchoo over 3 years ago - 1 comment

#255 - #254 fix nan values confusing downstream None checks

Pull Request - State: closed - Opened by calchoo over 3 years ago - 1 comment

#254 - TypeError: object of type 'float' has no len()

Issue - State: closed - Opened by calchoo over 3 years ago
Labels: bug

#253 - enable QOS priority setting in slurm

Issue - State: open - Opened by calchoo over 3 years ago
Labels: enhancement

#252 - Fix mavis config TypeError when invalid tool is given

Pull Request - State: closed - Opened by mattdoug604 over 3 years ago - 1 comment

#251 - add formal support for MuTect input

Pull Request - State: closed - Opened by mattdoug604 over 3 years ago - 4 comments

#250 - Fix mavis config TypeError when invalid tool is given

Pull Request - State: closed - Opened by mattdoug604 over 3 years ago - 3 comments

#249 - add formal support for MuTect input

Pull Request - State: closed - Opened by mattdoug604 over 3 years ago - 4 comments

#248 - Feature/test singularity

Pull Request - State: closed - Opened by creisle over 3 years ago - 2 comments

#247 - Feature/split config pkg

Pull Request - State: closed - Opened by creisle over 3 years ago - 1 comment

#246 - Error during MAVIS setup

Issue - State: closed - Opened by sarahdada over 3 years ago - 12 comments
Labels: SV caller

#245 - Convert to pytest syntax

Pull Request - State: closed - Opened by creisle over 3 years ago - 1 comment
Labels: code-style

#244 - Feature/use pandas

Pull Request - State: closed - Opened by creisle over 3 years ago - 1 comment

#243 - Feature/use docker

Pull Request - State: closed - Opened by creisle over 3 years ago - 1 comment
Labels: devops

#242 - Feature/docs and types

Pull Request - State: closed - Opened by creisle over 3 years ago - 1 comment

#241 - Use snakemake to manage mavis scheduling

Pull Request - State: closed - Opened by creisle over 3 years ago - 2 comments

#240 - Annotate sv caller outputs standalone

Issue - State: closed - Opened by MorganHow over 3 years ago - 2 comments
Labels: enhancement, awaiting reply

#239 - #237 Fix paths in annotation doc

Pull Request - State: closed - Opened by calchoo over 3 years ago - 1 comment

#238 - OSX Installation Issues - exited with status error 1

Issue - State: closed - Opened by zhemingfan almost 4 years ago - 6 comments
Labels: bug

#237 - MAVIS annotation page images not loading

Issue - State: open - Opened by zhemingfan almost 4 years ago
Labels: documentation