Skip to content

Preparation for Bioc submission #54

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
mbstadler merged 45 commits into from
Aug 8, 2025
Merged

Preparation for Bioc submission #54

mbstadler merged 45 commits into from
Aug 8, 2025

Conversation

@csoneson
Copy link
Collaborator

@csoneson csoneson commented Jun 2, 2025 •
edited
Loading

TODOs:

  • Rename master branch to devel
  • Add example to linkMultipleVariants() (or consider whether the function should be removed)
  • Remove the deprecated arguments (cause warnings in BiocCheck)

csoneson added 30 commits June 1, 2025 16:25
@csoneson
Remove dependency on deprecated zlibbioc
c28f1c8
@csoneson
Add BiocManager to Suggests to address R CMD check warning
bf206bb
@csoneson
Escape braces in documentation
370e6ab
@csoneson
Test against Bioc devel on GHA
7e790a3
@csoneson
Depend on R>=4.5.0
9d6d7c9
@csoneson
Add URL and BugReports fields
dcf2136
@csoneson
Cleanup, utils.R
03bab67
@csoneson
Cleanup, vignette
7064338
@csoneson
Cleanup, generateQCReport.R
ef8df50
@csoneson
Cleanup, plotTotals.R
838bf64
@csoneson
Cleanup, relabelMutPositions.R
bed42f6
@csoneson
Cleanup, summarizeExperiment.R
5e2ca1e
@csoneson
Cleanup, calculateFitnessScore.R
cbd2cd5
@csoneson
Cleanup, calculateRelativeFC.R
f675a64
@csoneson
Cleanup, plotResults.R
35e9172
@csoneson
Cleanup, collapseMutantsByAA.R
2a6d658
@csoneson
Cleanup, digestFastqs
82071a8
@csoneson
Cleanup, linkMultipleVariants.R
76d024b
@csoneson
Add import
1c3a48a
@csoneson
Cleanup, plotDistributions.R
1255ed0
@csoneson
Cleanup, plotFiltering.R
c5a9cb6
@csoneson
Cleanup, plotPairs.R
d6c1453
@csoneson
Swap %>% for |>
e71468f
@csoneson
Import rowData<-
182bebc
@csoneson
Bump version, update NEWS
f7950c2
@csoneson
Use expect_true(is_ggplot(.)) instead of expect_s3_class(., "ggplot")
1560e1e
@csoneson
Add chunk labels to vignette
2d72661
@csoneson
Fix a couple of long lines
3b1928b
@csoneson
Remove deprecated arguments to digestFastqs
2975358
@csoneson
Set default values of collapse parameters
5579e3d
@csoneson csoneson marked this pull request as ready for review July 31, 2025 18:13
csoneson and others added 14 commits August 4, 2025 12:33
@csoneson
Harmonize findClosestRefSeq with findClosestRefSeqEarlyStop (only com…
96ec0b3 
…pare until the end of the shortest of the variable and wildtype sequences)
@mbstadler
ignore test coverage for write failures
80c6260
@mbstadler
export and test C complement function
ec1a439
@mbstadler
ignore unit test coverage of hard/impossible to trigger failures in r…
fb60010 
…eached_end_of_file and get_next_seq
@mbstadler
ignore hard to trigger file open error for test coverage in openFastq
03e225c
@csoneson
Add some more tests, ignore lines that are not recognized by covr
20b42b3
@mbstadler
Merge branch 'bioc' of github.com:fmicompbio/mutscan into bioc
24a66e7
@mbstadler
add test_compareToWildtype and corresponding unit tests
8219b74
@mbstadler
ignore coverage of lines that are unreachable through the R API
544a5a5
@mbstadler
ignore coverage for lines that are hard to trigger in tests in variou…
d9c4704 
…s helper functions
@mbstadler
add test coverage of digestFastqsCpp
a1525ce
@mbstadler
add unit test coverage for makeBaseHGVS, makeAAHGVS and groupSimilarS…
22fd02f 
…equences
@csoneson
Skip likely unreachable sections
ccb6a0c
@csoneson
Add unit tests
cc199f8
@mbstadler mbstadler merged commit 189fc1c into master Aug 8, 2025
6 checks passed
@mbstadler mbstadler deleted the bioc branch August 8, 2025 06:09
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@csoneson @mbstadler