Skip to content
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

[WIP] New release #240

Merged
merged 94 commits into from
Feb 15, 2024
Merged

[WIP] New release #240

merged 94 commits into from
Feb 15, 2024

Conversation

HadrienG
Copy link
Owner

@HadrienG HadrienG commented Sep 13, 2023 •
edited
Loading

  • amplicon support
  • performance improvements
  • update doc with new amplicons options
  • style formatting
  • various bug fixes

Tessa Duk and others added 30 commits October 13, 2021 15:10
added test.txt
ed478ec
added possibility of amplicon sequencing and choosing level of read q…
87847ad 
…uality
deleted test.txt
50ec59f
Style changes according to PEP 8
10f0134
removed quality_bin options
a0e0634
improve flow
471ecc2
A2BCR-25 working tests
7112649
@ThijsMaas
Merge pull request #2 from ENPICOM/amplicon
47f16ed 
Amplicon
@ThijsMaas
Fixed tests.
8684d73 
Fixed read length bug.
@ThijsMaas
Removed print statement
b47fdac
@ThijsMaas
Removed unused import statements
53cd244
@ThijsMaas
More code cleanup and test added for amplicon read
456d8c4
@ThijsMaas
Merge pull request #4 from ENPICOM/amp-seq-fix
9cb368d 
Amplicon sequencing cleanup
@ThijsMaas
More option for model generation
a2f2e43
@ThijsMaas
Revert "More option for model generation"
6ca615d 
This reverts commit a2f2e43.
@ThijsMaas
Added default amplicon sequence type
053e45c
@ThijsMaas
Fized default
874af2a
@ThijsMaas
ignore
b7d6915
@ThijsMaas
ignore eggs
9b96034
@gdrosos
Remove unused dependency: future
dd71fab
@gdrosos
Improve formatting
f6d71ad
@HadrienG
unpin deps
97005d0
@HadrienG
migrate to pytest
1e18951
@HadrienG
tomutable -> MutableSeq()
da31452
@HadrienG
fix crash on empty error models
0e9fd7a
@HadrienG
numpt deprecations
f204bd8
@HadrienG
GC -> gc_fraction (biopython deprecation)
a8b354b
@HadrienG
update test matrix + switch github ci to pytest
e2d75bd
@HadrienG
quote version number in ci matrix
9f083c4
@HadrienG
test compat python>3.11
e3b623e
ThijsMaas and others added 19 commits December 19, 2023 16:29
@ThijsMaas
Merge branch 'experiment/fragment-length' into amplicon-performance-a…
e6db5da 
…nd-features
@ThijsMaas
removed import
df39237
@HadrienG
Merge pull request #246 from ENPICOM/amplicon-performance-and-features
fcd3490 
Amplicon performance update and features
@HadrienG
Merge pull request #247 from HadrienG/isize
716a700 
Fix for insert size distributions
@HadrienG
update hiseq and novaseq profiles
aec500d
@HadrienG
Merge pull request #248 from HadrienG/hiseq_novaseq_updates
fb425d1 
update hiseq and novaseq profiles
@StefanLelieveld
added new miSeq and Nextseq error models
2debb42
@StefanLelieveld
added legacy MiSeq error model to fix the test_amp test
fe9c5f4
@ThijsMaas
init storing mutations
8633b9f
@ThijsMaas
format and fix
968d6e7
@ThijsMaas
Fix mut sequence output
823fd75
@ThijsMaas
Add indel storing and fix cleanup
7108eab
@ThijsMaas
comment
87cf604
@ThijsMaas
snp -> sub
886fdea
@HadrienG
Merge pull request #250 from HadrienG/storing-mutations
e8ff9ca 
Saving inserted mutations/sequencing errors to a vcf file
@StefanLelieveld
removed types from precomputed_error_models
cac4365
@HadrienG
Merge pull request #249 from HadrienG/nextSeq-miSeq-error-models
cd714b1 
New MiSeq and NextSeq error models
@HadrienG
comment out raise statement used while debugging
3e25e0a
@HadrienG
sequence_type is optional since meta is the default
ef4908a
@HadrienG
Copy link
Owner Author

HadrienG commented Feb 15, 2024 •
edited
Loading

@ThijsMaas @StefanLelieveld I will make some updates to the documentation today, then unless you have any objections I'll make the 2.0 release

@ThijsMaas
Copy link
Collaborator

@ThijsMaas @StefanLelieveld I will make some updates to the documentation today, then unless you have any objections I'll make the 2.0 release

Great! Let us know if you need any contributions to the documentation from us.

@StefanLelieveld
Copy link
Collaborator

Perfect timing with the release! Today I will complete the submission of the manuscript. Indeed, if you need contributions from me or Thijs let us know.

@HadrienG HadrienG merged commit d25d840 into master Feb 15, 2024
3 checks passed
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.
4 participants
@HadrienG @ThijsMaas @StefanLelieveld @gdrosos