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[WIP] New release#240

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HadrienG merged 94 commits intomasterHadrienG/InSilicoSeq:masterfrom devHadrienG/InSilicoSeq:devCopy head branch name to clipboardFeb 15, 2024

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Commits on Oct 13, 2021

• added test.txt

  

  Tessa Duk

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Commits on Oct 14, 2021

• added possibility of amplicon sequencing and choosing level of read quality

  

  Tessa Duk

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• deleted test.txt

  

  Tessa Duk

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Commits on Oct 28, 2021

• Style changes according to PEP 8

  

  Tessa Duk

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Commits on Oct 29, 2021

• removed quality_bin options

  

  Tessa Duk

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• improve flow

  

  Tessa Duk

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• A2BCR-25 working tests

  

  Tessa Duk

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Commits on Feb 16, 2022

• Merge pull request #2 from ENPICOM/amplicon

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  ThijsMaas

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Commits on Mar 9, 2022

• Fixed tests.

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  ThijsMaas

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Commits on Oct 5, 2022

• Removed print statement

  ThijsMaas

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Commits on Nov 7, 2022

• Removed unused import statements

  ThijsMaas

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• More code cleanup and test added for amplicon read

  ThijsMaas

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• Merge pull request #4 from ENPICOM/amp-seq-fix

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  ThijsMaas

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Commits on Jan 13, 2023

• More option for model generation

  ThijsMaas

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Commits on Jan 25, 2023

• Revert "More option for model generation"

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  ThijsMaas

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Commits on Feb 6, 2023

• Added default amplicon sequence type

  ThijsMaas

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• Fized default

  ThijsMaas

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Commits on Jul 12, 2023

• ignore

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Commits on Jul 13, 2023

• ignore eggs

  ThijsMaas

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Commits on Aug 11, 2023

• Remove unused dependency: future

  gdrosos

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• Improve formatting

  gdrosos

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Commits on Sep 12, 2023

• unpin deps

  HadrienG

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Commits on Sep 13, 2023

• migrate to pytest

  HadrienG

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• tomutable -> MutableSeq()

  HadrienG

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• fix crash on empty error models

  HadrienG

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• numpt deprecations

  HadrienG

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• GC -> gc_fraction (biopython deprecation)

  HadrienG

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• update test matrix + switch github ci to pytest

  HadrienG

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• quote version number in ci matrix

  HadrienG

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• test compat python>3.11

  HadrienG

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• use the correct dict in draft/coverage mode

  HadrienG

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• version bump (1.6.0)

  HadrienG

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• add sequence_type arg to small generate test

  HadrienG

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• Merge branch 'master' into ENPICOM-amp-seq-fix

  HadrienG

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• Merge pull request #239 from HadrienG/ENPICOM-amp-seq-fix

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  HadrienG

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• Merge pull request #238 from gdrosos/master

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  HadrienG

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Commits on Sep 14, 2023

• Merge branch 'master' into updateMaster

  ThijsMaas

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• Fix test

  ThijsMaas

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• Merge pull request #8 from ENPICOM/updateMaster

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  ThijsMaas

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Commits on Sep 21, 2023

• Added readcounts parser. Added readcounts file input, added alternative n_reads flow for readcounts. Added test.

  ThijsMaas

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• Merge remote-tracking branch 'upstream/dev' into improve-amplicon-seq

  ThijsMaas

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Commits on Oct 6, 2023

• Merge pull request #242 from ENPICOM/improve-amplicon-seq

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  HadrienG

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Commits on Nov 13, 2023

• Style update with Black, isort and flake8.

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  ThijsMaas

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Commits on Nov 22, 2023

• restore main

  ThijsMaas

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• restore main functionality

  ThijsMaas

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Commits on Nov 23, 2023

• Added new dev dependencies

  ThijsMaas

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• Separate pipenv run commands

  ThijsMaas

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• Black requirements

  ThijsMaas

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• Split app.py

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  ThijsMaas

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• Single temp file for each cpu, reduces concat work

  ThijsMaas

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Commits on Nov 24, 2023

• Also added tomli for black on python versions < 3.11

  ThijsMaas

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• Dont run codecov on forks

  ThijsMaas

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• Merge branch 'styling-formatting-rework' into amplicon-performance-and-features

  ThijsMaas

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• remove line

  ThijsMaas

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• Merge pull request #245 from ENPICOM/styling-formatting-rework

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  HadrienG

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• Warning instead of assertion

  ThijsMaas

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• Remove joblib

  ThijsMaas

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Commits on Nov 27, 2023

• info to debug

  ThijsMaas

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  f5a4e96

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• Fix coverage variable bug

  ThijsMaas

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• fix n_reads vs n_read_pairs issue

  ThijsMaas

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• Fix unrounded issue

  ThijsMaas

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Commits on Nov 28, 2023

• fix cap of 500 on insert size distribution

  HadrienG

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• linting

  HadrienG

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Commits on Nov 29, 2023

• Added new fragment length params and fixes tests

  ThijsMaas

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Commits on Nov 30, 2023

• fix isort

  ThijsMaas

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Commits on Dec 19, 2023

• docstrings

  ThijsMaas

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• removed list()

  ThijsMaas

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• Restored default functionality. Add logging

  ThijsMaas

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• Merge branch 'experiment/fragment-length' into amplicon-performance-and-features

  ThijsMaas

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• removed import

  ThijsMaas

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Commits on Jan 8, 2024

• Merge pull request #246 from ENPICOM/amplicon-performance-and-features

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  HadrienG

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• Merge pull request #247 from HadrienG/isize

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  HadrienG

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Commits on Feb 1, 2024

• update hiseq and novaseq profiles

  HadrienG

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• Merge pull request #248 from HadrienG/hiseq_novaseq_updates

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  HadrienG

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• added new miSeq and Nextseq error models

  StefanLelieveld

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• added legacy MiSeq error model to fix the test_amp test

  StefanLelieveld

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Commits on Feb 5, 2024

• init storing mutations

  ThijsMaas

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• format and fix

  ThijsMaas

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• Fix mut sequence output

  ThijsMaas

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• Add indel storing and fix cleanup

  ThijsMaas

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• comment

  ThijsMaas

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Commits on Feb 7, 2024

• snp -> sub

  ThijsMaas

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Commits on Feb 12, 2024

• Merge pull request #250 from HadrienG/storing-mutations

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  HadrienG

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• removed types from precomputed_error_models

  StefanLelieveld

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Commits on Feb 13, 2024

• Merge pull request #249 from HadrienG/nextSeq-miSeq-error-models

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  HadrienG

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• comment out raise statement used while debugging

  HadrienG

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• sequence_type is optional since meta is the default

  HadrienG

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Commits on Feb 15, 2024

• ignore case in moel names

  HadrienG

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• update iss generate doc

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• update readthedocs config

  HadrienG

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• update readthedocs config

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• update model qualities and read length

  HadrienG

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• remove todo ...

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• add thijs and stefan as authors on the doc website

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