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Switch from HIVSeqinR to HIVIntact#23

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Donaim wants to merge 47 commits intomastercfe-lab/proviral:masterfrom hivintact-final-resultscfe-lab/proviral:hivintact-final-resultsCopy head branch name to clipboard

+753-331

Commits

Commits on Jul 21, 2023

• Add HIVIntact analysis, for #10.

  

  donkirkby

  authored and

  Donaim

  committed
  55536fb

• Install mafft and blast in GitHub Actions, for #10.

  

  donkirkby

  authored and

  Donaim

  committed
  1d54987

• Enable more checks in HIVIntact

  Donaim

  committed
  6b77cac

• Specify writable workdir for hivintact

  Donaim

  committed
  28ae510

• Update dependencies in the README file

  Donaim

  committed
  9aadb15

• Add HIVIntact to our python dependencies

  Donaim

  committed
  7cfd902

• Generate table_precursor table from hivintact output

  Donaim

  committed
  7f4eba1

• Remember intact sequences

  Donaim

  committed
  891b4a8

• Update hivintact errors list

  Donaim

  committed
  b88c4e4

• Improve hivintact errors priority and translation

  Donaim

  committed
  0bca5be

• Bump HIVIntact from cfe-1.2 to cfe-1.3

  Donaim

  committed
  6ad62bd

• Generate proviral_landscape for HIVIntact runs too

  Donaim

  committed
  7e15cf0

• Singularity: make HIVIntact the default and the only app

  Donaim

  committed
  719a14b

Commits on Jul 24, 2023

• Switch to csv outputs in HIVIntact

  Donaim

  committed
  a1294df

• Rename "hivseqinr_results_tar" argument to "detailed_results_tar"

  Donaim

  committed
  5c378e9

Commits on Sep 19, 2023

• Bump HIVIntact from 1.3 to 1.4

  Donaim

  committed
  56d06d9

• Do not translate HIVIntact errors to HIVSeqinR ones

  Donaim

  committed
  eae7b0f

Commits on Sep 20, 2023

• Fix table precursor construction

  Donaim

  committed
  775f100

• Add missing codes to the HIVINACT_ERRORS_TABLE

  Donaim

  committed
  120fe49

Commits on Mar 7, 2024

• fix the check for when to use HIVSeqinR results

  Donaim

  committed
  5367241

• Various code improvements

  Donaim

  committed
  95ae330

Commits on Jul 8, 2024

• Switch to CFEIntact

  Donaim

  committed
  9d725a1

• Update Pipfile.lock

  Donaim

  committed
  1c5eca6

• Update cfeintact command

  Donaim

  committed
  3a0bf9d

• Bump CFEIntact version

  Donaim

  committed
  2345afa

• Use CFEIntact's python API instead of operating system's shell

  Donaim

  committed
  bc1d1ea

• Do not install cfeintact twice

  Donaim

  committed
  514221c

Commits on Jul 9, 2024

• Fix column name of CFEIntact errors.csv

  Donaim

  committed
  1819951

• Improve reading of .SAM files

  Show description for 05aac4f
  Donaim

  committed
  05aac4f

• Small refactoring of utils.py

  Donaim

  committed
  49022e0

• Add a separate proviral_landscapes.py script

  Donaim

  committed
  3d53ae8

• Fix defect column value for intact sequences

  Donaim

  committed
  c1698b4

• Move all landscapes stuff to landscapes.py

  Donaim

  committed
  0925e73

Commits on Jul 12, 2024

• Bump CFEIntact version

  Donaim

  committed
  c1ed309

Commits on Jul 16, 2024

• Bump CFEIntact version

  Donaim

  committed
  eea0151

Commits on Jul 26, 2024

• Bump CFEIntact version

  Donaim

  committed
  6d18b36

Commits on Jul 27, 2024

• Bump CFEIntact version

  Donaim

  committed
  2b9a7b6

• Update CFEIntact errors table

  Donaim

  committed
  e68bfe5

Commits on Jul 28, 2024

• Bump CFEIntact version

  Donaim

  committed
  75fcf9c

• Bump CFEIntact version

  Donaim

  committed
  731556b

Commits on Jul 29, 2024

• Fix landscape generation based on sample_name

  Donaim

  committed
  9454ade

• Fix ignoring intact sequences in table_precursor and landscapes_plots

  Donaim

  committed
  87aaffb

• Bump CFEIntact version

  Donaim

  committed
  5fc9340

Commits on Jul 30, 2024

• Bump pandas version

  Donaim

  committed
  28950eb

• Fix reading of SAM files

  Show description for 6098677
  Donaim

  committed
  6098677

• Add missing UnknownNucleotide CFEIntact defect code

  Donaim

  committed
  9f874da

• Add missing SequenceDivergence CFEIntact defect code

  Donaim

  committed
  92c8d39