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Commits on May 12, 2025

• add citation

  martinghunt

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Commits on Jan 14, 2025

• Merge pull request #45 from martinghunt/mafft

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  martinghunt

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• update changelog

  martinghunt

  committed
  c4646f6

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• delete temp mafft install files

  martinghunt

  committed
  8bbcb0f

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Commits on Dec 11, 2024

• Fixes to work with viridian

  martinghunt

  committed
  c6c9d9d

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• Add option --use_mafft for global align

  martinghunt

  committed
  84e9923

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Commits on Feb 24, 2023

• Merge pull request #44 from martinghunt/remove_global_aln_indels

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  martinghunt

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• run black

  martinghunt

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  f1599c3

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• Add command line option --indel_max_fix_length

  martinghunt

  committed
  b38c7b0

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• typo min -> max

  martinghunt

  committed
  d81f874

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• Add function remove_small_indels_in_msa

  martinghunt

  committed
  3d615c5

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Commits on Dec 12, 2022

• Fix indel positions and tests

  martinghunt

  committed
  998f853

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• run black

  martinghunt

  committed
  b0ef562

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• normalise indel postiions in global align

  martinghunt

  committed
  5391653

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Commits on Sep 23, 2022

• update changelog

  martinghunt

  authored
  e35a1e9

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• run black

  martinghunt

  committed
  d6af33c

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• Consistent indel calling

  martinghunt

  committed
  015fc37

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Commits on Aug 2, 2022

• Merge pull request #43 from martinghunt/homopolymer_fix

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  martinghunt

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• apt-get update at the start

  martinghunt

  committed
  162be61

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• Upade changelog

  martinghunt

  committed
  9cd9815

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• Add option --hp_min_fix_length to fix homoplymers

  martinghunt

  committed
  4276ce8

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Commits on Jul 19, 2022

• Merge pull request #41 from martinghunt/global_align_end_gaps_fix

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• No end gap penalty for final alignment

  martinghunt

  committed
  014c59e

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Commits on Jul 18, 2022

• Bug fix gaps at end of global alignment

  martinghunt

  committed
  1011439

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Commits on Jul 1, 2022

• Merge pull request #40 from martinghunt/no_norm_global_align

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  martinghunt

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• Skip bcftools norm when using global align method

  martinghunt

  committed
  7a3fa49

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Commits on Jun 20, 2022

• Version bump 0.4.0

  martinghunt

  committed
  de95175

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Commits on May 24, 2022

• Merge pull request #39 from martinghunt/paftools_optional

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  martinghunt

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• Only on master branch and PRs

  martinghunt

  committed
  d088af3

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• Temporarily add paftools_optional branch to trigger github actions build

  martinghunt

  committed
  057e8bf

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• Add github actions

  martinghunt

  committed
  35c3880

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• Only check minimap2 found if using global align

  martinghunt

  committed
  b8ec178

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Commits on Feb 8, 2022

• Add option --use_non_acgt

  martinghunt

  committed
  a6938f9

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Commits on Feb 2, 2022

• Merge pull request #36 from martinghunt/global_align_output

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• run black

  martinghunt

  committed
  7fce292

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