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fix handling of ambiguous sites in edge cases

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@rneher rneher released this 06 May 12:44
· 552 commits to master since this release
v0.5.6
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This release is part bug-fix and part adding functionality to allow recovery of ambiguous bases for Fasta input (previously only available for VCF input).

  • Fix handling of ambiguous sites in compressed alignment, see PR#87 for a detailed description.
  • Enabling Recovery of Ambig Sites for Fasta-Input
    recover_var_ambigs() function has added functionality so that when called it not only recalculates the mutations, but also replaces node.sequence with a reconstructed sequence that includes ambiguous bases present in the original.
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