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HybPiper version 2.1.8

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@chrisjackson-pellicle chrisjackson-pellicle released this 25 Jun 04:08
· 154 commits to master since this release
  • Add new subcommand hybpiper filter_by_length, used to filter the sequence output of hybpiper retrieve sequences by absolute length and/or length relative to mean length in target file representatives. This is done on a per-sample/per-gene basis, rather than the sample-level filtering available in hybpiper retrieve_sequences. See wiki for more information.
  • Update the regex used to check target file fasta header formatting, to capture scenarios where a name contains multiple dashes and also ends with a dash.
  • In the fix_targetfile.py module, remove the import of Bio.Align.Applications.MafftCommandline and call MAFFT via subprocess (see issue#147).
  • In the gene_recovery_heatmap.py module, cast the dataframe from the seq_lengths_file to object dtype to avoid a deprecation warning .
  • Add option --no_heatmap to command hybpiper paralog_retriever (see issue#150).
  • Fix an Exonerate-related debug message in exonerate_hits.py.