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xlavir v0.5.2 (2021-11-09) - bugfix patch release
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@peterk87 peterk87 released this 09 Nov 13:19
· 22 commits to master since this release
v0.5.2
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Learn about vigilant mode.

Fixes and changes from PR #15

Fixes:

  • low coverage coordinate output off by one (xlavir.tools.mosdepth.get_interval_coords_bed)
  • error on no Pangolin reports found (e.g. non-SARS-CoV-2 report) (xlavir.tools.pangolin.get_info)
  • user QC thresholds not being used (xlavir.xlavir.run)
  • not showing all QC fail comments (xlavir.qc.create_qc_stats_dataframe)
  • consensus sequences being too long for Excel cell character limit (32,767 characters); longer sequences are chunked into 80 character segments with one segment per line in consensus sheet (xlavir.tools.consensus.read_fasta)

Changes:

  • Ignore and skip unsupported VCFs instead of throwing NotImplementedError (xlavir.tools.variants.get_info)
  • In consensus sheet, only add QC comments on FASTA header rows if necessary (xlavir.io.xl.add_comments)
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