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Version 0.9.8
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@etal etal released this 01 Jun 19:39
· 226 commits to master since this release
v0.9.8
b218280

Continuing a focus on stability and compatibility with other software:

  • Support for reading CRAM files with an optional user-provided local FASTA
    file for the reference genome sequence. (#555; thanks @johnegarza)
  • Call Rscript subprocess with safer flags for the R environment. Previously,
    --vanilla ignored R environments with the library path in a non-default
    location specified in the user's .Rprofile. Now, --no-restore and
    --no-environ ensure a clean environment but still respect the user's
    .Rprofile settings beyond that. (#491; thanks @pablo-gar)
  • Compatibility with the latest release of pandas. (#502, #523)

This release also fixes some regressions reported since the release of CNVkit
0.9.7 (which introduced a number of new performance optimizations).

  • scatter: A bug when plotting a region of a chromosome. (#536, #457; thanks tskir)
  • scatter: An IndexError when plotting entire chromosomes, e.g. chr7. (#541,
    #461, #535; thanks @tskir)
  • fix: A bug that occurred after automatic bias corrections, introducing
    NaN-valued rows in placed of rejected bins, leading to a downstream crash in
    CBS segmentation. (#551, #436, #547; thanks @johnegarza)
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