v0.1.4

• Multiple bug fixes.

• Reworked filter_contigs

  • Added a 'lite' mode for filter_contigs where it just checks for v/j/c gene call mis-match. Toggled with simple = True.
  • Split the filtering between and productive and non-productive contigs:
    • Replaced rescue_igh option with keep_highest_umi option which applies to all locus.

• Updated the isotype dictionary to allow for mouse genes which seems to address #70.

• Added more tests.

• Updated ddl.pp.calculate_threshold to reflect the updated shazam's disToNearest functionalities.

• Added sanitization functions to check for data stored in dandelion is relatively compliant with airr-standards (barring missing columns from 10x's data or scirpy's transferred data.

• Updated transfer of boolean columns to anndata to be stored as string rather than category during filter_contigs.

• Updated h5py requirement to be >=3.1.0. 2.10.0 should still work though. This led to some updates to how AnnData was storing info from dandelion after filter_contigs. Should update the tutorial in the next version.

TODO before merging:

• complete 10x output parser
• address #54

Ongoing:

• Slight issue with integration with scirpy scverse/scirpy#283, but should be solved. Will edit tests when the the pr is merged.

• Need to create larger fixtures to get access to some steps within the functions.

• Also need to test a mouse fixture. Maybe i should merge a large mouse fixture?