v0.5.41

removed dev dependencies from setup.py, removed install reqs from dev-reqs (#158)

v0.5.40

Fixed 10x3p model UMI length and added extra progress printing (#160)

• Changed 10x3p model to have a 12bp UMI.

• Fixing progress bars and counts if a .bai but no .pbi is present.

• Added hard progress logging in sift.

• Fixing unit test for 10x3p model.

• Updated tests to use a single thread.

• fixed various bugs and tests (#163)

Co-authored-by: James Webber [email protected]

v0.5.39

Fixed issue with tags in reads passed through the sift command (#154)

• Removed code that overwrote read tags from the sift model.

v0.5.38

Now points to Jonn's fork of pomegranate to fix heap overflow. (#152)

v0.5.37

Added read ignore list option to sift (#151)

• Added optional parameter for reads to ignore.

v0.5.36

Filter out non-conforming cDNA molecules and write some stats on how they fail the filter. (#149)

• Added sift - a new subcommand to filter out cDNA sequences that do not conform to a specified model.

Co-authored-by: Jonn Smith [email protected]

v0.5.35

Now segment model quality tag (XQ) is segmented along with the SG tag. (#148)

v0.5.34

Added tagfix command to correct position tags post-alignment and other minor updates. (#144)

• Added tagfix command to update reads after alignment.
• Added documentation for tagfix.
• Changed Slide-seq XQ tag to XR to prevent XQ tag from being
  overriden.
• Other minor updates.

v0.5.33

Fixed issues in segment with bulk libraries. (#141)

• Fixed issues in segment with bulk libraries.

• Added better logging in segment for model annotations.
• segment now cues off the model annotation_segments for what annotations are required on output.
• segment now has repeatable order for it tag output (READ_CLIPPED_SEQS_LIST_TAG)
• Split bam_utils.has_cbc_and_umi into two methods.
• Added two new tags for demultiplexing indices in bulk (and other) libraries.
• Now LibraryModel.has_umi_annotation will cue off of both the raw and final UMI tags.
• Now LibraryModel.has_cell_barcode_annotation will cue off of both the raw and final CBC tags.
• Updated all models that annotate UMIs to annotate both the final and raw UMI tags.
• Fixed typo in the mas_15_bulk_10x5p_single_internal array_element_structure.
• Updated tests for segment to validate against expected output for 3 models (mas_15_bulk_10x5p_single_internal, mas_10_sc_10x5p_single_none, mas_15_sc_10x5p_single_none).
• Added unit test file for the model.

v0.5.32

Updated bulk model name to reflect internal multiplexing. (#139)