v0.6.4

Exposed more correct_umi parameters (#184)

• Exposed parameters for umi_correct
• Updated correct_umi docs.

v0.6.3

get_segments(...) now returns three things rather than two (#183)

v0.6.2

Add a pseudocount for num_reads to prevent a rare divide-by-zero error (#182)

v0.6.1

Fix parsing of zero-length segments (#181)

v0.6.0

Kvg hierarchical models (#173)

• Refactored models into a hierarchical format

• Updated inspect to have a BLAST-like display. Now includes option to ingest a second bam file to visualize corrected CBC and UMI.

• Sift now verifies that the entirety of the cDNA structure is present.

• Added SC tag, containing segment cigar strings.

• Added umi_correct tool. (#172)

• Added sift documentation

• Changed default # threads for correct to 1 because of memory use.

• Refactoring into a hierarchical HMM constitutes a #minor version bump.

• Removed scsplit.

• Updated annotate to only read in one model from a bam file.

• Further updates for PR review.

• Replaced mas10 test data.

• Regenerated test data.

• Now only supports one model per bam file.

Co-authored-by: Jonn Smith [email protected]
Co-authored-by: James Webber [email protected]
Co-authored-by: BumpVersion Action bumpversion@github-actions
Co-authored-by: Jonn Smith [email protected]

v0.5.46

pass bam header as dict for subprocesses (#168)

• fix syntaxwarning in python 3.8: is not "" is not recommended

• changed create_bam_header_with_program_group to return a dict, for use with subprocesses

v0.5.45

bump python req (#169)

• fix syntaxwarning in python 3.8: is not "" is not recommended

• bumped max python version to <3.8 rather than <=3.7.9

v0.5.44

fix syntaxwarning in python 3.8: is not "" is not recommended (#167)

v0.5.43

Refactor tests to be more independent (#165)

• converting tests to use pathlib.Path instead of os
  converting stream tests to use CliRunner with input=fh

• removed slow fixtures, added intermediate files for filter
  tweaked some test code to look more consistent

• use isolated_filesystem to not keep test output files

• created a new fixture for test_correct and made the piped version of the test work

v0.5.42

An almost-entirely pointless change: tweaked how subcommands were added at runtime (#159)