Releases | Open Source Science

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 jonn-smith@users.noreply.github.com Co-authored-by: James Webber jamestwebber@users.noreply.github.com Co-authored-by: BumpVersion Action bumpversion@github-actions Co-authored-by: Jonn Smith jonn@broadinstitute.org

- Python
Published by github-actions[bot] over 3 years ago

https://github.com/broadinstitute/longbow - v0.5.46

pass bam header as dict for subprocesses (#168)

fix syntaxwarning in python 3.8: is not "" is not recommended
changed createbamheaderwithprogram_group to return a dict, for use with subprocesses

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.44

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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.42

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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.41

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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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 jamestwebber@users.noreply.github.com

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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.

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.38

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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.37

Added read ignore list option to sift (#151)

Added optional parameter for reads to ignore.

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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 jonn@broadinstitute.org

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - v0.5.35

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

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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.

- Python
Published by github-actions[bot] almost 4 years ago

https://github.com/broadinstitute/longbow - 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 (READCLIPPEDSEQSLISTTAG)
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.

- Python
Published by github-actions[bot] about 4 years ago

https://github.com/broadinstitute/longbow - v0.5.32

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

- Python
Published by github-actions[bot] about 4 years ago

https://github.com/broadinstitute/longbow - v0.5.31

Updated the mas10 model segment names. (#138)

- Python
Published by github-actions[bot] about 4 years ago

https://github.com/broadinstitute/longbow - v0.5.30

Updated default models to have more intuitive names (#137)

Updated default models and segment names.
Removed old / vestigial models.
Minor renames for some models.
Changed all Ancient Roman segments to have more descriptive names.
Updated tests to reflect the models currently baked into longbow.
Other minor refactoring.

- Python
Published by github-actions[bot] about 4 years ago

https://github.com/broadinstitute/longbow - v0.5.29

Fixed CD bumpversion github action

Now using jasonamyers/github-bumpversion-action@v1.0.4 which includes a fix for the patch that was introduced because of https://github.blog/2022-04-12-git-security-vulnerability-announced/

Added VIM to docker image (#134)

Added vim to docker container
Updated Dockerfile to allow for new versions of packages.
Added in samtools library dependencies for new pysam.
Pinned pysam version.
Fixed the longbow correct tests to work with padded data.

Hotfix for some correct stats and parsing model info from bam headers (#126)

Fixing barcode corrected stats in the case of padded barcodes.
Fixed header parsing for model information.

- Python
Published by github-actions[bot] about 4 years ago