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Recent Releases of https://github.com/broadinstitute/strainge

https://github.com/broadinstitute/strainge - StrainGE 1.3.9

  • [FIX] KeyError in straingst cluster with newer version of Pandas (#12)

- Python
Published by lrvdijk over 2 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.9

  • [FIX] KeyError in straingst cluster with newer version of Pandas (#12)

- Python
Published by lrvdijk over 2 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.8

  • [FIX] Incorrect alleles array initialization in StrainGR call (#33)

- Python
Published by lrvdijk over 2 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.8

  • [FIX] Fix incorrect size initialization of the alleles array

- Python
Published by lrvdijk over 2 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.7

Another maintenance release.

  • [FIX] Prevent another potential DivisionByZero

- Python
Published by lrvdijk about 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.6

Maintenance release.

  • [ENH] CI improvements

- Python
Published by lrvdijk about 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.5

Maintenance release

  • [FIX] Prevent division by zero in jaccard computation

- Python
Published by lrvdijk about 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.4

Maintenance release

  • [FIX] Use of old method that didn't exist anymore
  • [FIX] Increase minimum sckit-bio version that fixes an incompatibility with the latest scipy

- Python
Published by lrvdijk about 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.3

  • [FIX] Force SciPy version dependency to be <1.9. Another dependency, scikit-bio, currently has some incompatibilities with SciPy 1.9 (https://github.com/biocore/scikit-bio/issues/1818).

- Python
Published by lrvdijk over 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.2

Another small bugfix release.

  • [FIX] Fix a logging issue with straingst kmerize with filter (-F) enabled. Also give a nicer error instead of an exception if no output filename given (#13, #14).
  • [IMPV] Give a warning if computing k-mer count filter thresholds failed (e.g., if k-mer count distribution is too messy)

- Python
Published by lrvdijk over 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3.1

This is a small bugfix release.

  • [FIX] Fix the parse_straingst function, which now detects whether we're reading a new-style (v1.3) StrainGST TSV or not, and adjusts behavior accordingly. Fixing this function also fixes the straingr prepare-ref command, and now also supports new-style StrainGST files (#11).

- Python
Published by lrvdijk over 3 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.3

Changelog:

  • [FEAT] Add a new StrainGST output mode (enabled with --separate-outputs), which splits the sample statistics and reported strains in separate TSVs. These TSVs are more easily read and combined in Pandas or R (#7).
  • [FIX] Removed straingr view VCF verbose level 2, as pysam does not allow us to write VCF entries with a single allele (#10).

- Python
Published by lrvdijk almost 4 years ago

https://github.com/broadinstitute/strainge - v1.2

Remove unsupported pyvcf dependency for VCF output, and use pysam instead.

Should fix pip install strainge again.

- Python
Published by lrvdijk about 4 years ago

https://github.com/broadinstitute/strainge - v1.1.5

Add NumPy as runtime dependency to fix PyPI package

- Python
Published by lrvdijk over 4 years ago

https://github.com/broadinstitute/strainge - v1.1.4

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - v1.1.3

Fix some edge cases where strains were incorrectly assigned a very low abundance.

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - StrainGE v1.1.2

Don't perform relative abundance calculation if no strains identified.

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - StrainGE v1.1.1

Fix use of wrong variable name

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.1

  • Improved relative abundance calculation
  • Various bugfixes and improvements

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - v1.0.3

  • Fix numpy build dependency (https://github.com/pypa/pip/issues/9542)
  • Fix issue with uninitialized matrix entries in cluster
  • Fix some over-agressive database pruning strategies

- Python
Published by lrvdijk almost 5 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.0.2

Packaging improvements. First Zenodo archived release.

- Python
Published by lrvdijk about 5 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.0.1

Packing improvements

- Python
Published by lrvdijk about 5 years ago

https://github.com/broadinstitute/strainge - StrainGE 1.0

First stable release of StrainGE.

- Python
Published by lrvdijk about 5 years ago