StrainGE 1.3.9

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

StrainGE 1.3.8

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

StrainGE 1.3.7

Another maintenance release.

• [FIX] Prevent another potential DivisionByZero

StrainGE 1.3.6

Maintenance release.

• [ENH] CI improvements

StrainGE 1.3.5

Maintenance release

• [FIX] Prevent division by zero in jaccard computation

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

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 (scikit-bio/scikit-bio#1818).

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)

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).

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).