search

sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
Other
167 stars 52 forks source link

Require pysam>=0.21.0; fix mpileup call #335

Closed martinghunt closed 1 year ago

martinghunt commented 1 year ago

Closes #327

Update to pysam 0.21.0, and fix the bcftools/mpileup call.

The VCF of this updated mpileup has slightly different values (read counts/depths etc changed a tiny bit), but not enough to worry about. Tests/test files updated accordingly.