Fixed - Added missing default option to arparse instance in smolecule command. - Copy across contigs with no aligned reads during `medaka stitch`. - Quote strings in bash scripts to allow filenames with spaces.
1.3.2
Fixed - Typo in `medaka_consensus` causing a syntax error.
1.3.1
Added - Option to output VCF record for all reference positions from `medaka variant`.
1.3.0
Changed - Haploid variant calling reverted to old-style methodology. Fixed - Early exits on error in `medaka_consensus` and `medaka_variant`. - `INFO` field of VCFs is now correctly `.` when empty.
1.2.6
Changed - Rewrote inference data loading code for clarity. - Removed pinned BioPython pin. - Formally update htslib program requirements to 1.11. Removed - Support for Python 3.5. Fixed - Corner case in consensus stitching.
1.2.5
Fixed - Variant annotation when more than one CHROM record in VCF.