v1.1

Features

• Added support to output unaligned regions in XMFA format (--unaligned). This output format contains a list of all unaligned sequence due to: (i) unrelated sequence, (ii) failure to extend past match (MUM) boundaries/sensitivity limitations, and (iii) subset relationships. This output file is further described in the documentation --> http://harvest.readthedocs.org/en/latest/.
• Updated MUMi parameter to allow for setting a maximum MUMi value to enable bypassing the distribution cutoff

Bug fixes

• Fixed minor bug when parsing multiple GenBank files for harvesttools annotation import
• Updated branch lengths via harvest-tools
• Fixed bug that produced VCF output without repeat filtering, even if enabled
• Fixed issue where empty fasta file was causing index errors
• Fixed exit code to be 0 on –h (Issue #4)
• Updated docs to indicate CXXFLAGS=’-fopenmp’ must be provided to configure for openmp support
• Added support for harvesttools v1.2 (see: https://github.com/marbl/harvest-tools/releases/tag/v1.2)

Changes

• Added –V, --version parameter
• Allow columns with Ns to be marked as pass in VCF
• Allow any fasta file present in -d, regardless of extension, to be used
• Disallow genome file names containing spaces or the following special characters: . , [ ] { } ( ) ! ; " ' * ? < > |
• Default repeat filtering disabled, removing NUCmer dependency. Repeat filtering still possible via bed format support and harvest-tools; see harvesttools documentation for further details.