Code Refactoring:
- Improved code structure, readability and the documentation
- Fixed consistency between counts and read info table
- Improved test coverage by adding more unit and integration tests
Bug fixes:
- Fixed bug where bowtie2 multi-mappers were not properly counted as junction and spanning reads
Other:
- Improved and updated README
- Added snp_or_indel info into read info table
Full Changelog: 0.5.5...0.6.0