Changes
- Added support for current PacBio BAM format of alignments (legacy *.cmp.h5 still supported)
- Moved documentation to readthedocs
- Improved installation procedure by bundling installation of Python dependencies
- Deprecated the --align option due to limited use-cases and limited support with aligned BAM inputs
- Cleaned up codebase
Citation
John Beaulaurier, Xue-Song Zhang, Shijia Zhu, Robert Sebra, Chaggai Rosenbluh, Gintaras Deikus, Nan Shen, Diana Munera, Matthew K. Waldor, Andrew Chess, Martin J. Blaser, Eric E. Schadt & Gang Fang. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat. Commun. 6, 7438 (2015).