- Improve error message when read length is too short for MM tag
- Fix HP tag parse
- The HP tag parser was not handling all possible binary int representations in BAM format
- Fixes #47
- Support alignment input in CRAM format
- Added progress bar to bam processing step
- Clarified error message when an unmapped alignment file is input
- Fix parse error in MM/ML methylation tags
- An infrequent error occurred when a reverse-mapped read ends (in sequenced orientation) with a C base annotated by the MM tag
- Fixes #41
Initial update to the new binary version of aligned_bam_to_cpg_scores, replacing the similarly named python script
with a faster solution that should be simpler to install and run on linux systems. The new version has
near feature parity with the previous python script. See updated README contents for details.
Final released state of the python implementation prior to new binary v2 release. Includes various minor bug fixes and runtime improvements compared to v1.1.0.
Includes several new features, such as denovo modsites mode, and addresses previously reported bugs
Initial release of the python implementation.