[0.3.1] (26 Jun 2023)

This is a minor release of Dorado. It introduces various bug fixes, as well as performance and usability enhancements. Of particular note, this release introduces the ability to resume simplex basecalling if interrupted, adds RNA002 models, improves the speed of modified base calling and duplex calling, and solves an issue whereby Dorado users were experiencing segmentation faults on version of Linux with older glibc.

• 08218cd - Added --resume-from for simplex basecalling.
• 790a002 - Mitigate simplex scaling performance regression on mGPU systems.
• e0c1beb - Turn off all logging if stdout and stderr point to the same file to avoid curruption
• ae1e5e3 - Support for http proxies in dorado download via dorado_proxy and dorado_proxy_port envvars.
• a62465c - Added warning if user tries to use duplex with fast model
• 99f7483 - Improved error reporting on OSX
• 4f61c18 - Removed source of error related to race-condition
• b1405ab - Added new RNA002 models with V3 architecture
• e75e327 - Aligner throws error when reference path does not exist
• a977916 - Refactor of progress bar and account for filtered reads
• f162705 - Fix the build when compiling with VS2017
• 84ecf32 - Update Koi to v0.3.3
• d6463b3 - Refactor aligner/hts nodes
• c46a2a3 - Fix segfault on Ubuntu 16.04
• 2a96f89 - Improve performance of mod base calling by changing encoding format
• 612ba20 - Node performance stats monitoring
• dc9ea3b - CRFModel: perform clamp on torch tensors in-place. Use torch::InferenceMode
• bf18314 - Solve various bugs in duplex pairing algorithm
• 164ca6e - Add support for running sanitizers as part of CI
• 379fc21 - Add RG tag to duplex pipeline
• 68b5b81 - Add missing dependencies for Mac
• 628722d - Add error checking to pod5 api calls
• c48ab08 - Progress bar fixes for Windows
• ce68b55 - Update metal-cpp so we can make use of NS::SharedPtr<>
• 53aec51 - Update Readme to include roadmap
• 5ea6705 - Adding smoke tests