v0.4.0

[0.4.0] (9 Oct 2023)

This release of Dorado introduces barcode demultiplexing, barcode trimming, simplex read splitting, and updated models for calling 6mA and 5mC/5hmC modified bases. Furthermore, it contains improvements to duplex pairing for increased yield, basecalling speed enhancements and reductions to memory consumption, bug fixes, and additional tests for enhanced stability.

• e836fa4 - New all-context and updated CpG-context 5mC/5hmC models
• e4aca76 - Handle custom batch sizes that exceed maximum safe batch size
• ad463ea - Updated all-context 6mA model
• 21d25a3 - SSL host verification enabled and dorado download HTTPS proxy support improved
• 8ae95e7 - Enable simplex read splitting
• 1210607 - Fix mean-qscore calculation with trimming
• d27666e - Beam search optimisation
• 46e68c1 - Report the error we get back from httplib if a download fails
• 89db1e1 - Support ChEBI codes for modified bases
• 92097ca - Add options to dorado aligner
• 4cb9862 - Fix Linux ccache usage
• 692ecd3 - Fixed issues with internal representation of signal during duplex calling
• 80efe8c - Fix std::logic_error (issue #205)
• d92547a - Make CUDA kernel profiling to stderr available via --devopts
• 69bf701 - Refactoring to support further duplex developments
• 510e2e9 - Verify models when downloaded using dorado download
• 12476ee - Improve memory usage diagnostics in Metal
• 3172413 - Fix non-determinism in selecting matrix multiplication sub-routine during basecalling
• f14b418 - Provide NVIDIA driver version in server API
• 207871e - Use DORADO_GPU_BUILD rather than !defined(__x86_64__)
• d16ccbe - Get tests that use CUDA working when ASAN is enabled
• 41bfb99 - Update duplex pairing heuristics to improve duplex yield
• 87c2c6e - Change ReadPair to take full ownership of its data, and drop ReadPtr
• 88aa9f3 - Only use pre-compiled headers if ccache isn't available
• c04c145 - Bump Koi version to 0.3.9
• 6b8064d - Separate out data shared by both Duplex and Simplex reads into ReadCommon class
• 34e9b55 - Flip RNA signal for modified basecalling
• 636ac83 - CRFModel: Update to use KoiActivation and corresponding Koi host functions
• cd50a01 - Add parent ID tag (pi:Z:parentid) to split reads so that original read can be inferred
• 2956bf6 - Add support for barcode trimming
• 92dee85 - Fix segfault in modified basecalling
• fe22d21 - Add support for read groups with barcoding
• 2f69da6 - Allow basecalling from single files rather than a directory
• c22e46f - Support ambiguous motifs for modified basecalling
• 882da60 - Refactor to create separate utils lib target
• b792bba - Enforce const-west style via clang-format
• 611a4ea - Skip code signing on x64 to prevent crashes
• a6a1902 - Fix various deficiencies of the iOS htslib build
• 5ff8034 - Add barcode check for both ends
• e42b8c8 - Remove mux from pairing cache key to reduce memory consumption by up to 4x
• 93d052b - Setup signing of executables on macOS
• a45b97c - Bump RNA004 models to V3.0.1 with corrected scaling
• 7e152fd - Reinstate ReadFilterNode tests
• c3e412e - Add duplex commandline test
• 3ba422b - Don't perform adapter trimming on RNA signals
• 066b815 - Add barcoding support to Dorado
• 09cc44f - Add unit test coverage report generation
• b2e54b8 - Fix typo for 5fC modification
• 829dba3 - Enforce that values passed to a sink are mutable rvalues
• 8aa7722 - Remove dependence of dorado_lib on dorado_models_lib
• cd6d2bf - Extend the lifetime of the NNTasks in the metal backend
• abed8ee - Bug fixes for iOS build
• 64b3ae3 - Clarify --min-qscore option in help
• 225a153 - Further restrict Metal kernel run times to improve stability of basecalling on Apple silicon
• 3ae95e4 - Refactor modified basecalling code
• 8ec58f0 - Option for --guard-gpus no longer used in duplex
• 1f3cade - Add CUDAGuard before cache clear to reduce CUDA memory consumption
• dae5e30 - Move ModBaseCallerNode to using an unordered_set for working reads, like BasecallerNode
• b43adfa - Improvements to pipeline API