v0.3.2

[0.3.2] (13 Jul 2023)

This release of Dorado introduces basecalling models for the RNA004 chemistry, better identification of duplex read pairs and improved read Q score estimation. It also incorporates various important bug fixes which improve the stability and usability of Dorado.

• 4ce0cb0 - Add RNA004 models
• 24b6c4e - Retry basecalling on CUDA OOM after clearing allocator cache
• 3897ba5 - Add troubleshooting guide to README.md
• 9d55b44 - Fix bug with resume file header parsing
• f9289e2 - Improvements to duplex read splitting algorithm for improved accuracy
• 2869dbc - Solve memory leak during modified base calling
• 4d8ca17 - Fix race condition which was introducing nondeterministic basecalls
• ddb6f71 - Fix aligner regressions from pipeline change
• a57987f - Add R941 v3.3 5mCG 5hmCG models
• ba40e53 - Refactor of basecalling pipeline management strategy
• 26be1a0 - Query enabled Apple silicon cores, not all cores
• 185058e - Replace empty value with "Unknown" in read group tags to satisfy SAM specification
• d953f33 - Add time ordered reads pair cache strategy to PairingNode to support greater variety of ways to run duplex basecalling
• d2700dd - Fix to enable Duplex basecalling on CPU. This will be slow but functionally correct.
• f5ccd0d - Add channel/mux/start_time/start_time_ms to the duplex read
• 0ee5a9b - Fixes to host OOM issues
• 2fe609b - Exclude some non-informative bases at read start from mean qscore calculation
• 3090328 - Fix no output when stdout == stderr and both are the tty
• 7e70de7 - Add support for compute 6.1 (GTX 1080 Ti) plus handling CUDA failures
• 995d0fb - Runner creation refactor
• 9d21036 - Modbase smoke test BLAS fix
• 30658c4 - Add ScopedAutoReleasePool to prevent autorelease leaks on MacOS
• cf502e3 - Update sample rate check to allow some tolerance