Merge branch '0.3.3_release' into 'master'

0.3.3 release

See merge request machine-learning/dorado!508

CHANGELOG.md

@@ -2,6 +2,35 @@
 
 All notable changes to Dorado will be documented in this file.
 
+# [0.3.3] (8 Aug 2023)
+
+This release of Dorado introduces improvements to Duplex pair identification for improved duplex yields, faster basecalling on A100 and H100, improvements to modified base calling speed on Apple silicon, and major enhancements to the portability of Dorado binaries.
+
+ * 7307146b55096ee339b1da953b5acf05d112e124 - Major reduction to required GPU memory, especially for A100/H100. Allows greater batch size and consequently improved basecalling speed
+ * 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled.
+ * 39ffb35a90a2389b9f45ba229e908136e770991f - Report the duplex rate percentage
+ * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices
+ * 481438a3415e009174e5f0406d90ad9fd0868339 - Improve performance of basecalling of Fast model on M silicon by 6% by inlining of function used during decode
+ * fe8dbf2af44900bcb60e602653cf01dc119b702b - Improve basecalling stability on Apple silicon by limiting run time of LSTM kernel to avoid CB submission errors
+ * 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy
+ * 752e094b5c4769ff4375249a23ab51d51cf9486b - Upgrade to OpenSSL3
+ * 447b5592758ddf1d26d6ae72a43e836259b53836 - Switch to target-based includes CMake builds - Prevents dependent projects from copying all nclude paths and link libs
+ * b0d10a985e3f4e8d43778367a1710c67d1cde544 - Fix edge case where it is possible to spawn no basecaller worker threads
+ * 1650b83106c3a06e038b98badc3c529e12046630 - Fix issue with inability to find `CUPTI` library during compilation on some systems
+ * e4ba3e55fe3e8cd83d59a2f89a415a63be672b94 - Add missing `SA:Z` tag to alignments generated by Dorado
+ * c5a4cfcabb93084c6d5a4d0e069daefc5cc261b1 - Fix various linker errors
+ * bf72fdd7f2f21491f85930f55f7bf0f9231eac4e - Dorado will error out gracefully if no POD5s are provided
+ * bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux
+ * e14a7e61a6a3e60c0516342df7516b0ba5b92e62 - Improvements to error handling on Apple Silicon devices (Metal command buffer error handling)
+ * ca1d191ffba5cc1397e4b704e3dab1014fa07175 - Improvements to read ids for non-split reads
+ * 5d9238a809656d6fab59713c7ab8346790efd2cc - Revamp `AsyncQueue` interface
+ * 6a3ccb6af5a56527571bf4938447bf85ab5c38e5 - Removed RNA003 model which is obsolesced by RNA004
+ * 1a94facbad52db0908eae3a7fe3242d525cbd6da - Add summary stats and progress bar for basecalling from Fast5
+ * 072ed964276fc8e26f0a705c89055cece900edbf - Add pipeline restart capability and pairing cache retention option to termination
+ * 01acbd5628948bf934985777bcade6bf51103200 - Stop progress bar cutting out near the end of the run
+ * 211968cd38fee6fa7476a4033a2b59ca37b19199 - Add suppression for false-positive vptr issues in older Xcodes
+ * 1e14d2af7bff07c62b0286f17e1d61a7b99390fb - Reduce unnecessary startup cost by setting an upper limit on the maximum batchsize to 10,240
+ * 09c5b28f51707c72df1436967d5da28f850beef1 - Speed up the fixed cost of auto batchsize detection on mGPU systems by running in parallel
 
 # [0.3.2] (13 Jul 2023)
 

README.md

@@ -17,10 +17,10 @@ If you encounter any problems building or running Dorado, please [report an issu
 
 ## Installation
 
- - [dorado-0.3.2-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.2-linux-x64.tar.gz)
- - [dorado-0.3.2-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.2-linux-arm64.tar.gz)
- - [dorado-0.3.2-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.2-osx-arm64.tar.gz)
- - [dorado-0.3.2-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.2-win64.zip)
+ - [dorado-0.3.3-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.3-linux-x64.tar.gz)
+ - [dorado-0.3.3-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.3-linux-arm64.tar.gz)
+ - [dorado-0.3.3-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.3-osx-arm64.tar.gz)
+ - [dorado-0.3.3-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.3-win64.zip)
 
 ## Platforms
 

cmake/DoradoVersion.cmake

@@ -1,6 +1,6 @@
 set(DORADO_VERSION_MAJOR 0)
 set(DORADO_VERSION_MINOR 3)
-set(DORADO_VERSION_REV 2)
+set(DORADO_VERSION_REV 3)
 
 find_package(Git QUIET)
 if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")