From b3644668bdf7ef1b97a9d8d43dac09be11aef393 Mon Sep 17 00:00:00 2001 From: Christopher Seymour Date: Thu, 1 Aug 2024 10:30:21 +0000 Subject: [PATCH] Merge branch 'slee/release-v0.7.3' into 'master' v0.7.3 release See merge request machine-learning/dorado!1135 (cherry picked from commit c34a8b354e3f58f851ae6fd187844f2198849fc1) b34c5d0e v0.7.3 release --- CHANGELOG.md | 13 +++++++++++++ README.md | 8 ++++---- cmake/DoradoVersion.cmake | 2 +- 3 files changed, 18 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cd05858b4..9c0691489 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,19 @@ All notable changes to Dorado will be documented in this file. +# [0.7.3] (1 Aug 2024) + +This release of Dorado updates `dorado correct` to fix handling of high copy repeats and avoid shutdown hanging. It also includes `dorado demux` improvements to reduce false matches in midstrand barcode detection and ensure correct file naming, along with other fixes. + +* 5dc78ab677fbf4c67467ecfc4fb89438dc68c8d4 - Remove limit on number of overlaps considered during all-vs-all alignment in `dorado correct` +* 2741de70278dd47850c548266d8b3bff5b387aaf - Prevent hang during shutdown of `dorado correct` and prevent out of memory errors +* 37d316c4db26df6121f5c09410eb8bd966ab6b75 - Remove unused `--read-ids` and `--threads` parameters from `dorado correct` +* ddb13dea5144769e0a5542321aa03867f06024c1 - Increase the threshold for midstrand barcode detection to reduce false matches +* 845a3ad37f2a7d2b7e62fcd50ff1971f47c139c3 - Fix misnaming by `dorado demux` of barcode file for barcodes ending in a letter (e.g., `12a`) +* 56d3e8e2ea55b4873e0ef4f35c144d210b20755e - Fix seq/qual orientation when demultiplexing aligned BAMs +* 5ddfc2fa6d639fa52c735184a2c92e9ce4306a3c - Fix bug causing CUDA illegal memory access with v5 RNA SUP and mods + + # [0.7.2] (18 June 2024) This release of Dorado resolves basecalling failures when running v5 SUP models on CPU-only devices or v5 RNA HAC on Apple silicon. It also fixes bugs in `dorado demux` and `dorado correct`, and corrects `sm` and `sd` tags to match the Dorado SAM specification. diff --git a/README.md b/README.md index 971993513..78e57b101 100644 --- a/README.md +++ b/README.md @@ -22,10 +22,10 @@ If you encounter any problems building or running Dorado, please [report an issu First, download the relevant installer for your platform: - - [dorado-0.7.2-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.2-linux-x64.tar.gz) - - [dorado-0.7.2-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.2-linux-arm64.tar.gz) - - [dorado-0.7.2-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.2-osx-arm64.zip) - - [dorado-0.7.2-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.2-win64.zip) + - [dorado-0.7.3-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.3-linux-x64.tar.gz) + - [dorado-0.7.3-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.3-linux-arm64.tar.gz) + - [dorado-0.7.3-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.3-osx-arm64.zip) + - [dorado-0.7.3-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.3-win64.zip) Once the relevant `.tar.gz` or `.zip` archive is downloaded, extract the archive to your desired location. diff --git a/cmake/DoradoVersion.cmake b/cmake/DoradoVersion.cmake index 543793d86..04e47e9aa 100644 --- a/cmake/DoradoVersion.cmake +++ b/cmake/DoradoVersion.cmake @@ -1,6 +1,6 @@ set(DORADO_VERSION_MAJOR 0) set(DORADO_VERSION_MINOR 7) -set(DORADO_VERSION_REV 2) +set(DORADO_VERSION_REV 3) find_package(Git QUIET) if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")