From cc9f9c9e0fa1e7739ccf87f01b6ea4fc7ff6e76b Mon Sep 17 00:00:00 2001 From: Joyjit Daw Date: Mon, 22 Apr 2024 10:16:50 -0400 Subject: [PATCH 1/4] update version number to 0.6.1 --- CHANGELOG.md | 14 ++++++++++++++ README.md | 8 ++++---- cmake/DoradoVersion.cmake | 2 +- 3 files changed, 19 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 89828a42..2b3eb198 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,20 @@ All notable changes to Dorado will be documented in this file. +# [0.6.1] (23 April 2024) + +This release of Dorado fixes some critical bugs in `dorado aligner` primarily related to using presets correctly. + +* TBD - Make sm/sd tags for pA and quantile scaling consistent +* a2abf83852e895b1016c690769b59c06587684fe - Fix incorrect overriding of minimap2 options when minimap2 preset is specified +* 1cc207a166b1cafcbd012f5c70b5c817c788c7f3 - Fix bug causing unclassified records from `dorado demux` to be unreadable by samtools +* 298277150ad2522ca6c1928c4981782ce2893a5a - Fix issue with allocating memory on unused GPU during basecalling +* fa79f4a77fca737704d8a9e08d0495b9988f88ef - Fix reverse strand alignments when re-mapping a SAM/BAM file with `dorado aligner` +* 3b2c8252d1a40bb0f941ca2ceca0849be15d15fa - Propagate `sv` tag to split reads +* 11675a565da9af52de89a3f6614d15e57d10765d - Fix bug where errors were being swalled in HtsFile class +* 73046e19fd443dfb48f3fbb82c0b37c5c7cfb8d5 - Fx type in Warnings.cmake + + # [0.6.0] (2 April 2024) This release of Dorado improves performance for short read basecalling and RBK barcode classification rates, introduces sorted and indexed BAM generation in Dorado aligner and demux, and updates the minimap2 version and default mapping preset. It also adds GPU information to the output BAM or FASTQ and includes several other improvements and bug fixes. diff --git a/README.md b/README.md index 6dee444e..fc6cbf62 100644 --- a/README.md +++ b/README.md @@ -19,10 +19,10 @@ If you encounter any problems building or running Dorado, please [report an issu ## Installation - - [dorado-0.6.0-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-linux-x64.tar.gz) - - [dorado-0.6.0-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-linux-arm64.tar.gz) - - [dorado-0.6.0-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-osx-arm64.zip) - - [dorado-0.6.0-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-win64.zip) + - [dorado-0.6.1-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.1-linux-x64.tar.gz) + - [dorado-0.6.1-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.1-linux-arm64.tar.gz) + - [dorado-0.6.1-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.1-osx-arm64.zip) + - [dorado-0.6.1-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.1-win64.zip) ## Platforms diff --git a/cmake/DoradoVersion.cmake b/cmake/DoradoVersion.cmake index 92a8c968..919d8a12 100644 --- a/cmake/DoradoVersion.cmake +++ b/cmake/DoradoVersion.cmake @@ -1,6 +1,6 @@ set(DORADO_VERSION_MAJOR 0) set(DORADO_VERSION_MINOR 6) -set(DORADO_VERSION_REV 0) +set(DORADO_VERSION_REV 1) find_package(Git QUIET) if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git") From 89564b8962cd4e2bc445b741f95301da3d96182c Mon Sep 17 00:00:00 2001 From: Joyjit Daw Date: Mon, 22 Apr 2024 13:08:00 -0400 Subject: [PATCH 2/4] fix typos in changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b3eb198..33d3935a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,8 +12,8 @@ This release of Dorado fixes some critical bugs in `dorado aligner` primarily re * 298277150ad2522ca6c1928c4981782ce2893a5a - Fix issue with allocating memory on unused GPU during basecalling * fa79f4a77fca737704d8a9e08d0495b9988f88ef - Fix reverse strand alignments when re-mapping a SAM/BAM file with `dorado aligner` * 3b2c8252d1a40bb0f941ca2ceca0849be15d15fa - Propagate `sv` tag to split reads -* 11675a565da9af52de89a3f6614d15e57d10765d - Fix bug where errors were being swalled in HtsFile class -* 73046e19fd443dfb48f3fbb82c0b37c5c7cfb8d5 - Fx type in Warnings.cmake +* 11675a565da9af52de89a3f6614d15e57d10765d - Fix bug where errors were being swallowed in HtsFile class +* 73046e19fd443dfb48f3fbb82c0b37c5c7cfb8d5 - Fx typo in Warnings.cmake # [0.6.0] (2 April 2024) From 8c420385cd94d6046e38b8c1fc376dc171f21bfa Mon Sep 17 00:00:00 2001 From: Joyjit Daw Date: Tue, 23 Apr 2024 10:49:27 -0400 Subject: [PATCH 3/4] add another change to changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 33d3935a..3e175979 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ All notable changes to Dorado will be documented in this file. This release of Dorado fixes some critical bugs in `dorado aligner` primarily related to using presets correctly. * TBD - Make sm/sd tags for pA and quantile scaling consistent +* 3e060db5a35ab09fecbeef9754cc545ba400edf1 - Skip stripping of SQ header lines in dorado demux --no-classify * a2abf83852e895b1016c690769b59c06587684fe - Fix incorrect overriding of minimap2 options when minimap2 preset is specified * 1cc207a166b1cafcbd012f5c70b5c817c788c7f3 - Fix bug causing unclassified records from `dorado demux` to be unreadable by samtools * 298277150ad2522ca6c1928c4981782ce2893a5a - Fix issue with allocating memory on unused GPU during basecalling From 064ef3729e91e9d1b88b9092909aaaa2919ee09c Mon Sep 17 00:00:00 2001 From: Joyjit Daw Date: Tue, 23 Apr 2024 13:17:10 -0400 Subject: [PATCH 4/4] clarify content of the release and remove a line from changelog --- CHANGELOG.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e175979..fcf3dfee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,9 +4,8 @@ All notable changes to Dorado will be documented in this file. # [0.6.1] (23 April 2024) -This release of Dorado fixes some critical bugs in `dorado aligner` primarily related to using presets correctly. +This release of Dorado fixes bugs in `dorado aligner` related to using presets incorrectly and in `dorado demux` which were causing demultiplexed outputs to be malformed. -* TBD - Make sm/sd tags for pA and quantile scaling consistent * 3e060db5a35ab09fecbeef9754cc545ba400edf1 - Skip stripping of SQ header lines in dorado demux --no-classify * a2abf83852e895b1016c690769b59c06587684fe - Fix incorrect overriding of minimap2 options when minimap2 preset is specified * 1cc207a166b1cafcbd012f5c70b5c817c788c7f3 - Fix bug causing unclassified records from `dorado demux` to be unreadable by samtools @@ -16,7 +15,6 @@ This release of Dorado fixes some critical bugs in `dorado aligner` primarily re * 11675a565da9af52de89a3f6614d15e57d10765d - Fix bug where errors were being swallowed in HtsFile class * 73046e19fd443dfb48f3fbb82c0b37c5c7cfb8d5 - Fx typo in Warnings.cmake - # [0.6.0] (2 April 2024) This release of Dorado improves performance for short read basecalling and RBK barcode classification rates, introduces sorted and indexed BAM generation in Dorado aligner and demux, and updates the minimap2 version and default mapping preset. It also adds GPU information to the output BAM or FASTQ and includes several other improvements and bug fixes.