From 461c4d0e321bbab37a59d9e2f9c96c07a135f1a1 Mon Sep 17 00:00:00 2001 From: Susie Lee Date: Tue, 1 Aug 2023 20:12:21 +0100 Subject: [PATCH 1/7] [skip-ci] Release updates --- CHANGELOG.md | 19 +++++++++++++++++++ README.md | 8 ++++---- cmake/DoradoVersion.cmake | 2 +- 3 files changed, 24 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb1175da2..77247aa21 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,25 @@ All notable changes to Dorado will be documented in this file. +# [0.3.3] (3 Aug 2023) + +This release of Dorado introduces: duplex pairing improvements - improve duplex yields; reduction in memory requirement; improved mod base performance on M1; statically linked binaries - user requires very few dependencies to install + +* bcdeb8f0093bc5c01ef42befecda7f524b894aee - Static builds of (macOS|Linux)+(arm|x64) +* 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Metal modbases: fix slow mod base calling on macOS +* e14a7e61a6a3e60c0516342df7516b0ba5b92e62 - Improve Metal command buffer error handling +* ca1d191ffba5cc1397e4b704e3dab1014fa07175 - [ReadSplit] Fix read ids for non-split reads +* 5d9238a809656d6fab59713c7ab8346790efd2cc - Revamp AsyncQueue interface +* 3f0af88fa77dabd19a56245be2892b61750a297d - Changed uuid to be based on subread id, instead of split point. +* 6a3ccb6af5a56527571bf4938447bf85ab5c38e5 - Removed RNA003 model +* 1a94facbad52db0908eae3a7fe3242d525cbd6da - Fast5 stats +* 0abea5fb58545a679fcc1638ababe2a866789921 - 5mCG@v0.1 medmad compatible models +* eec657d113aa12ec2819fd6d597c4691e03ec374 - Prefer static libs to dynamic ones +* 072ed964276fc8e26f0a705c89055cece900edbf - Add pipeline restart capability and pairing cache retention option to termination +* efba0c874716d5adb213f7f39ecaf48c9e150f56 - mlhub single read eval triggers +* 01acbd5628948bf934985777bcade6bf51103200 - Stop progress bar cutting out near the end of the run +* 211968cd38fee6fa7476a4033a2b59ca37b19199 - Add suppression for false-positive vptr issues in older Xcodes + # [0.3.2] (13 Jul 2023) diff --git a/README.md b/README.md index 7ef0613f1..16ddf39b0 100644 --- a/README.md +++ b/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 diff --git a/cmake/DoradoVersion.cmake b/cmake/DoradoVersion.cmake index f6e6d3c5f..ffc549330 100644 --- a/cmake/DoradoVersion.cmake +++ b/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") From 34da7010c82ab65387b8bfad39227b35416dc82f Mon Sep 17 00:00:00 2001 From: Mike Vella Date: Wed, 2 Aug 2023 14:02:14 +0100 Subject: [PATCH 2/7] [skip-ci] changelog enhancements --- CHANGELOG.md | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 77247aa21..9143b19de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,22 +4,19 @@ All notable changes to Dorado will be documented in this file. # [0.3.3] (3 Aug 2023) -This release of Dorado introduces: duplex pairing improvements - improve duplex yields; reduction in memory requirement; improved mod base performance on M1; statically linked binaries - user requires very few dependencies to install - -* bcdeb8f0093bc5c01ef42befecda7f524b894aee - Static builds of (macOS|Linux)+(arm|x64) -* 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Metal modbases: fix slow mod base calling on macOS -* e14a7e61a6a3e60c0516342df7516b0ba5b92e62 - Improve Metal command buffer error handling -* ca1d191ffba5cc1397e4b704e3dab1014fa07175 - [ReadSplit] Fix read ids for non-split reads -* 5d9238a809656d6fab59713c7ab8346790efd2cc - Revamp AsyncQueue interface -* 3f0af88fa77dabd19a56245be2892b61750a297d - Changed uuid to be based on subread id, instead of split point. -* 6a3ccb6af5a56527571bf4938447bf85ab5c38e5 - Removed RNA003 model -* 1a94facbad52db0908eae3a7fe3242d525cbd6da - Fast5 stats -* 0abea5fb58545a679fcc1638ababe2a866789921 - 5mCG@v0.1 medmad compatible models -* eec657d113aa12ec2819fd6d597c4691e03ec374 - Prefer static libs to dynamic ones -* 072ed964276fc8e26f0a705c89055cece900edbf - Add pipeline restart capability and pairing cache retention option to termination -* efba0c874716d5adb213f7f39ecaf48c9e150f56 - mlhub single read eval triggers -* 01acbd5628948bf934985777bcade6bf51103200 - Stop progress bar cutting out near the end of the run -* 211968cd38fee6fa7476a4033a2b59ca37b19199 - Add suppression for false-positive vptr issues in older Xcodes +This release of Dorado introduces improvements to duplex pair detection for improved duplex yields, improvements to modified base calling speed on Apple silicon, and major enhancements to the portability of Dorado binaries. + + * bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux + * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices + * 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 + * 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy + * 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 # [0.3.2] (13 Jul 2023) From b45c4715206bd7823705ad261ef8fc6de2b2787f Mon Sep 17 00:00:00 2001 From: Mike Vella Date: Mon, 7 Aug 2023 13:09:45 +0100 Subject: [PATCH 3/7] [skip-ci] changelog enhancements --- CHANGELOG.md | 36 +++++++++++++++++++++++------------- 1 file changed, 23 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9143b19de..294287f50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,19 +4,29 @@ All notable changes to Dorado will be documented in this file. # [0.3.3] (3 Aug 2023) -This release of Dorado introduces improvements to duplex pair detection for improved duplex yields, improvements to modified base calling speed on Apple silicon, and major enhancements to the portability of Dorado binaries. - - * bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux - * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices - * 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 - * 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy - * 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 +This release of Dorado introduces improvements to Duplex pair identification for improved duplex yields, improvements to modified base calling speed on Apple silicon, and major enhancements to the portability of Dorado binaries. + +* 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 +* 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 +* 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield +* bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux +* 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices +* 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 +* 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy +* 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 # [0.3.2] (13 Jul 2023) From 2cd4648316312d4220856fdae0f52ade5a17f264 Mon Sep 17 00:00:00 2001 From: Mike Vella Date: Mon, 7 Aug 2023 13:10:41 +0100 Subject: [PATCH 4/7] [skip-ci] changelog enhancements --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 294287f50..d2224a972 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ This release of Dorado introduces improvements to Duplex pair identification for * 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 -* 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield +* 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled. * bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices * e14a7e61a6a3e60c0516342df7516b0ba5b92e62 - Improvements to error handling on Apple Silicon devices (Metal command buffer error handling) From 956136502d37c30f507af371fbc6b305e678576a Mon Sep 17 00:00:00 2001 From: Mike Vella Date: Mon, 7 Aug 2023 13:11:08 +0100 Subject: [PATCH 5/7] [skip-ci] changelog enhancements --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d2224a972..4ccc85c53 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ This release of Dorado introduces improvements to Duplex pair identification for * 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 +* 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 * 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled. From 9956ac70f4016ddf6953aeebc4d5cd9e7bd46220 Mon Sep 17 00:00:00 2001 From: Mike Vella Date: Tue, 8 Aug 2023 09:49:11 +0100 Subject: [PATCH 6/7] [skip-ci] Changelog update --- CHANGELOG.md | 51 ++++++++++++++++++++++++++------------------------- 1 file changed, 26 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4ccc85c53..333a5f1f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,31 +2,32 @@ All notable changes to Dorado will be documented in this file. -# [0.3.3] (3 Aug 2023) - -This release of Dorado introduces improvements to Duplex pair identification for improved duplex yields, improvements to modified base calling speed on Apple silicon, and major enhancements to the portability of Dorado binaries. - -* 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 -* 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 -* 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled. -* bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux -* 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices -* 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 -* 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy -* 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 +# [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 + * 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 + * 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 + * 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled. + * bcdeb8f0093bc5c01ef42befecda7f524b894aee - Improvements to portability of Dorado binaries via use of static linking on macOS and Linux + * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices + * 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 + * 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy + * 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 # [0.3.2] (13 Jul 2023) From b75c9a2d9faae739d7f2f8a4a7b04879d9080314 Mon Sep 17 00:00:00 2001 From: Chris Seymour Date: Tue, 8 Aug 2023 16:56:47 +0100 Subject: [PATCH 7/7] [ci-skip] update changelog --- CHANGELOG.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 333a5f1f0..4694f20f5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,28 +7,30 @@ All notable changes to Dorado will be documented in this file. 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 - * 8073364fa8e4390d21da56216a2ef0d78b57f206 - Improvements to Duplex pairing algorithm for increased Duplex yield. Situations where complement read is truncated are now handled. + * 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 - * 65b8b8a81a202d0166ca2d0ea4724941aa3102a4 - Major speed upgrade to modified base calling on Apple silicon devices * 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 - * 0abea5fb58545a679fcc1638ababe2a866789921 - Upgrade dna_r9.4.1_e8 5mCG models to version 0.1 for improved accuracy * 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)