From cd7ea52e83abc310d599159cf5020467e228f154 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Sun, 30 Jul 2023 11:09:55 +0300 Subject: [PATCH] chore: final corrections to 4.4.2 changelog, upgrade to release versions --- build.gradle.kts | 2 +- changelogs/v4.4.2.md | 21 +++++++++++---------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/build.gradle.kts b/build.gradle.kts index 8fe92421a..1436cff33 100644 --- a/build.gradle.kts +++ b/build.gradle.kts @@ -133,7 +133,7 @@ val toObfuscate: Configuration by configurations.creating { val obfuscationLibs: Configuration by configurations.creating -val mixcrAlgoVersion = "4.4.0-18-kmapper2-for-long-read-data-" +val mixcrAlgoVersion = "4.4.2" val milibVersion = "" val mitoolVersion = "" val repseqioVersion = "" diff --git a/changelogs/v4.4.2.md b/changelogs/v4.4.2.md index d1573e7fb..d8709b3ed 100644 --- a/changelogs/v4.4.2.md +++ b/changelogs/v4.4.2.md @@ -1,17 +1,18 @@ -## New features +## 🚀 New features -- Now one can import tags from sequence headers by parsing its content with regular expressions -- New presets for amplicons/rna-seq sequenced by long-read sequencers such as Pacific Biosciences - and Oxford Nanopore: _generic-ont_, _generic-ont-with-umi_, _generic-pacbio_, _generic-pacbio-with-umi_ +- Two-fold `align` step speedup for most of the protocol-specific presets (see the list below) +- Import tags from sequence headers by parsing its content with regular expressions +- Highly optimized generic presets for amplicon/rna-seq sequence by long-read sequencers such as Pacific Biosciences and Oxford Nanopore: `generic-ont`, `generic-ont-with-umi`, `generic-pacbio`, `generic-pacbio-with-umi` -## Bug fixes +## 🐞 Bug fixes - Fixes crush when input contains quality scores > 70 - Fixes excessive memory consumption issue for long read data +- Fix for crush in `assemble` with UMI tags but with consensus assembler turned off -## Other minor adjustments -- long-read J gene aligner optimization -- aligner changed for flairr-seq preset to long-read dedicated one -- quality trimming is disabled for long-read aligner -- removed qc reports for clustered alignments and clones +## 👷 Other minor adjustments +- Long-read J gene aligner optimization +- FLAIRR-seq preset optimized with new long-read-optimized aligner +- Quality trimming is disabled for long-read aligner +- Removed qc reports for clustered alignments and clones - The following presets have been optimized by specifying a single reverse/direct alignment mode and now work faster: `takara-human-rna-bcr-umi-smartseq`, `takara-human-rna-bcr-umi-smarter`,`takara-human-rna-tcr-umi-smartseq`,`takara-human-rna-tcr-umi-smarter-v2`,`takara-human-rna-tcr-smarter`,`takara-mouse-rna-bcr-smarter`,`takara-mouse-rna-tcr-smarter`,`10x-sc-xcr-vdj`,`10x-sc-5gex`,`abhelix-human-rna-xcr`,`bd-human-sc-xcr-rhapsody-cdr3`,`bd-mouse-sc-xcr-rhapsody-cdr3`,`bd-sc-xcr-rhapsody-full-length`,`cellecta-human-rna-xcr-umi-drivermap-air`,`illumina-human-rna-trb-ampliseq-sr`,`illumina-human-rna-trb-ampliseq-plus`,`irepertoire-human-rna-xcr-repseq-sr`,`irepertoire-human-rna-xcr-repseq-lr`,`irepertoire-mouse-rna-xcr-repseq-sr`,`irepertoire-mouse-rna-xcr-repseq-lr`,`irepertoire-human-rna-xcr-repseq-plus`,`irepertoire-mouse-rna-xcr-repseq-plus`,`irepertoire-human-dna-xcr-repseq-sr`,`irepertoire-human-dna-xcr-repseq-lr`,`milab-human-rna-ig-umi-multiplex`,`milab-human-rna-tcr-umi-race`,`milab-human-rna-tcr-umi-multiplex`,`milab-human-dna-tcr-multiplex`,`milab-human-dna-xcr-7genes-multiplex`,`milab-mouse-rna-tcr-umi-race`,`neb-human-rna-xcr-umi-nebnext`,`qiagen-human-rna-tcr-umi-qiaseq` \ No newline at end of file