chore: final corrections to 4.4.2 changelog, upgrade to release versions

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 = ""

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`