changelog and final dependency upgrade

build.gradle.kts

@@ -133,12 +133,12 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.4.2-82-fix-version"
-// may be blank (will be inherited from mixcr-algo)
-val mitoolVersion = ""
+val mixcrAlgoVersion = "4.5.0"
 // may be blank (will be inherited from mixcr-algo)
 val milibVersion = ""
 // may be blank (will be inherited from mixcr-algo)
+val mitoolVersion = ""
+// may be blank (will be inherited from mixcr-algo)
 val repseqioVersion = ""
 
 val picocliVersion = "4.6.3"

changelogs/v4.5.0.md

@@ -0,0 +1,48 @@
+## 🚀  New features
+
+### Multi-chain clone assembly for single-cell data
+
+Now MiXCR calculates Heavy-Light antibody and Alpha-Beta and Gamma-Delta TCR combined clones for single-cell data. Two new commands were introduced to enable this functionality: `groupClones` and `exportCloneGroups`, the first command calculate multi-chain clones form assembled clonotypes and writes result in binary format, the second export information about combined clonotypes.
+
+All single-cell presets now automatically produce combined multi-chain output in both binary and textual formats, see files with names matching `*.clone.groups.tsv` pattern in the output folder.  
+
+### New characteristics in clonotype export
+
+- Export biochemical properties of gene regions with `-biochemicalProperty <geneFeature> <property>` or `-baseBiochemicalProperties <geneFeature>` export options. Available in export for alignments, clones and SHM tree nodes. Available properties: `Hydrophobicity`, `Charge`, `Polarity`, `Volume`, `Strength`, `MjEnergy`, `Kf1`, `Kf2`, `Kf3`, `Kf4`, `Kf5`, `Kf6`, `Kf7`, `Kf8`, `Kf9`, `Kf10`, `Rim`, `Surface`, `Turn`, `Alpha`, `Beta`, `Core`, `Disorder`, `N2Strength`, `N2Hydrophobicity`, `N2Volume`, `N2Surface`.
+- Export isotype with `-isotype [<(primary|subclass|auto)>]`
+- Export `-mutationRate [<gene_feature>]` in `exportShmTreesWithNodes`, `exportClones` and `exportCloneGroups` command: number of mutations relative to corresponding germline divided by the target sequence size. For `exportClones` and `exportCloneGroups` CDR3 is not included in calculation.
+
+### Support for wider set of input formats
+
+- Support for `cram` files as input for `analyze` and `align` commands. Optionally, a reference to the genome can be specified by `--reference-for-cram`
+- Fixed usage of BAM input for `analyze` and `align`, if file contains both paired and single reads
+
+### Algorithm enhancements
+
+- Global consensus assembly algorithm, applied in `assemble` to collapse UMI/Cell groups into contigs, now have much better seed selection empirical step for multi-consensus assembly scenarios. This significantly increases sensitivity during assembly of secondary consensuses from the same group of sequences.
+- New constrain in low-quality reads mapping procedure preventing cross-cell read mapping.
+
+## 📚  Preset updates
+
+- Additional improvement of clone filters in `10x-sc-xcr-vdj` preset.
+- Tag pattern upgrade for `cellecta-human-rna-xcr-umi-drivermap-air`. Now UMI includes a part of the C-gene primer to increase diversity, and R2 is also used for payload.
+- Assembling feature fix for `irepertoire-human-rna-xcr-repseq-plus` preset. Now `{CDR2Begin:FR4End}`.
+- New preset for BD full-length protocol with enhanced beads V2 featuring B384 whitelists: `bd-sc-xcr-rhapsody-full-length-enhanced-bead-v2`.
+- New preset for Takara Bio SMART-Seq Mouse TCR (with UMIs): `takara-mouse-rna-tcr-umi-smarseq`.
+- Presets for new Cellecta kits: `cellecta-human-dna-xcr-umi-drivermap-air`, `cellecta-human-rna-xcr-full-length-umi-drivermap-air`, `cellecta-mouse-rna-xcr-umi-drivermap-air`.
+- Presets for iRepertoire RepSeq+ kits with UMI: `irepertoire-mouse-rna-xcr-repseq-plus-umi-pe`, `irepertoire-human-rna-xcr-repseq-plus-umi-se`,`irepertoire-human-rna-xcr-repseq-plus-umi-pe`.
+- `isotype` field added to `exportClones` for presets supporting isotype identification.
+- Split by C-gene enabled in `thermofisher-human-rna-igh-oncomine-lr` and `cellecta-human-rna-xcr-umi-drivermap-air` presets to facilitate isotype separation.
+- Default consensus assembly parameters `maxNormalizedAlignmentPenalty` and `altSeedPenaltyTolerance` are adjusted to increase sensitivity.
+- The `--split-by-sample` option is now set to `true` by default for all `align` presets, as well as all presets that inherit from it. This new default behavior applies unless it is directly overridden in the preset or with `--dont-split-by-sample` mix-in.
+- `exportAlignments` now reports UMI and/or Cell barcodes by default for presets with barcodes.
+
+## 🛠️  Minor improvements & fixes
+
+- Fixed possible crash with `--dry-run` option in `analyze`
+- More informative help message that appears when using a deprecated preset and incorrectly suggests using `--assemble-contigs-by` instead of `--assemble-clonotypes-by`.
+- When split-by-tags is enabled, `exportClone` and `exportShmTreesWithNodes` now output read count as the sum of reads for given tags selection, more complicated formula was used in previous versions
+- `exportAlignments` by default now include the column `topChains`. `exportClones` function reports `topChains` for single cell presets.
+- Fixed calculation of `geneFamilyName` for genes like `IGHA*00` (without the number before `*` symbol)
+- Better formatting in `listPresets` command. Added grouping by vendor, labels and optional filtering
+- Validation of input types in `align` or `analyze` by given tag pattern