MiXCR v4.1.2

Major changes

• Command findShmTrees now can build trees from inputs with different tags
• Added --impute-germline-on-export and --dont-impute-germline-on-export to exportAlignments and exportClones
  commands

Minor improvements

• Now, instead of specifying separately multiple tags of the same type (i.e. CELL1+CELL2+CELL3) in filters, one can use
  convenient aliases (like allTags:Cell, allTags:Molecule). This also facilitates creation of a more generic base
  presets implementing common single-cell and UMI filtering strategies.
• Several command line interface improvements
• Migration from <tag_name> to <tag_type> semantics in export columns and --split-by-tag options

Fixes

• fixes bug with saveOriginalReads=true on align leading to errors down the pipeline
• analyze now correctly terminates on first error
• correct progress reporting in align with multiple input files provided by file name expansion mechanism
• fix --only-observed behaviour in exportShmTreesWithNodes
• fix missing tile in heatmap
• fix some cases of usage of -O...

Presets

• Fixed issue with mouse presets from MiLaboratories
• Fixed presets with whitelists
• Fixed missing material type and species in several presets
• Added template switch region trimming for RACE protocols
• Added presets for
  • Thermo Fisher Oncomine kits
  • ParseBio single-cell protocols
  • iRepertoire kits
  • Preset for protocol described in Vergani et al. (2017)
  • Cellecta AIR kit