milaboratory/mixcr: MiXCR v3.0

Major changes New command assembleContigs for assembling longest possible contig TCR/IG receptor sequences from several intersecting sequences containing clonal sequence. E.g. assemble all possible sequence information outside CDR3. New command analyze for running optimized mixcr pipelines with one single command. Two pipelines which cover most practical cases are implemented analyze amplicon and analyze shotgun. New file format .clna for storing clones with alignments including alignments clones mapping Complete refactoring of command line interface New option --resume for resuming aborted / partially completed execution Implemented -nFeatureImputed and -aaFeatureImputed to export gene feature sequences imputing unavailable regions from germline sequences up to the full feature sequecn (marking imputed regions lowercase) LZ4 based compression .vdjca/.clna files, 3 ~ 4 fold file size reduction (built into file formats, enabled by default) Species option --species is now mandatory #342 Removed --chains option for align action #292 Added export field -positionInReference Now export fields like -nMutationsRelative supports alignment-attached gene features (e.g. this allows to export all mutations of V gene inside CDR3 sub-regions: -nMutationsRelative VCDR3Part VRegionWithP) Now align action prints library-level warnings and citation notice Refactored command line interface of exportReadsForClones Dropped support for Java 7 Minor changes fixes for #292 #280 #279 #208 #203 #421 --noMerge option renamed to --no-merge in assemble actio