MiXCR v2.1.6

Major changes

• (beta) Added JSON-formatted reports. Use --json-report option in align, extendAlignments, assemblePartial or assemble actions to create JSON report or append it to already existing report file (jsonl). This feature is intended to simplify batch analysis, and analysis automation. E.g. jq util can be used to aggregate information from multi-json-report files.
• Report file appends are made atomic. Now you can safely specify the same report file name in several invocations of MiXCR, even if you run several instances of MiXCR in parallel. Should also work for NFS and other remote FS, suppporting file locking.
• Added chains column in export (-chains and -topChains)

Minor changes

• Several new counters added to align report
• Added proper filtering for alleles with wildcard symbols in featureToAlign region
• Fixed bug in align report (wrong total count in rare cases) #265
• Documentation added for filterAlignments