MiXCR v1.5

Major changes

• Analysis mode for RNA-Seq data. Use -p rna-seq in align action.
• Possible set of D genes is limited by loci of V and J genes in current rearrangement
• Default output format for exportAlignmentsPretty changed for the new one which is more compact and vivid
• Two new filtering options in exportAlignmentsPretty: --cdr3-contains and --read-contains
• Default value for -OjParameters.parameters.floatingRightBound changed to false
• New parameters: -OincludeDScore and -OincludeCScore for align action. If set to true score of D or C gene will be added to total alignment score
• New action: mergeAlignments to merge several *.vdjca files into one

Minor changes

• Additional micro filtration step for paired-end read aligner (work in very rare cases)
• Fixed bug leading to incorrect behaviour if readsLayout=Unknown
• Correct progress reporting with -n option in align action.
• Added export options -vHitsWithoutScores (same for J and D genes)
• Added support for optional compression of .vdjca and .clns files (when specifying additional .gz extension: e.g. mixcr align inut.fastq output.vdjca.gz etc.)
• Correct handling of quotes in parameters overriding