milaboratory/mixcr: MiXCR v3.0.8

Major changes Alignments are forced to the corresponding edge if the same V/J gene is detected in the opposite PE read mate Average quality threshold (-OaverageQualityThreshold=...) in assembleContigs increased to 20 Added exportAlignmentsForClones action All indels in homopolimeric stretches are now shifted left in all alignment algorihtms Smarter base V/J/C hit selection in assembleContigs Read quality trimming (see help for --trimming-window-size and --trimming-quality-threshold options in align) (disabled by default until 3.1) Fix exception in -mutationsDetailed and similar export options Fixes in step skipping logic in analyze (additional automatic parameter adjustment for VDJC libraries covering only VRegion) Several more fixes for assembleContigs Minor changes Fixes incorrect numbers in assemble report Fix for filterAlignmentsActio