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

• Fixes incorrect numbers in assemble report
• Fix for filterAlignmentsAction