GUIDE

guide to some of the directories here:

enclone               most of the code up to "printing"
enclone_args          argument processing
enclone_com           inter-processs communication (experimenal)
enclone_core          core definitions, etc.
enclone_denovo        experimental code for making VDJ references
enclone_exec          just the actual main program
enclone_help          help menus from the command line
enclone_main          this includes the enclone main program guts
enclone_paper         calculations for enclone paper
enclone_print         prints clonotypes in the sense of creating the "pictures" (much of core logic)
enclone_proto         stuff for communicating with Loupe, and reused for other purposes
enclone_ranger        entry point for cellranger
enclone_stuff         things called by enclone_main and enclone_ranger
enclone_tail          last part of the code
enclone_tools         miscellaneous binaries
enclone_vars          variable definitions
enclone_version       determine current version string
enclone_visual        experimental GUI client

credits               credits
fonts                 DejaVuSansMono, in case not otherwise available
img                   images for site
pages                 pages on site and source code for such
target                where rust puts compilation stuff