allergome 1-100 group 3 has pep 66 multiple
rebuild pkgdown when internet
add annotation files to dropbox phip
push to dev version
debug 1:100
epitopefindr log
--
indexGroups line 135 section still allows merge of duplicated should fix
also some peptides havae NA group, thus fails groupMSA
add progress into to log add job complete to log add newline after pregress bars / remove progress bars when they are done
fix indexgroups algorithm
-- epitoep 88 has 768 splits
make indexgorups faster
alinging groups are always the same. 1 from each?. not necessarily
groups.csv only assigning each peptide ot its last group.
also creates thousands of groups make peptide.once == FALSE by default until ready
try crop out one peptide option
-- make epitopefindr method write.files = TRUE if false, skil MSA skip fwrite in epfind add return of the three spreadsheets epitopekey epitopesummary finalalignments (also initial sequences and starting alignments?) add groups.csv to output? make groupMSA compatible with epitopekey