This is based on the mac-build branch but I could rebase to master if that isn't accepted. The changes are in the readInMSA function. Currently, the function advances the index for every buffer (line) that doesn't start with > which fails for multiline fastas (which are the default for gisaid and NCBI).
This is based on the
mac-buildbranch but I could rebase to master if that isn't accepted. The changes are in thereadInMSAfunction. Currently, the function advances the index for every buffer (line) that doesn't start with>which fails for multiline fastas (which are the default for gisaid and NCBI).