Multi-fasta file support for --add-to-library about kraken HOT 2 CLOSED

Multi-fasta files weren't originally supported because Kraken used to use a file that mapped files to taxa. (This made sense when working only with completed microbial genomes, but has since been shown to be problematic.) One of the component programs, set_lcas, would then open each file one at a time, and use the map information to assign correct taxonomic information to the file's k-mers. The set_lcas program actually supported multi-fasta files for quite a while, but the scripts and changes to other programs to support those files weren't present until now.

As of the most recent commit, adding multi-fasta files to a DB should no longer require many, many files in the filesystem, and also will not utilize the clumsy .ffn hack that just confused matters and ate up disk space unreasonably.

from kraken.

Thanks @DerrickWood . That helps tremendously.

from kraken.