Update to fix issue #1 pointed out by ctberthiaume.
This issue did not exists on Ubuntu 13.04 64bit with MUMmer 3.23, muscle
3.8.31 and blast+ 2.2.28; however on CentOS 5.9 with the same program
versions, I verified this bug.
This fixes the bug, all tests pass on both test systems.
Merge branch 'master' into genodo
Updated and simplified logging output to single file and screen.
Removed logs directory, all logging now in Master.log in baseDirectory.
Updating the log output.
FormatBlastDB now outputs to Master.log
Added nameOrId as the specifier for what is displayed in the output
binary and snp tables.
Updated the output of Panseq to include a core and accessory fasta file,
based on the run settings.
Updating BlastResults
more changes
Refactoring BlastResults and pan/core/accessory output