Merge branch 'lean'
Merge remote-tracking branch 'origin/lean'
Merge branch 'lean'
Added support for queryFile, to specify an input file, rather than generating a pangenome for the run.
PhylogenyFileCreator.pm now uses array of arrays instead of a hash to transpose the data into a phylip file. Also added a standalone phylogeny_creator.pl file to manipulate the data from the commandline.
Remove debugging log prints.
Merge branch 'table'
Log4p.conf is back
If providing a query file in lieu of creating a pan-genome, Panseq will now utilize the locus names instead of creating arbitrary ones.
Update for specified queryFile
fixed out of bounds error on _transposeArray
Earlier unlinking of temp files.
Updated permissible characters in fasta headers.
remove and add newline for every line in _combineAndSanitizeFastaFiles
Added PanGenome.pm log to output.
Fixed bug in rare instance, where fasta header ">" was included as part of name.
Adjusting NovelIterator to maximal efficiency.
Merge remote-tracking branch 'origin/master' into lean
Removed given/when in favor of elsif.
Also multi-core NovelIterator throws no errors.
Fixed race condition where the iterator number plus system time was not enough to generate unique names. The programmed iterated fast enough to clobber the old name. Added two 6 digit integer random number generations to the file name.