Merge remote-tracking branch 'origin/lean'
Added the faq.tmpl
version update
Updated MANIFEST to reflect current version.
Removed .htaccess from MANIFEST
Added Test::Pretty to list of dependencies.
updated gitignore
Moved fragment info _(34..56) into Roles::GetNewIdStartEnd.pm, updated SegmentMaker.pm and NovelRegionFinder.pm with this.
Turned logging of STDERR back on.
Fixed hard-coded 20 splits for blast run. Now splits to number of cores.
update coverage
Changes for deltaFilter branch
Added percent identity filtering for nucmer stage.

This includes a delta-filter before the coords file is generated, to
incorporate the percentIdentityCutoff into the pan-genome generation as
well. Suggested by Anson Wong.
sequence coverage update.
missing semicolon
updating unique mode

need to ensure seed strain is also checked.
comment added in NovelRegionFinder.pm
sqlite conversion for PanGenome
Changed blastdb max size to 1TB, from 1GB.
Upped the max_target_seqs value for BlastRun in Panseq.pm to 1 million.