Bug fix
Output filename now includes entire input filename.
Bug fix
Changed a parameter from int to double.
Centromere locations are now hard-wired in HumanGenome.cc rather than requiring an external file.
Updated these fasta-auxiliary files to reflect changes in Lachesis' input file parsing.
Big update!  The INI files now have several new parameters (DRAFT_ASSEMBLY_FASTA, REF_ASSEMBLY_FASTA, RE_SITE_SEQ, CLUSTER_NONINFORMATIVE_RATIO, ORDER_DRAW_DOTPLOTS, REPORT_MAKE_HEATMAP) and several parameters have been removed (DRAFT_ASSEMBLY_NAMES_FILE, REF_ASSEMBLY_NAMES_FILE, RE_COUNTS_FILE, CLUSTER_DO_NONINFORMATIVE, REPORT_CHART_OUTFILE).  The goal of these changes is to make the INI files more user-friendly and easier to use.  The process of using grep to create *.names files and using CountMotifsInFasta.pl to create *.counts_*.txt file is now automated by Lachesis.
Big update!  The INI files now have several new parameters (DRAFT_ASSEMBLY_FASTA, REF_ASSEMBLY_FASTA, RE_SITE_SEQ, CLUSTER_NONINFORMATIVE_RATIO, ORDER_DRAW_DOTPLOTS, REPORT_MAKE_HEATMAP) and several para