MSite.cpp: adding a loop to pass the header when trying to determine if a file is a counts file
hmr.cpp and pmd.cpp: adding code to skip the header when reading sites
methcounts.cpp: refactoring to move the header code into counts_header.chpp
recovered.cpp: refactoring to move the header stuff into counts_header
smmetric-cpgs.cpp: refactoring to move the header stuff into counts_header
xcounts.cpp: refactoring to move the header stuff into counts_header
unxcounts.cpp: refactoring to move the header stuff into counts_header
uniq.cpp: adding a variable to control the max buffer size which matters for some strange data sets with hundreds of thousands of reads at the same mapping location