methcounts.cpp: adding option to include a header in the counts output
covered.cpp: minor fix in output when no args given
symmetric-cpgs.cpp: added a function to print any header if it exists, which involves just printing leading lines that begin with # symbol
bam_record_utils.hpp: added a function to get the target length from the header without specifying the internal header inside the bam_header object
MSite.hpp and MSite.cpp: added a constructor from a char array with length. Also moved the logic of parsing strings to construct MSite into an initialize function which allows the same thing to be done without constructing a new object
xcounts.cpp: adding this file to compress the counts files as small as possible
dnmtools.cpp: adding the xcounts command
Makefile.am: adding the xcounts.cpp file to the sources
unxcounts.cpp: adding a tool to convert back from the xcounts format
Makefile.am and dnmtools.cpp: adding the unxcounts command
recovered.cpp: using getline then initalize the sites so that skipping the header is easier
xcounts.cpp: removing output of chromosomes to stderr each time they change, not forcing a null char after the part of the buffer to be written, and making the buffer at most 128 bytes