compress counts

[andrewdavidsmith]

• 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
• unxcounts.cpp: major changes for speed