remove dead code
add some Graph tests
decouple BamIo from Options struct
TestBamIo/openBam -> parameterized test vs loop based
add "bam_file_index" to LibraryConfig object
make sure to initialize LibraryConfig::bam_file_index
fwd declare instead of include ReadCountsByLib
add serialization of missing member in BamConfig

_max_read_window_size was left out!
add (currently undocumented) -C / -R options

-C cache.xml will dump the command line options, bam_config, and bam
summary data to cache.xml

-R cache.xml (which must be the only option) will load that data which
lets it skip the initial pass over the bam to build the flag
distribution.
add ConfigLoader class to handle cache/restore from xml
add bam_config_path to options

instead of relying on argv[optind] externally
add support for -C / -R cache restore options to main program
update region summary to include:

tid, start, end, up to first 10 read names