rename LegacyConfig -> BamConfig

I'm about to make this class parse the bams as well, to collect the
statistics currently being gathered in main()
move bam parsing to BamConfig object
More code cleanup:

add flag to Read class to indicate whether or not to cache the
sequence/quality data (it isn't needed when computing read stats).

cache LibraryInfo associated with a read on the read instance.

remove unused variables total_{phy,seq}_coverage

stop passing reference_len as a parameter and use stored value
in BamConfig object

create "add_per_lib_read_counts_to_region" function in breakdancer
that uses merge_maps to update read counts.