push reg_name into BreakDancerData in preparation for mischief
removing some dead code
take region_data private. mischief is coming!
add BasicRegion class:

switch "regs" and "reg_name" from map<int, ...> to vector<...>
make sure to destroy bam iterator
remove reg_idx variable, pull read_count... maps into BreakDancer class
add merge_maps function

there were some ugly blocks of code trying to do things like:

for k in b.keys():
    a[k] += b[k]

which is much more verbose in C++. merge_maps merges b into resolving
conflicts with a supplied combine callable
change roi read counts from map<int,...> to vector and

cleaned up a few const/iterator problems as well
Updated how the bam2cfg.pl output is stored:

instead of storing a bunch of maps keyed on library name, we now have a
LibraryInfo structure and a single map with values of said type.
rename nreads_ -> nreads_per_bam
remove some redundant checks to see if things exist in maps
Revert "remove some redundant checks to see if things exist in maps"

This reverts commit 896a2b3e5a26d9104bec6c492390b90cbb7b7548.
after reverting the previous commit...

it turns out that the clink map needs special treatment. this commit
restores everything that was reverted in the last one except for the
changes to the clink map. note to self, it looks like it is trying to be
an adjacency matrix for an undirected graph, so we may be able to cut
the storage requirement in half...
make a few iterators const.
change SVtype map to ConfigMap
replace some use of bam1_t with Read class
add strand_e enum (FWD, REV) to use instead of '+'/'-'

rename 'read' to read_regions
move read_density into BreakDancer object

we should ultimately make it a property of a library or bam file object.
I need to figure out what is up with the CN_lib option first.