count pairs with RF as ARP_RF for PE data

NORMAL_RF isn't really a thing for PE.
allow breakdancer to read sam files
make RawBamEntry non-copyable
add is_leftmost and pair_overlap functions to Read
add BamWriter class
more test cases for bam io
remove comments
encapsulate BreakDancer::read_density map
refactor option/config caching
add function to merge LibraryFlagDistributions
start refactoring config related code
add BOOST_BUILD_OPTS cmake flag

to do things like cmake <...> -DBOOST_BUILD_OPTS=-j8 for
parallel compilation of boost
store bam aux data as vector<uint8_t> instead of std::string

it's uint8_t natively and we were casting it (to char for string).
stop passing bam header to memfns that have acces to it
refactoring
ditch some namespaces
add ReadClassifier concept

i'm trying to get rid of all the nested/chained if statements that
decide on the final breakdancer read flag.
update build system

added deps target (make deps will build boost and samtools first)

require c++11 support
fix some tag mismatches (class/struct) and remove unused vars
simplify pe read classifier