... bam_file(s) > output
Requires bamtools API library at run time, and c++0x for compile.
git clone https://github.com/pezmaster31/bamtools
cd bamtools
mkdir build
cd build
cmake ..
make
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib
g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x