Build instructions for developers:
Assuming that blasr and blaser_libcpp is placed under //depot/software/smrtanalysis/bioinformatics/ext/pi

  $ cd <bam2bax>
  $ module load boost
  $ mkdir build; cd build; cmake ..
  $ make
  $ ../tests/bin/test_bam2bax # to test bam2bax exe


Build instructions for users:
  $ cd <bam2bax>
  $ mkdir build; cd build; 
  $ cmake -DPacBioBAM_INCLUDE_DIRS=<path_to_include_dir> \
      -DHTSLIB_INCLUDE_DIRS=<path_to_include_dir> \
      -DPacBioBAM_LIBRARIES=<path_to_lib_so_or_a> \
      -DHTSLIB_LIBRARIES=<path_to_lib_so_or_a> \
      -DPBDATA_INCLUDE_DIRS=<path_to_include_dir> 
      -DPBDATA_LIBRARIES=<path_to_lib_so_or_a> \
      -DPBIHDF_INCLUDE_DIRS=<path_to_include_dir> 
      -DPBIHDF_LIBRARIES=<path_to_lib_so_or_a> \
      -DBLASR_INCLUDE_DIRS=<path_to_include_dir> 
      -DBLASR_LIBRARIES=<path_to_lib_so_or_a> \
      -DHDF5_INCLUDE_DIRS=<path_to_include_dir> 
      -DHDF5_CPP_LIBRARIES=<path_to_lib_so_or_a> \
      -DHDF5_LIBRARIES=<path_to_lib_so_or_a> \
      -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \
      ../

  $ make
  $ ../tests/bin/test_bam2bax # to test bam2bax exe

# e.g.,
#cmake -DPacBioBAM_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/pbbam/include \
#      -DHTSLIB_INCLUDE_DIRS=$smrtanalysis/bioinformatics/lib/cpp/htslib \
#      -DPacBioBAM_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/pbbam/lib/libpbbam.a \
#      -DHTSLIB_LIBRARIES=$smrtanalysis/bioinformatics/lib/cpp/htslib/libhts.a \
#      -DPBDATA_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata \
#      -DPBDATA_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/pbdata/libpbdata.a \
#      -DPBIHDF_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf \
#      -DPBIHDF_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/hdf/libpbihdf.a \
#      -DBLASR_INCLUDE_DIRS=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/ \
#      -DBLASR_LIBRARIES=$smrtanalysis/bioinformatics/ext/pi/blasr/libcpp/alignment/libblasr.a \
#      -DHDF5_INCLUDE_DIRS=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/include \
#      -DHDF5_CPP_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5_cpp.a \
#      -DHDF5_LIBRARIES=$smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404/lib/libhdf5.a \
#      -DBam2Bax_EXE_LINKER_FLAGS="-Wl,--no-as-needed -ldl -pthread -lrt " \
#      ../
