File: README.md

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[![Build Status](https://travis-ci.org/PacificBiosciences/blasr_libcpp.svg?branch=master)](https://travis-ci.org/PacificBiosciences/blasr_libcpp)

#What is blasr_libcpp#

**Blasr_libcpp** is a *library* used by **blasr** and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment:
+ pbdata  
   - contains source code for handling Pacbio sequences and can build lib ```libpbdata```.
+ hdf 
   - contains source code for handling Pacbio hdf5 files (e.g., *.pls.h5, *.rgn.h5, *.bas.h5) and builds ```libpbhdf```.
+ alignment 
   - contains source code for aligning Pacbio reads to target sequences used in blasr and builds ```libblasr```.

For more information, see
* https://github.com/PacificBiosciences/blasr_libcpp/wiki

## Building
The simplest way is:
```
NOPBBAM=1 ./configure.py
make -j all
```
That will skip pbbam, and it will download HDF5 headers.