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libmaus

libmaus is a collection of data structures and algorithms. It contains

• I/O classes (single byte and UTF-8)
• bitio classes (input, output and various forms of bit level manipulation)
• text indexing classes (suffix and LCP array, fulltext and minute (FM), ...)
• BAM sequence alignment files input/output (simple and collating)

and many lower level support classes.

The main development branch of libmaus is hosted by github at

https://github.com/gt1/libmaus

Compilation

libmaus uses the GNU autoconf/automake tool set. It can be compiled on Linux using:

autoreconf -i -f
./configure
make

Running autoreconf requires a complete set of tools including autoconf, automake, autoheader, aclocal and libtool.

A full list of configuration parameters can be obtained by calling

./configure --help

libmaus can use functionality from several other code bases. This includes:

• snappy [http://code.google.com/p/snappy/] : a fast and lightweight Lempel-Ziv type compression/decompression library. This can be used for the compression of temporory files (as used in name collating BAM input for instance).
• io_lib [http://sourceforge.net/p/staden/code/HEAD/tree/io_lib/] : This is part of the Staden package. libmaus can use this library for SAM and CRAM file input.
• SeqAN [http://www.seqan.de/] : libmaus contains a wrapper class for consensus computation. The actual consensus computation is done by SeqAN. libmaus only offers a somewhat simplified interface.
• kmlocal [http://www.cs.umd.edu/~mount/Projects/KMeans/] : libmaus can use this kmeans clustering code for the requantisation of FastQ quality values.

The compilation on Darwin (MacOS X) may require the installation of the following packages:

• pkg-config [http://www.freedesktop.org/wiki/Software/pkg-config/]
• boost [http://www.boost.org/]

pkg-config will be installed on most Linux systems. The boost libraries are required if libmaus is to be compiled using non recent versions of the GNU compiler, as they contain some classes offering functionality that has meanwhile been added to the C++ standard (shared_ptr, unique_ptr, unordered_map, ...).

Compilation of boost for libmaus on Darwin

The following lines called in an unpacked boost source tree should be sufficient to compile and install a version of the boost libraries usable by libmaus:

INSTPREFIX=${HOME}/libs/boost
./bootstrap.sh --prefix=${INSTPREFIX}
./b2 --prefix=${INSTPREFIX} --build-type=minimal \
	--layout=system toolset=darwin variant=release link=static \
	address-model=32_64 threading=multi cxxflags="-arch i386 -arch x86_64"
./b2 --prefix=${INSTPREFIX} --build-type=minimal \
	--layout=system toolset=darwin variant=release link=static \
	address-model=32_64 threading=multi cxxflags="-arch i386 -arch x86_64" install

Compilation of libmaus on Darwin

After installing boost, libmaus can be compiled and installed in ${HOME}/libmaus using:

export CPPFLAGS="-I${HOME}/libs/boost/include/"
export CFLAGS="-arch i386 -arch x86_64 -O2"
export CXXFLAGS="-arch i386 -arch x86_64 -O2"
export LDFLAGS="-L${HOME}/libs/boost/lib/"
export LIBS="-arch i386 -arch x86_64"
export CC="/usr/bin/gcc"
export CXX="/usr/bin/g++"
export CPP="/usr/bin/cpp"
export CXXCPP="/usr/bin/cpp"
bash configure --prefix=${HOME}/libmaus --disable-shared-libmaus --disable-asm \
	--disable-dependency-tracking
make install