libmaus2

libmaus2 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.

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The main development branch of libmaus2 is hosted by gitlab at

https://gitlab.com/german.tischler/libmaus2

Release packages can be found at

https://gitlab.com/german.tischler/libmaus2/tags

Please make sure to choose a package containing the word “release” in it’s name if you intend to compile libmaus2 for production (i.e. non development) use.

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Compilation

libmaus2 uses the GNU autoconf/automake tool set. It can be compiled on Linux using:

libtoolize
aclocal
autoreconf -i -f
./configure
make

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

The release packages come with a configure script, so running libtoolize, aclocal etc should not be necessary, i.e.

./configure
make

should be sufficient to compile libmaus2.

A full list of configuration parameters can be obtained by calling

./configure --help

libmaus2 can use functionality from several other code bases. This includes:

• snappy [https://github.com/google/snappy] : a fast and lightweight Lempel-Ziv type compression/decompression library. This can be used for the compression of temporary files (as used in name collating BAM input for instance).
• io_lib [https://github.com/jkbonfield/io_lib] : This is part of the Staden package. libmaus2 can use this library for SAM and CRAM file input. The minimum version of io_lib required is 1.14.13.
• libsecrecy [https://gitlab.com/german.tischler/libsecrecy] : a library for data encryption and decryption allowing random access on the read side The url scheme used is libsecrecy[keyname]:path, where providing a key name is not necessary for decryption.

libmaus2 requires some form of atomic shared pointer. This can be either std::atomic< std::shared_ptr<> > (which is not supported by at lot of systems yet, including gcc version at least up to version 11) or boost::atomic_shared_ptr. This means on most systems you need to have the boost libraries (e.g. libboost-dev on Ubuntu) installed to compile libmaus2.