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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.
-------------------------------------------------------------------------------
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.
-------------------------------------------------------------------------------
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.
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