$Id: README 4276 2023-01-25 06:58:38Z peter $

About yat

This directory contains the yat library. For an overview of the project, visit

http://dev.thep.lu.se/yat

Configuring and building yat

1. If you checked out this project from the subversion repository you must run 'bootstrap' to initialize the build system.
2. Issue './configure' to create the Makefiles. Optionally run configure with '--enable-debug', which will turn on debug options.
3. Compile with 'make'.
4. 'make doc' will generate documentation.
5. Optionally do 'make check' to run test programs.
6. Issue 'make install' to install the package on your system, documentation will not be installed if documentation was not generated above. Default installation location is /usr/local; this can be changed with './configure --prefix=/dir/to/install/to'.
7. Optionally do 'make installcheck' to verify that intallation completed correctly.

The configure script has additional options; ./configure --help will offer you those choices or refer to Requirements below.

Compile Flag Variables

Compile flags (CPPFLAGS (preprocessor), CXXFLAGS (compiler), and LDFLAGS (linker)) can be set at via configure, e.g.:

#> ./configure CPPFLAGS=-I/my/local/path/include

This setting will be used both when building the source into libyat as well as propagated into script yat-config. If you only want the variable propagated to yat-config, you can instead set variables with prefix YAT_CONFIG_:

#> ./configure YAT_CONFIG_CXXFLAGS=

Similarly, if you only want the variable used when building libyat, and not propagated to output of yat-config or pkg-config, you can use flags with prefix INTERNAL_:

#> ./configure INTERNAL_CXXFLAGS="-g 03"

Requirements

From version 0.18, yat needs a C++11 compliant compiler to build. In addition, there are a few packages and programs required for compiling yat and generate supporting material. The configure script will look for required programs and report failure to meet the requirements. Here we list some of the requirements, but omit required standard utilities such as echo and sed since these are normally available.

Required packages

GSL

GNU Scientific Library, ​GSL version 1.13 or later. If you have GSL installed in a non-standard location, ./configure --with-gsl=DIR can be useful to provide the location of GSL. The gsl-config script, which is used to retrieve needed compiler and linker flags, is expected to be found in DIR/bin/. The check for existing GSL can be turned off with option --without-gsl. This can be useful, for example, if gsl-config is not available at configure time but header file will be available at make time.

BLAS

A C implementation of Basic Linear Algebra Subprograms (​BLAS) is required. GSL comes with a reference implementation, but you should consider getting a hardware optimized implementation. ATLAS provides optimized BLAS (see below).

The configure script searches for many different BLAS libraries in a specific order (for details refer to m4/yat_cblas.m4). If you want to use a specific CBLAS library, ./configure --with-cblas=LIB may be useful. Note, however, that the chosen/detected CBLAS library is not hard-coded into the installed libyat, but a user can choose a different CBLAS when she links her application. A way to access which CBLAS was detected during the configuration is to access the yat-config script directly or via the autoconf macros included in the distribution. If you do want to hard-code a choice of CBLAS into the installed libyat, you may provide the appropriate value to LIBS. The following line, for example:

#> ./configure LIBS=-lcblas

will hard-code the choice of -lcblas into libyat.

Boost

​Boost version 1.66 or later. If you have Boost installed in a non-standard location, ./configure --with-boost=DIR can be useful to provide the location of Boost. Boost header files are expected to be found in DIR/include/ and boost libraries are expected to be found in DIR/lib/. The configure script tries to detect libraries boost_thread, boost_thread and boost_iostreams. The name of a boost library typically depends on its configuration (see boost's naming convention) and there may be several versions/configurations of the same library installed. The configure tries to pick one of the available libraries, wchih can be overridden with ./configure --with-boost-thread=foo, `configure --with-boost-system=foo, and --with-boost-iostreams=foo`, respectively. The check for boost can be turned off with --without-boost.

quiet nan

Quiet NaN's must be supported.

infinity

infinity for type double must be supported.

Optional packages

HTSLIB and Samtools

In order to enable functionality related to bam files htslib (​http://www.htslib.org) version 1.10 (or newer) must be available. Header file <htslib/sam.h> is required as well as 'libhts'. If you have header files installed outside compiler's search path (in e.g. '/path/to/htslib/sam.h', you can help the compiler with ./configure CPPFLAGS=-I/path/to. If library is installed outside linker's search path, in e.g. <libdir>, you can run `./configure LDFLAGS=-L<lib dir>`. You can build yat without bam support by running ./configure --without-htslib.

The samtools program (version 1.2 or newer) is needed for some tests related to bam functionality. If samtools is not found by configure, these tests will be skipped. If you have samtools available outside PATH, you can help configure to find it with `./configure SAMTOOLS=/path/to/samtools`.

The bcftools program is needed for some tests. If bcftools is not found by configure, these tests will be skipped. If you have bcftools available outside your PATH, you can help configure to find it with ./configure BCFTOOLS=/path/to/bcftools.

ZLIB

Zlib available from ​http://www.zlib.net/ is required to build samtools and consequently needed to build yat too, unless you turn off samtools support (please refer to samtools section above). Header file zlib.h and library libz are required. If installed in an unconventional location you can help the compiler/linker with `CPPFLAGS=-I<include dir> and LDFLAGS=-L<lib dir>`, respectively.

ATLAS

GSL supplies a reference implementation of BLAS. You may want to consider using hardware optimized BLAS. The ​ATLAS software provides an automatic hardware optimized BLAS library.

The detection of ATLAS is supported by the yat configuration script but in many cases the ATLAS libraries are installed in non-conventional directory locations. As an example, on Fedora 8, ATLAS libraries are located in /usr/lib/atlas or /usr/lib64/atlas depending on your hardware architecture. If you have ATLAS installed and the configure script fails to locate it, try to add the location to the atlas libraries when running configure:

#> ./configure LDFLAGS="-L/usr/lib64/atlas"

C++11 Compliant Compiler

The configure script will test that the compiler is in C++11 mode and supports features such as rvalue and std::atomic. If you run configure with option --enable-cxx11

#> ./configure --enable-cxx11

and the compiler is not in C++11 mode, the configure script will try different options such as '-std=cxx11' to turn on support for C++11 features.

Doxygen

​Doxygen 1.5 (or newer) is required for generation of the API documentation. If doxygen application is missing, generation of API documentation is disabled. You can turn off doxygen usage with

#> ./configure DOXYGEN=no

Documentation

The API documentation for the latest release is available in HTML and can be found through http://dev.thep.lu.se/yat. If you wish to build a local copy, issue make doc and you will find the documents in directory doc/html/.

Developers

See file README.developer for developer specific information.

Mac OS X

On Mac OS X you can create a universal library, a library that works on multiple systems. You can do this by specifying multiple -arch options to the compiler (but not to the preprocessor):

#> ./configure CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \

CXXCPP="g++ -E" --disable-dependency-tracking

This will produce a universal yat library with 4 architectures. If your OS X does not support both Power-PC and Intel-based processors, you can omit these architectures. Also, required libraries, GSL and CBLAS, need to be available as universal libraries with desired architectures.

Copyright (C) 2003 Jari Häkkinen, Peter Johansson
Copyright (C) 2004 Jari Häkkinen
Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Peter Johansson
Copyright (C) 2022 Jari Häkkinen, Peter Johansson
This file is part of yat library, http://dev.thep.lu.se/yat
The yat library is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 3 of the
License, or (at your option) any later version.
The yat library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with yat. If not, see <http://www.gnu.org/licenses/>.