The smithlab_cpp library

This library contains code that has been used in the Smith lab for several years, and that we now depend on for several of our data analysis tools. Many of those tools use older versions of this source code in subdirectories of other repos.

Requirements

• A C++ compiler that knows C++11. The GNU g++ compiler works well for this after version 5.3.
• The GNU Scientific Library, GSL, which is likely already on your system, or easily installed through a package manager.
• The zlib library, which we use for I/O of files in gzip format. You likely have this on your system.
• Optional: The HTSLib library, which we use for I/O of SAM and BAM format files.

Building and installing the smithlab_cpp library

Assuming you downloaded the release X.X the tarball libsmithlab_cpp-X.X.tar.gz, you would do the following:

$ tar -xvf libsmithlab_cpp-X.X.tar.gz
$ cd libsmithlab_cpp-X.X
$ ./configure
$ make
$ make install

If you do not want to contaminate your system's directories with our code, you can modify the 3rd step above to:

$ ./configure --prefix=/some/unimportant/directory

It is also a very good idea to run the configure script as follows:

$ ./configure CXXFLAGS='-O3 -Wall'

This will make the resulting library code faster and much smaller, as the defaults compile with -g for debugging.

Using the source directly from the repo

If you clone the repo and attempt to use the source directly, you are likely to run into more problems than if you use a release. I will do everything I can to provide support for the releases, but I may not help if you have problems using the source repo directly.

This README.md file is written just as we are turning smithlab_cpp into a library and not a collection of source files. If you want to use it the way it has been used from 2010-2019, then you can use the original_makefile.mk which should still be in this repo. Just like this:

$ make -f original_makefile.mk OptionParser.o
g++ -Wall -std=c++11 -c -o OptionParser.o OptionParser.cpp

Now that we are using both the Zlib and HTSLib libraries, it is more important that we have a build system that can check for these. So this repo no longer contains a Makefile.