Adding a README

Author: andrewdavidsmith

README.md

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+# 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](https://zlib.net), which we use for I/O of files
+  in gzip format. You likely have this on your system.
+- Optional: The [HTSLib library](http://htslib.org), 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` but instead you must
+generate one. If you want