vicidel / smithlab_cpp

C++ code library that includes functions used in many of the Smith lab projects

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

If you want to build this code to use our htslib wrapper, you will need to run like this:

$ ./configure --enable-hts

You must also have HTSlib installed in some standard place on your system. If you have it installed in some other place, then you will need to set variables (CPPFLAGS and LDFLAGS) when running the configure script.

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 Makefile in this repo without running the ./configure script:

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

Note: if you run the ./configure script it will overwrite the Makefile indicated above. If that happens, just get a new one. The ./configure script must be obtained using autotools if you cloned this repo; if you downloaded this code as a "release" then the configure script should be present already.

TODO

This code needs lots of changes. I'm listing them here for the present and hope to take care of each with separate issues on GitHub. The result should be less total code overall in smithlab_cpp.

• bisulfite_utils.*pp code should disappear. It has nothing useful, and any functionality it does contain likely belongs in methpipe.
• The RNG.*pp code should also disappear. It should be replaced with the stl random code (since c++11) in applications.
• The sim_utils.*pp code has not been used in any of our tools for a very long time, and should be removed.
• QualityScore.*pp likely should be removed, as we only use sequencing quality scores in specific places, and in those places have chosen to re-implement anything that would be here.
• `smithlab_os.* Any use of character arrays should be replaced with strings for filenames. Implementation of many functions in the cpp file is sloppy.
• smithlab_utils.*pp: lots to replace here. Many functions seem redundant with functions elsewhere. Not sure of we need the smithlab namespace. Likely the copy_if function should be removed. We should test of the alphabet conversion functions are all needed.
• There might be redundancy between several functions that span GenomicRegion.*pp, chromosome_utils.*pp and smithlab_os.*pp, especially in relation to reading files that contain genomes.