kevyin / interop

C++ Library to parse Illumina InterOp files

Quick Start

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The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.

The InterOp files supported by this library include:

• CorrectedIntMetricsOut.bin
• ErrorMetricsOut.bin
• ExtractionMetricsOut.bin
• ImageMetricsOut.bin
• QMetricsOut.bin
• TileMetricsOut.bin
• IndexMetricsOut.bin

This library is written in C++98 and provides bindings for C# using the SWIG interface. This support includes examples and unit tests for both languages.

Documentation

Content	Description
Main	Index page for the documentation
Install	Describes how to install Illumina InterOp from binaries and the source code
Applications	Describes applications that transform binary InterOp data into text
Examples	How to examples showing how to use the Illumina InterOp C++ API
Modules	Short descriptions of the most useful code in the Illumina InterOp API
Changes	Changes between releases of the source code
Issues	Have a question? Need a feature? Found a bug? Interact with the developers here.

Install

From Source

$ git clone https://github.com/Illumina/interop.git
$ mkdir build
$ cd build
$ cmake ../interop
$ cmake --build .

Building with InterOp

GCC/Clang

g++ example1.cpp -l interop_lib -L <install_dir>/lib64 -I <install_dir>/include

For CLang, just substitute g++ with clang++.

Known Limitations

There are several known limitations to the current library:

1. You cannot build a shared library on Windows. Our CMake build script disallows it for good reason, it currently does not work. You can still use a static library on Windows. There is one caveat, you can build a shared library for the SWIG bindings, e.g. C#.
2. The full logic of SAV including certain metrics and plots are not yet implemented.
3. Microsoft .Net less than v4.0.30319 is currently not supported (Same for Mono)
4. MinGW cannot compile the code when ENABLE_BACKWARDS_COMPATIBILITY=ON
5. We do not support Mono on Windows
6. If both Visual Studio and Mono are installed, the build script will only use Visual Studio for C#