C++ Library to parse Illumina InterOp files
GPL-3.0 License
The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k and NovaSeqX. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
We now support an interface to 3.8-3.12 Note that 3.10-3.12 are CentOS 7 or later while earlier versions support Centos 5 or later Note: dumptext has been deprecated in favor of imaging_table and will be removed in the next version
The InterOp files supported by this library include:
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.
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. |
Performance | Computation performance of the code |
Formats | Description of the binary formats for each InterOp file |
Python | Step by step tutorial using the Python binding |
Supported versions for binary distribution: 3.5-3.10.
** Python 2.7 support has been removed **
You should have NumPy already installed.
$ pip install interop
Test the installation
$ python -m interop --test
If you see this error:
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Then upgrade numpy and try again.
$ git clone https://github.com/Illumina/interop.git
$ mkdir build
$ cd build
$ cmake ../interop
$ cmake --build .
g++ example1.cpp -l interop_lib -L <install_dir>/lib64 -I <install_dir>/include
For CLang, just substitute g++ with clang++.
There are several known limitations to the current library:
The following images were generated using the applications provided by the InterOp package.