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 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.

Interop is licensed under PolyForm Strict License 1.0.0

We now support an interface to 3.8-3.14

Note that 3.10-3.14 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: - CorrectedIntMetricsOut.bin - ErrorMetricsOut.bin - ExtractionMetricsOut.bin - ExtendedTileMetricsOut.bin - ImageMetricsOut.bin - QMetricsOut.bin - TileMetricsOut.bin - IndexMetricsOut.bin - QMetrics2030Out.bin - QMetricsByLaneOut.bin - EmpiricalPhasingMetricsOut.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.

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Documentation

| Content | Description | | ----------------------------- | -------------------------------------------------------------------------------------| | [Main][MainPage] | Index page for the documentation | | [Install][InstallPage] | Describes how to install Illumina InterOp from binaries and the source code | | [Applications][AppsPage] | Describes applications that transform binary InterOp data into text | | [Examples][ExamplesPage] | How to examples showing how to use the Illumina InterOp C++ API | | [Modules][ModulesPage] | Short descriptions of the most useful code in the Illumina InterOp API | | [Changes][ChangesPage] | Changes between releases of the source code | | [Issues] | Have a question? Need a feature? Found a bug? Interact with the developers here. | | [Performance][PerfPage] | Computation performance of the code | | [Formats][BinaryFormats] | Description of the binary formats for each InterOp file | | [Python][PythonBinding] | Step by step tutorial using the Python binding |

[MainPage]: http://illumina.github.io/interop/index.html [InstallPage]: http://illumina.github.io/interop/install.html [AppsPage]: http://illumina.github.io/interop/apps.html [ExamplesPage]: http://illumina.github.io/interop/examples.html [ModulesPage]: http://illumina.github.io/interop/modules.html [ChangesPage]: http://illumina.github.io/interop/changes.html [Issues]: https://github.com/Illumina/interop/issues [PerfPage]: http://illumina.github.io/interop/perf.html [BinaryFormats]: http://illumina.github.io/interop/binary_formats.html [PythonBinding]: http://illumina.github.io/interop/python_binding.html

Install

Python

Supported versions for binary distribution: 3.8-3.14.

Python 2.7, 3.5, 3.6, 3.7 support has been removed

You should have NumPy already installed.

~~~~~{.sh} $ pip install interop ~~~~~

Test the installation

~~~~~{.sh} $ 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.

From Source

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

Building with InterOp

GCC/Clang

~~~~~{.sh} g++ example1.cpp -l interoplib -L dir>/lib64 -I /include ~~~~~