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https://github.com/illumina/interop

C++ Library to parse Illumina InterOp files
https://github.com/illumina/interop

cpp csharp illumina-sequencing interop python python-3-8 python-3-9 python27 python3 python35 python36 python37 swig

Last synced: 7 days ago
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C++ Library to parse Illumina InterOp files

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README 

        
Quick Start

===========



[![TravisCI_Status][tcistatus]][tcihome]

[![AppVeyor_status][acistatus]][acihome]

[![Coverity_status][covstatus]][covhome]



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:

  - 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.



[tcistatus]:https://travis-ci.org/Illumina/interop.svg?branch=master

[tcihome]:https://travis-ci.org/Illumina/interop



[acistatus]:https://ci.appveyor.com/api/projects/status/5hwirymkc10uf13d/branch/master?svg=true

[acihome]:https://ci.appveyor.com/project/ezralanglois/interop/branch/master



[covstatus]:https://scan.coverity.com/projects/7744/badge.svg

[covhome]:https://scan.coverity.com/projects/illumina-interop



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: 3.5-3.10.



** Python 2.7 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 interop_lib -L /lib64 -I /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. Microsoft .Net less than v4.0.30319 is currently not supported (Same for Mono)

  3. MinGW cannot compile the code when ENABLE_BACKWARDS_COMPATIBILITY=ON

  4. We do not support Mono on Windows

  5. If both Visual Studio and Mono are installed, the build script will only use Visual Studio for C#

  6. We do not support 32-bit builds

  7. MinGW W64 4.9.x and prior will not link properly

  8. Visual Studio 12 2013 is not supported for the C# Bindings (Results in heap corruption)

  9. We support .NET Core 2.x or later

  10. Big endian systems are currently not supported

  11. We do not support compilers earlier than 4.8.x - too many compiler bugs



SAV Analysis Tab

----------------



The following images were generated using the applications provided by

the InterOp package.



![Example Plots](docs/images/example_plots.png)