{"id":15009264,"url":"https://github.com/illumina/interop","last_synced_at":"2025-10-25T01:32:24.741Z","repository":{"id":40530807,"uuid":"50213716","full_name":"Illumina/interop","owner":"Illumina","description":"C++ Library to parse Illumina InterOp files","archived":false,"fork":false,"pushed_at":"2025-03-13T22:20:23.000Z","size":25236,"stargazers_count":75,"open_issues_count":4,"forks_count":28,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-04-09T20:04:16.377Z","etag":null,"topics":["cpp","csharp","illumina-sequencing","interop","python","python-3-8","python-3-9","python27","python3","python35","python36","python37","swig"],"latest_commit_sha":null,"homepage":"http://illumina.github.io/interop/index.html","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Illumina.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-01-22T23:21:29.000Z","updated_at":"2025-03-13T22:17:32.000Z","dependencies_parsed_at":"2023-02-17T00:31:36.274Z","dependency_job_id":"f2ad0db6-0fdb-47ea-a1d3-2bf4126c5473","html_url":"https://github.com/Illumina/interop","commit_stats":{"total_commits":516,"total_committers":6,"mean_commits":86.0,"dds":"0.21124031007751942","last_synced_commit":"5fd23ff188087649db633e4ebe6622bad2f26b8a"},"previous_names":[],"tags_count":63,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Finterop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Finterop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Finterop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Illumina%2Finterop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Illumina","download_url":"https://codeload.github.com/Illumina/interop/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248103865,"owners_count":21048245,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cpp","csharp","illumina-sequencing","interop","python","python-3-8","python-3-9","python27","python3","python35","python36","python37","swig"],"created_at":"2024-09-24T19:24:05.221Z","updated_at":"2025-10-25T01:32:19.721Z","avatar_url":"https://github.com/Illumina.png","language":"C++","readme":"Quick Start\n===========\n\n[![TravisCI_Status][tcistatus]][tcihome]\n[![AppVeyor_status][acistatus]][acihome]\n[![Coverity_status][covstatus]][covhome]\n\nThe Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by\nIllumina sequencers including **NextSeq 1k/2k** and NovaSeqX. These libraries are backwards compatible and capable of supporting prior releases of the software,\nwith one exception: GA systems have been excluded.\n\n***\n\u003e We now support an interface to 3.8-3.13\n\u003e Note that 3.10-3.13 are CentOS 7 or later while earlier versions support Centos 5 or later\n\u003e Note: dumptext has been deprecated in favor of imaging_table and will be removed in the next version\n***\n\nThe InterOp files supported by this library include:\n  - CorrectedIntMetricsOut.bin\n  - ErrorMetricsOut.bin\n  - ExtractionMetricsOut.bin\n  - ExtendedTileMetricsOut.bin\n  - ImageMetricsOut.bin\n  - QMetricsOut.bin\n  - TileMetricsOut.bin\n  - IndexMetricsOut.bin\n  - QMetrics2030Out.bin\n  - QMetricsByLaneOut.bin\n  - EmpiricalPhasingMetricsOut.bin\n\nThis library is written in C++98 and provides bindings for C# using the SWIG interface. This\nsupport includes examples and unit tests for both languages.\n\n[tcistatus]:https://travis-ci.org/Illumina/interop.svg?branch=master\n[tcihome]:https://travis-ci.org/Illumina/interop\n\n[acistatus]:https://ci.appveyor.com/api/projects/status/5hwirymkc10uf13d/branch/master?svg=true\n[acihome]:https://ci.appveyor.com/project/ezralanglois/interop/branch/master\n\n\n[covstatus]:https://scan.coverity.com/projects/7744/badge.svg\n[covhome]:https://scan.coverity.com/projects/illumina-interop\n\n\nDocumentation\n-------------\n\n| Content                       | Description                                                                          |\n| ----------------------------- | -------------------------------------------------------------------------------------|\n| [Main][MainPage]              | Index page for the documentation                                                     |\n| [Install][InstallPage]        | Describes how to install Illumina InterOp from binaries and the source code          |\n| [Applications][AppsPage]      | Describes applications that transform binary InterOp data into text                  |\n| [Examples][ExamplesPage]      | How to examples showing how to use the Illumina InterOp C++ API                      |\n| [Modules][ModulesPage]        | Short descriptions of the most useful code in the Illumina InterOp API               |\n| [Changes][ChangesPage]        | Changes between releases of the source code                                          |\n| [Issues]                      | Have a question? Need a feature? Found a bug? Interact with the developers here.     |\n| [Performance][PerfPage]       | Computation performance of the code                                                  |\n| [Formats][BinaryFormats]      | Description of the binary formats for each InterOp file                              |\n| [Python][PythonBinding]       | Step by step tutorial using the Python binding                                       |\n\n[MainPage]: http://illumina.github.io/interop/index.html\n[InstallPage]: http://illumina.github.io/interop/install.html\n[AppsPage]: http://illumina.github.io/interop/apps.html\n[ExamplesPage]: http://illumina.github.io/interop/examples.html\n[ModulesPage]: http://illumina.github.io/interop/modules.html\n[ChangesPage]: http://illumina.github.io/interop/changes.html\n[Issues]: https://github.com/Illumina/interop/issues\n[PerfPage]: http://illumina.github.io/interop/perf.html\n[BinaryFormats]: http://illumina.github.io/interop/binary_formats.html\n[PythonBinding]: http://illumina.github.io/interop/python_binding.html\n\nInstall\n-------\n\n### Python\n\nSupported versions for binary distribution: 3.8-3.13.\n\n** Python 2.7, 3.5, 3.6, 3.7 support has been removed **\n\nYou should have NumPy already installed.\n\n~~~~~~~~~~~~~{.sh}\n$ pip install interop\n~~~~~~~~~~~~~\n\nTest the installation\n\n~~~~~~~~~~~~~{.sh}\n$ python -m interop --test\n~~~~~~~~~~~~~\n\nIf you see this error:\n\n    RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa\n\nThen upgrade numpy and try again.\n\n### From Source\n\n~~~~~~~~~~~~~{.sh}\n$ git clone https://github.com/Illumina/interop.git\n$ mkdir build\n$ cd build\n$ cmake ../interop\n$ cmake --build .\n~~~~~~~~~~~~~\n\nBuilding with InterOp\n---------------------\n\n### GCC/Clang\n\n~~~~~~~~~~~~~{.sh}\ng++ example1.cpp -l interop_lib -L \u003cinstall_dir\u003e/lib64 -I \u003cinstall_dir\u003e/include\n~~~~~~~~~~~~~\n\nFor CLang, just substitute g++ with clang++. \n\n\nKnown Limitations\n-----------------\n\nThere are several known limitations to the current library:\n\n  1. You cannot build a shared library on Windows. Our CMake build script disallows it for good reason, it currently\n     does not work. You can still use a static library on Windows. There is one caveat, you can build a shared\n     library for the SWIG bindings, e.g. C#.\n  2. Microsoft .Net less than v4.0.30319 is currently not supported (Same for Mono)\n  3. MinGW cannot compile the code when ENABLE_BACKWARDS_COMPATIBILITY=ON\n  4. We do not support Mono on Windows\n  5. If both Visual Studio and Mono are installed, the build script will only use Visual Studio for C#\n  6. We do not support 32-bit builds\n  7. MinGW W64 4.9.x and prior will not link properly\n  8. Visual Studio 12 2013 is not supported for the C# Bindings (Results in heap corruption)\n  9. We support .NET Core 2.x or later\n  10. Big endian systems are currently not supported\n  11. We do not support compilers earlier than 4.8.x - too many compiler bugs\n\nSAV Analysis Tab\n----------------\n\nThe following images were generated using the applications provided by\nthe InterOp package.\n\n![Example Plots](docs/images/example_plots.png)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fillumina%2Finterop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fillumina%2Finterop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fillumina%2Finterop/lists"}