├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── enhancement-request.md │ ├── feature_request.md │ └── questions-and-inquiries.md └── workflows │ └── ccpp.yml ├── .gitignore ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── RELEASE.md ├── cmake ├── FindGperftools.cmake ├── gtest.cmake └── version.cmake ├── common ├── CMakeLists.txt ├── input_ouput_parameter_map.txt ├── src │ ├── counters.h │ ├── hts_exception.h │ ├── ioHandler.cpp │ ├── ioHandler.h │ ├── main_template.h │ ├── read.cpp │ ├── read.h │ ├── threadutils.h │ ├── typedefs.h │ ├── utils.cpp │ ├── utils.h │ ├── version.h.in │ └── version.h.release └── test │ ├── testIO.cpp │ ├── testRead.cpp │ └── testThreadUtils.cpp ├── ext └── googletest │ └── googletest-release-1.12.1.tar.gz ├── hts_AdapterTrimmer ├── CMakeLists.txt ├── README ├── src │ ├── hts_AdapterTrimmer.cpp │ └── hts_AdapterTrimmer.h └── test │ ├── hts_TestAdapterTrimmer.cpp │ └── test.txt ├── hts_CutTrim ├── CMakeLists.txt ├── README ├── src │ ├── hts_CutTrim.cpp │ └── hts_CutTrim.h └── test │ └── hts_TestCutTrim.cpp ├── hts_ExtractUMI ├── CMakeLists.txt ├── README ├── src │ ├── hts_ExtractUMI.cpp │ └── hts_ExtractUMI.h └── test │ └── hts_TestExtractUMI.cpp ├── hts_LengthFilter ├── CMakeLists.txt ├── README ├── src │ ├── hts_LengthFilter.cpp │ └── hts_LengthFilter.h └── test │ └── hts_TestLengthFilter.cpp ├── hts_NTrimmer ├── CMakeLists.txt ├── README ├── src │ ├── hts_NTrimmer.cpp │ └── hts_NTrimmer.h └── test │ └── hts_TestNTrimmer.cpp ├── hts_Overlapper ├── CMakeLists.txt ├── README ├── src │ ├── hts_Overlapper.cpp │ └── hts_Overlapper.h └── test │ ├── hts_TestOverlapper.cpp │ └── test.txt ├── hts_PolyATTrim ├── CMakeLists.txt ├── README ├── diagram.txt ├── src │ ├── hts_PolyATTrim.cpp │ └── hts_PolyATTrim.h └── test │ └── hts_TestPolyATTrim.cpp ├── hts_Primers ├── CMakeLists.txt ├── README ├── src │ ├── hts_Primers.cpp │ └── hts_Primers.h └── test │ └── hts_TestPrimers.cpp ├── hts_QWindowTrim ├── CMakeLists.txt ├── README ├── src │ ├── hts_QWindowTrim.cpp │ └── hts_QWindowTrim.h └── test │ └── hts_TestQWindowTrim.cpp ├── hts_SeqScreener ├── CMakeLists.txt ├── README ├── src │ ├── hts_SeqScreener.cpp │ └── hts_SeqScreener.h └── test │ └── hts_TestSeqScreener.cpp ├── hts_Stats ├── CMakeLists.txt ├── README ├── src │ ├── hts_Stats.cpp │ └── hts_Stats.h └── test │ └── hts_TestStats.cpp ├── hts_SuperDeduper ├── CMakeLists.txt ├── README ├── src │ ├── hts_SuperDeduper.cpp │ └── hts_SuperDeduper.h └── test │ └── hts_testSuperDeduper.cpp └── regression ├── chain.json ├── hts_AdapterTrimmer.json ├── hts_AdapterTrimmer.tab6 ├── hts_AdapterTrimmer.tab6.gz ├── hts_CutTrim.json ├── hts_CutTrim.tab6 ├── hts_CutTrim.tab6.gz ├── hts_ExtractUMI.json ├── hts_ExtractUMI.tab6 ├── hts_ExtractUMI.tab6.gz ├── hts_LengthFilter.json ├── hts_LengthFilter.tab6 ├── hts_LengthFilter.tab6.gz ├── hts_NTrimmer.json ├── hts_NTrimmer.tab6 ├── hts_NTrimmer.tab6.gz ├── hts_Overlapper.json ├── 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