├── .gitignore ├── CHANGES.md ├── LICENSE ├── Makefile ├── README.md ├── configure ├── ngs-bam ├── .gitignore ├── Makefile ├── Makefile.install ├── Makefile.libs ├── Makefile.rules ├── Makefile.vers ├── bam.cpp ├── bam.hpp ├── configure ├── examples │ ├── AlignTest.cpp │ ├── Makefile │ ├── Makefile.config │ └── README.md ├── ngs-bam.cpp ├── ngs-bam │ └── ngs-bam.hpp └── setup │ ├── install │ ├── install.perl │ ├── install.prl │ ├── konfigure.perl │ ├── ngs-bam │ ├── install │ ├── linux │ │ └── os.prl │ └── mac │ │ └── os.prl │ ├── os-arch.perl │ ├── os-arch.prl │ └── package.prl ├── ngs-java ├── .gitignore ├── Makefile ├── Makefile.java ├── Makefile.rules ├── Makefile.vers ├── build.xml ├── configure ├── examples │ ├── Makefile │ ├── examples │ │ ├── AlignSliceTest.java │ │ ├── AlignTest.java │ │ ├── DumpReferenceFASTA.java │ │ ├── FragTest.java │ │ ├── PileupTest.java │ │ ├── ReadGroupTest.java │ │ ├── RefTest.java │ │ └── SparkKMer.java │ └── expected.txt ├── gov │ └── nih │ │ └── nlm │ │ └── ncbi │ │ └── ngs │ │ ├── DownloadManager.java │ │ ├── FileCreator.java │ │ ├── HttpException.java │ │ ├── HttpManager.java │ │ ├── LMProperties.java │ │ ├── LibDependencies.java │ │ ├── LibManager.java │ │ ├── LibPathIterator.java │ │ ├── LibVersionChecker.java │ │ ├── Logger.java │ │ ├── Makefile │ │ ├── Manager.java │ │ ├── NGS.java │ │ ├── Version.java │ │ └── error │ │ ├── LibraryIncompatibleVersionError.java │ │ ├── LibraryLoadError.java │ │ ├── LibraryNotFoundError.java │ │ └── cause │ │ ├── ConnectionProblemCause.java │ │ ├── DownloadDisabledCause.java │ │ ├── InvalidLibraryCause.java │ │ ├── JvmErrorCause.java │ │ ├── LibraryLoadCause.java │ │ ├── OutdatedJarCause.java │ │ ├── PrereleaseReqLibCause.java │ │ └── UnsupportedArchCause.java ├── ngs │ ├── Alignment.java │ ├── AlignmentIterator.java │ ├── ErrorMsg.java │ ├── Fragment.java │ ├── FragmentIterator.java │ ├── Package.java │ ├── Pileup.java │ ├── PileupEvent.java │ ├── PileupEventIterator.java │ ├── PileupIterator.java │ ├── Read.java │ ├── ReadCollection.java │ ├── ReadGroup.java │ ├── ReadGroupIterator.java │ ├── ReadIterator.java │ ├── Reference.java │ ├── ReferenceIterator.java │ ├── ReferenceSequence.java │ ├── Statistics.java │ └── itf │ │ ├── AlignmentIteratorItf.java │ │ ├── AlignmentItf.java │ │ ├── FragmentIteratorItf.java │ │ ├── FragmentItf.java │ │ ├── PileupEventIteratorItf.java │ │ ├── PileupEventItf.java │ │ ├── PileupIteratorItf.java │ │ ├── PileupItf.java │ │ ├── ReadCollectionItf.java │ │ ├── ReadGroupIteratorItf.java │ │ ├── ReadGroupItf.java │ │ ├── ReadIteratorItf.java │ │ ├── ReadItf.java │ │ ├── Refcount.java │ │ ├── ReferenceIteratorItf.java │ │ ├── ReferenceItf.java │ │ ├── ReferenceSequenceItf.java │ │ └── StatisticsItf.java └── setup │ ├── install │ ├── install.perl │ ├── install.prl │ ├── konfigure.perl │ ├── ngs-java │ ├── install │ ├── linux │ │ └── os.prl │ └── mac │ │ └── os.prl │ ├── os-arch.perl │ ├── os-arch.prl │ └── package.prl ├── ngs-python ├── .gitignore ├── Makefile ├── Makefile.python ├── Makefile.rules ├── Makefile.vers ├── build.xml ├── configure ├── examples │ ├── AlignSliceTest.py │ ├── AlignTest.py │ ├── DumpReferenceFASTA.py │ ├── FragTest.py │ ├── Makefile │ ├── NGS_FastQ.py │ ├── PileupTest.py │ ├── RefTest.py │ └── expected.txt ├── ngs │ ├── Alignment.py │ ├── AlignmentIterator.py │ ├── ErrorMsg.py │ ├── Fragment.py │ ├── FragmentIterator.py │ ├── LibChecker.py │ ├── LibManager.py │ ├── Package.py │ ├── Pileup.py │ ├── PileupEvent.py │ ├── PileupEventIterator.py │ ├── PileupIterator.py │ ├── Read.py │ ├── ReadCollection.py │ ├── ReadGroup.py │ ├── ReadGroupIterator.py │ ├── ReadIterator.py │ ├── Refcount.py │ ├── Reference.py │ ├── ReferenceIterator.py │ ├── ReferenceSequence.py │ ├── Statistics.py │ ├── String.py │ └── __init__.py ├── setup.py └── setup │ ├── install │ ├── install.perl │ ├── install.prl │ ├── konfigure.perl │ ├── ngs-python │ ├── install │ ├── linux │ │ └── os.prl │ └── mac │ │ └── os.prl │ ├── os-arch.perl │ ├── os-arch.prl │ └── package.prl └── ngs-sdk ├── .gitignore ├── CONTENTS.txt ├── Makefile ├── Makefile.install ├── Makefile.libs ├── Makefile.rules ├── Makefile.vers ├── adapter ├── AlignmentItf.cpp ├── ErrBlock.cpp ├── ErrBlock.hpp ├── ErrorMsg.cpp ├── FragmentItf.cpp ├── Makefile ├── PileupEventItf.cpp ├── PileupItf.cpp ├── ReadCollectionItf.cpp ├── ReadGroupItf.cpp ├── ReadItf.cpp ├── Refcount.cpp ├── ReferenceItf.cpp ├── ReferenceSequenceItf.cpp ├── StatisticsItf.cpp ├── StringItf.cpp └── unix │ └── fat86 │ └── atomic32.h ├── configure ├── dispatch ├── AlignmentItf.cpp ├── ErrBlock.cpp ├── ErrorMsg.cpp ├── FragmentItf.cpp ├── Makefile ├── PackageItf.cpp ├── PileupEventItf.cpp ├── PileupItf.cpp ├── ReadCollectionItf.cpp ├── ReadGroupItf.cpp ├── ReadItf.cpp ├── Refcount.cpp ├── ReferenceItf.cpp ├── ReferenceSequenceItf.cpp ├── StatisticsItf.cpp ├── StringItf.cpp ├── VTable.cpp └── version.h ├── examples ├── .gitignore ├── AlignSliceTest.cpp ├── AlignTest.cpp ├── DumpReferenceFASTA.cpp ├── FastqTableDump.cpp ├── FragTest.cpp ├── Makefile ├── Makefile.config ├── PileupTest.cpp ├── RefTest.cpp └── expected.txt ├── language ├── Makefile ├── c++ │ ├── Alignment.cpp │ ├── AlignmentIterator.cpp │ ├── Fragment.cpp │ ├── FragmentIterator.cpp │ ├── Makefile │ ├── Pileup.cpp │ ├── PileupEvent.cpp │ ├── PileupEventIterator.cpp │ ├── PileupIterator.cpp │ ├── Read.cpp │ ├── ReadCollection.cpp │ ├── ReadGroup.cpp │ ├── ReadGroupIterator.cpp │ ├── ReadIterator.cpp │ ├── Refcount.cpp │ ├── Reference.cpp │ ├── ReferenceIterator.cpp │ ├── ReferenceSequence.cpp │ ├── Statistics.cpp │ └── StringRef.cpp ├── java │ ├── .gitignore │ ├── Makefile │ ├── jni.h │ ├── jni_AlignmentIteratorItf.cpp │ ├── jni_AlignmentIteratorItf.h │ ├── jni_AlignmentItf.cpp │ ├── jni_AlignmentItf.h │ ├── jni_ErrorMsg.cpp │ ├── jni_ErrorMsg.hpp │ ├── jni_FragmentItf.cpp │ ├── jni_FragmentItf.h │ ├── jni_Package.cpp │ ├── jni_Package.h │ ├── jni_PileupEventIteratorItf.cpp │ ├── jni_PileupEventIteratorItf.h │ ├── jni_PileupEventItf.cpp │ ├── jni_PileupEventItf.h │ ├── jni_PileupIteratorItf.cpp │ ├── jni_PileupIteratorItf.h │ ├── jni_PileupItf.cpp │ ├── jni_PileupItf.h │ ├── jni_ReadCollectionItf.cpp │ ├── jni_ReadCollectionItf.h │ ├── jni_ReadGroupIteratorItf.cpp │ ├── jni_ReadGroupIteratorItf.h │ ├── jni_ReadGroupItf.cpp │ ├── jni_ReadGroupItf.h │ ├── jni_ReadIteratorItf.cpp │ ├── jni_ReadIteratorItf.h │ ├── jni_ReadItf.cpp │ ├── jni_ReadItf.h │ ├── jni_Refcount.cpp │ ├── jni_Refcount.h │ ├── jni_ReferenceIteratorItf.cpp │ ├── jni_ReferenceIteratorItf.h │ ├── jni_ReferenceItf.cpp │ ├── jni_ReferenceItf.h │ ├── jni_ReferenceSequenceItf.cpp │ ├── jni_ReferenceSequenceItf.h │ ├── jni_StatisticsItf.cpp │ ├── jni_StatisticsItf.h │ ├── jni_String.cpp │ ├── jni_String.hpp │ ├── jni_md.h │ └── libngs-java-ncbi.vers └── python │ ├── Makefile │ ├── py_AlignmentIteratorItf.cpp │ ├── py_AlignmentIteratorItf.h │ ├── py_AlignmentItf.cpp │ ├── py_AlignmentItf.h │ ├── py_ErrorMsg.hpp │ ├── py_FragmentIteratorItf.cpp │ ├── py_FragmentIteratorItf.h │ ├── py_FragmentItf.cpp │ ├── py_FragmentItf.h │ ├── py_PackageItf.cpp │ ├── py_PackageItf.h │ ├── py_PileupEventIteratorItf.cpp │ ├── py_PileupEventIteratorItf.h │ ├── py_PileupEventItf.cpp │ ├── py_PileupEventItf.h │ ├── py_PileupIteratorItf.cpp │ ├── py_PileupIteratorItf.h │ ├── py_PileupItf.cpp │ ├── py_PileupItf.h │ ├── py_ReadCollectionItf.cpp │ ├── py_ReadCollectionItf.h │ ├── py_ReadGroupIteratorItf.cpp │ ├── py_ReadGroupIteratorItf.h │ ├── py_ReadGroupItf.cpp │ ├── py_ReadGroupItf.h │ ├── py_ReadIteratorItf.cpp │ ├── py_ReadIteratorItf.h │ ├── py_ReadItf.cpp │ ├── py_ReadItf.h │ ├── py_Refcount.cpp │ ├── py_Refcount.h │ ├── py_ReferenceIteratorItf.cpp │ ├── py_ReferenceIteratorItf.h │ ├── py_ReferenceItf.cpp │ ├── py_ReferenceItf.h │ ├── py_ReferenceSequenceItf.cpp │ ├── py_ReferenceSequenceItf.h │ ├── py_StatisticsItf.cpp │ ├── py_StatisticsItf.h │ ├── py_StringItf.cpp │ ├── py_StringItf.h │ └── py_ngs_defs.h ├── ngs ├── Alignment.hpp ├── AlignmentIterator.hpp ├── ErrorMsg.hpp ├── Fragment.hpp ├── FragmentIterator.hpp ├── Package.hpp ├── Pileup.hpp ├── PileupEvent.hpp ├── PileupEventIterator.hpp ├── PileupIterator.hpp ├── Read.hpp ├── ReadCollection.hpp ├── ReadGroup.hpp ├── ReadGroupIterator.hpp ├── ReadIterator.hpp ├── Reference.hpp ├── ReferenceIterator.hpp ├── ReferenceSequence.hpp ├── Statistics.hpp ├── StringRef.hpp ├── adapter │ ├── AlignmentItf.hpp │ ├── ErrorMsg.hpp │ ├── FragmentItf.hpp │ ├── PileupEventItf.hpp │ ├── PileupItf.hpp │ ├── ReadCollectionItf.hpp │ ├── ReadGroupItf.hpp │ ├── ReadItf.hpp │ ├── Refcount.hpp │ ├── ReferenceItf.hpp │ ├── ReferenceSequenceItf.hpp │ ├── StatisticsItf.hpp │ ├── StringItf.hpp │ └── defs.h ├── inl │ ├── Alignment.hpp │ ├── AlignmentIterator.hpp │ ├── Fragment.hpp │ ├── FragmentIterator.hpp │ ├── Package.hpp │ ├── Pileup.hpp │ ├── PileupEvent.hpp │ ├── PileupEventIterator.hpp │ ├── PileupIterator.hpp │ ├── Read.hpp │ ├── ReadCollection.hpp │ ├── ReadGroup.hpp │ ├── ReadGroupIterator.hpp │ ├── ReadIterator.hpp │ ├── Reference.hpp │ ├── ReferenceIterator.hpp │ ├── ReferenceSequence.hpp │ ├── Statistics.hpp │ └── StringRef.hpp ├── itf │ ├── AlignmentItf.h │ ├── AlignmentItf.hpp │ ├── ErrBlock.h │ ├── ErrBlock.hpp │ ├── ErrorMsg.hpp │ ├── FragmentItf.h │ ├── FragmentItf.hpp │ ├── PackageItf.hpp │ ├── PileupEventItf.h │ ├── PileupEventItf.hpp │ ├── PileupItf.h │ ├── PileupItf.hpp │ ├── ReadCollectionItf.h │ ├── ReadCollectionItf.hpp │ ├── ReadGroupItf.h │ ├── ReadGroupItf.hpp │ ├── ReadItf.h │ ├── ReadItf.hpp │ ├── Refcount.h │ ├── Refcount.hpp │ ├── ReferenceItf.h │ ├── ReferenceItf.hpp │ ├── ReferenceSequenceItf.h │ ├── ReferenceSequenceItf.hpp │ ├── StatisticsItf.h │ ├── StatisticsItf.hpp │ ├── StringItf.h │ ├── StringItf.hpp │ ├── VTable.h │ ├── VTable.hpp │ └── defs.h ├── unix │ ├── arm64 │ │ └── atomic32.h │ ├── fat86 │ │ └── atomic32.h │ ├── i386 │ │ └── atomic32.h │ └── x86_64 │ │ └── atomic32.h └── win │ ├── atomic32.h │ └── stdbool.h ├── setup ├── install ├── install.perl ├── install.prl ├── konfigure.perl ├── ngs-c++ │ ├── install │ ├── install.prl │ ├── linux │ │ └── os.prl │ └── mac │ │ └── os.prl ├── ngs-engine-dev │ ├── install │ ├── install.prl │ ├── linux │ │ └── os.prl │ └── mac │ │ └── os.prl ├── os-arch.perl ├── os-arch.prl └── package.prl ├── test ├── Makefile ├── ngs-test │ ├── Makefile │ └── main.cpp └── test_engine │ ├── AlignmentItf.hpp │ ├── Makefile │ ├── PileupEventItf.hpp │ ├── PileupItf.hpp │ ├── ReadCollectionItf.hpp │ ├── ReadGroupItf.hpp │ ├── ReadItf.hpp │ ├── ReferenceItf.hpp │ ├── ReferenceSequenceItf.hpp │ ├── StatisticsItf.hpp │ ├── test_engine.cpp │ └── test_engine.hpp └── win ├── build.xml ├── libadapter.files ├── libdispatch.files ├── libngs-c++.files ├── libtest_engine.files ├── ngs-sdk.files ├── ngs-test.files ├── vs2010 ├── .gitignore ├── ipch │ └── libadapter-2137bad9 │ │ └── libngs-adapt-c++-4ff9a6f5.ipch ├── lib-project.props ├── 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