├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── ChangeLog ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── genMakefile.R └── seqminer.R ├── README.md ├── appveyor.yml ├── cleanup ├── configure ├── configure.ac ├── configure.win ├── demo ├── 00Index ├── annotate.R ├── meta.workflow.R └── vcf.workflow.R ├── docs ├── Manual.html ├── Manual.html.bak.09052013 ├── Manual.html.bak.11112013 ├── Tutorial.html ├── annotation.html ├── benchmark.html ├── benchmark │ ├── README │ ├── data │ │ ├── rand.chr1.gene.100 │ │ └── rand.chr1.range.100 │ ├── extraction │ │ ├── seqminer │ │ │ ├── chr1.nonsyn.gene │ │ │ │ ├── cmd.sh │ │ │ │ └── script.oneByone.R │ │ │ └── chr1.nonsyn.range │ │ │ │ ├── cmd.sh │ │ │ │ └── script.oneByone.R │ │ └── va │ │ │ ├── chr1.nonsyn.gene │ │ │ └── script.chr1.readOneByOne.R │ │ │ └── chr1.nonsyn.range │ │ │ └── script.chr1.readOneByOne.R │ └── integration │ │ ├── gemini │ │ ├── README │ │ ├── annotate.sh │ │ └── import.sh │ │ ├── seqminer │ │ └── annotate.R │ │ └── va │ │ ├── README │ │ ├── annotate.R │ │ └── cmd.sh ├── css │ └── toc.css ├── data.set.html ├── index.html ├── js │ └── toc.min.js ├── query.html ├── script │ ├── appendGA.py │ └── appendToc.py ├── version └── workflow.png ├── inst ├── CITATION ├── benchmark │ ├── output.png │ └── seqminer2_benchmark_script.txt ├── bgen │ ├── all.anno.filtered.extract.bgen │ └── all.anno.filtered.extract.bgen.bgi ├── doc │ └── Manual.html ├── plink │ ├── all.anno.filtered.extract.bed │ ├── all.anno.filtered.extract.bim │ └── all.anno.filtered.extract.fam ├── rvtests │ ├── cfh.refFlat.txt │ ├── rvtest.MetaCov.assoc.gz │ ├── rvtest.MetaCov.assoc.gz.tbi │ ├── rvtest.MetaScore.assoc.anno.gz │ ├── rvtest.MetaScore.assoc.anno.gz.tbi │ ├── rvtest.MetaScore.assoc.gz │ ├── rvtest.MetaScore.assoc.gz.tbi │ ├── rvtest.MetaSkew.assoc.gz │ └── rvtest.MetaSkew.assoc.gz.tbi ├── tabanno │ ├── codon.txt │ ├── input.100.vcf.gz │ ├── input.demo.vcf │ ├── input.test.plain.txt │ ├── input.test.vcf │ ├── priority.epact.txt │ ├── priority.txt │ ├── test.bed │ ├── test.dbNSFP.gz │ ├── test.dbNSFP.gz.tbi │ ├── test.fa │ ├── test.fa.fai │ ├── test.gene.txt │ └── tmp.vcf ├── test-triallelic │ ├── bi.MetaCov.assoc.gz │ ├── bi.MetaCov.assoc.gz.tbi │ ├── bi.MetaScore.assoc.gz │ ├── bi.MetaScore.assoc.gz.tbi │ ├── test2.study1.MetaCov.assoc.gz │ ├── test2.study1.MetaCov.assoc.gz.tbi │ ├── test2.study1.MetaScore.assoc.gz │ ├── test2.study1.MetaScore.assoc.gz.tbi │ ├── test2.study2.MetaCov.assoc.gz │ ├── test2.study2.MetaCov.assoc.gz.tbi │ ├── test2.study2.MetaScore.assoc.gz │ ├── test2.study2.MetaScore.assoc.gz.tbi │ ├── test2.study3.MetaCov.assoc.gz │ ├── test2.study3.MetaCov.assoc.gz.tbi │ ├── test2.study3.MetaScore.assoc.gz │ ├── test2.study3.MetaScore.assoc.gz.tbi │ ├── tri.MetaCov.assoc.gz │ ├── tri.MetaCov.assoc.gz.tbi │ ├── tri.MetaScore.assoc.gz │ └── tri.MetaScore.assoc.gz.tbi ├── tests │ └── correct.Rdata └── vcf │ ├── 1000g.phase1.20110521.CFH.var.anno.vcf.gz │ ├── 1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi │ ├── all.anno.filtered.extract.bcf.gz │ ├── all.anno.filtered.extract.bcf.gz.bci │ ├── all.anno.filtered.extract.headerFixed.bcf.gz │ ├── all.anno.filtered.extract.headerFixed.bcf.gz.scIdx │ ├── all.anno.filtered.extract.headerFixed.vcf.gz │ ├── all.anno.filtered.extract.vcf.gz │ ├── all.anno.filtered.extract.vcf.gz.scIdx │ ├── all.anno.filtered.extract.vcf.gz.tbi │ └── refFlat_hg19_6col.txt.gz ├── man ├── SEQMINER.Rd ├── addJob.Rd ├── annotateGene.Rd ├── annotatePlain.Rd ├── annotateVcf.Rd ├── createSingleChromosomeBCFIndex.Rd ├── createSingleChromosomeVCFIndex.Rd ├── download.annotation.resource.Rd ├── getCovPair.Rd ├── getRefBase.Rd ├── hasIndex.Rd ├── isDirWritable.Rd ├── isInRange.Rd ├── isTabixRange.Rd ├── isURL.Rd ├── makeAnnotationParameter.Rd ├── newJob.Rd ├── newWorkflow.Rd ├── openPlink.Rd ├── readBGENToListByGene.Rd ├── readBGENToListByRange.Rd ├── readBGENToMatrixByGene.Rd ├── readBGENToMatrixByRange.Rd ├── readPlinkToMatrixByIndex.Rd ├── readSingleChromosomeBCFToMatrixByRange.Rd ├── readSingleChromosomeVCFToMatrixByRange.Rd ├── readVCFToListByGene.Rd ├── readVCFToListByRange.Rd ├── readVCFToMatrixByGene.Rd ├── readVCFToMatrixByRange.Rd ├── rvmeta.readCovByRange.Rd ├── rvmeta.readDataByGene.Rd ├── rvmeta.readDataByRange.Rd ├── rvmeta.readNullModel.Rd ├── rvmeta.readScoreByRange.Rd ├── rvmeta.readSkewByRange.Rd ├── rvmeta.writeCovData.Rd ├── rvmeta.writeScoreData.Rd ├── sub-.PlinkFile.Rd ├── tabix.createIndex.Rd ├── tabix.createIndex.meta.Rd ├── tabix.createIndex.vcf.Rd ├── tabix.read.Rd ├── tabix.read.header.Rd ├── tabix.read.table.Rd ├── validateAnnotationParameter.Rd ├── verifyFilename.Rd └── writeWorkflow.Rd ├── src ├── AnnotationController.h ├── AnnotationInputFile.h ├── AnnotationOutput.h ├── AnnotationOutputFile.h ├── AnnotationResult.h ├── AnnotationResultCollection.h ├── AnnotationString.h ├── BCFHeader.h ├── BCFReader.cpp ├── BCFReader.h ├── BGenFile.cpp ├── BGenFile.h ├── BGenIndex.cpp ├── BGenIndex.h ├── BGenVariant.cpp ├── BGenVariant.h ├── BedReader.h ├── BitReader.h ├── Codon.h ├── Common.h ├── CommonFunction.h ├── Exception.cpp ├── Exception.h ├── FileFormat.h ├── FileIO.cpp ├── FileIO.h ├── FreqTable.h ├── Gene.h ├── GeneAnnotation.h ├── GeneFormat.h ├── GeneLoader.cpp ├── GeneLoader.h ├── GenomeScore.h ├── GenomeSequence.h ├── HiCExtract.h ├── Indexer.h ├── LogFile.h ├── Makevars.in ├── Makevars.win ├── Maximum.h ├── MmapFile.cpp ├── MmapFile.h ├── ModelParser.h ├── OrderedMap.h ├── PatternMatch.cpp ├── PatternMatch.h ├── PeopleSet.cpp ├── PeopleSet.h ├── PlinkInputFile.cpp ├── PlinkInputFile.h ├── PlinkOutputFile.cpp ├── PlinkOutputFile.h ├── Priority.h ├── Profiler.cpp ├── Profiler.h ├── R_CPP_interface.cpp ├── R_CPP_interface.h ├── Range.h ├── RangeList.cpp ├── RangeList.h ├── Rannotation.cpp ├── Rannotation.h ├── SequenceUtil.h ├── SimpleMatrix.cpp ├── SimpleMatrix.h ├── SimpleTimer.h ├── SingleChromosomeBCFIndex.cpp ├── SingleChromosomeBCFIndex.h ├── SingleChromosomeVCFIndex.cpp ├── SingleChromosomeVCFIndex.h ├── StringTemplate.h ├── StringUtil.h ├── TabixData.h ├── TabixReader.h ├── TimeUtil.h ├── Type.h ├── TypeConversion.cpp ├── TypeConversion.h ├── Utils.cpp ├── Utils.h ├── VCFBuffer.h ├── VCFConstant.h ├── VCFExtractor.h ├── VCFFilter.h ├── VCFFunction.h ├── VCFHeader.cpp ├── VCFHeader.h ├── VCFIndividual.cpp ├── VCFIndividual.h ├── VCFInfo.cpp ├── VCFInfo.h ├── VCFInputFile.cpp ├── VCFInputFile.h ├── VCFOutputFile.h ├── VCFRecord.h ├── VCFUtil.cpp ├── VCFUtil.h ├── VCFValue.h ├── bam_endian.h ├── bcf.c ├── bcf.h ├── bcf_index.c ├── bcfutils.c ├── bedidx.c ├── bgen2genoLoader.cpp ├── bgen2genoLoader.h ├── bgzf.c ├── bgzf.h ├── config.h.in ├── khash.h ├── knetfile.c ├── knetfile.h ├── kseq.h ├── ksort.h ├── kstring.c ├── kstring.h ├── plink2genoLoader.cpp ├── plink2genoLoader.h ├── rvMetaLoader.cpp ├── rvMetaLoader.h ├── scbcf2genoLoader.cpp ├── scbcf2genoLoader.h ├── scvcf2genoLoader.cpp ├── scvcf2genoLoader.h ├── seqForStat.c ├── seqminer.c ├── seqminer_init.c ├── sqlite │ ├── shell.c │ ├── sqlite3.c │ ├── sqlite3.h │ └── sqlite3ext.h ├── tabix.h ├── tabixLoader.cpp ├── tabixLoader.h ├── tabix_index.c ├── vcf.c ├── vcf2genoLoader.cpp ├── vcf2genoLoader.h └── zstd │ ├── .gitattributes │ ├── .gitignore │ ├── CODE_OF_CONDUCT.md │ ├── CONTRIBUTING.md │ ├── COPYING │ ├── LICENSE │ ├── Makefile │ ├── README.md │ ├── TESTING.md │ ├── appveyor.yml │ ├── build │ ├── .gitignore │ ├── README.md │ ├── VS2008 │ │ ├── fullbench │ │ │ └── fullbench.vcproj │ │ ├── fuzzer │ │ │ └── fuzzer.vcproj │ │ ├── zstd.sln │ │ └── zstdlib │ │ │ └── zstdlib.vcproj │ ├── VS2010 │ │ ├── CompileAsCpp.props │ │ ├── datagen │ │ │ └── datagen.vcxproj │ │ ├── fullbench-dll │ │ │ └── fullbench-dll.vcxproj │ │ ├── fullbench │ │ │ └── fullbench.vcxproj │ │ ├── fuzzer │ │ │ └── fuzzer.vcxproj │ │ ├── libzstd-dll │ │ │ ├── libzstd-dll.rc │ │ │ └── libzstd-dll.vcxproj │ │ ├── libzstd │ │ │ └── libzstd.vcxproj │ │ └── zstd.sln │ ├── VS_scripts │ │ ├── README.md │ │ ├── build.VS2010.cmd │ │ ├── build.VS2012.cmd │ │ ├── build.VS2013.cmd │ │ ├── build.VS2015.cmd │ │ ├── build.VS2017.cmd │ │ ├── build.VS2017Community.cmd │ │ ├── build.VS2017Enterprise.cmd │ │ ├── build.VS2017Professional.cmd │ │ └── build.generic.cmd │ └── cmake │ │ ├── .gitignore │ │ ├── CMakeLists.txt │ │ ├── CMakeModules │ │ ├── AddZstdCompilationFlags.cmake │ │ └── GetZstdLibraryVersion.cmake │ │ ├── contrib │ │ ├── CMakeLists.txt │ │ ├── gen_html │ │ │ └── CMakeLists.txt │ │ └── pzstd │ │ │ └── CMakeLists.txt │ │ ├── programs │ │ ├── .gitignore │ │ └── CMakeLists.txt │ │ └── tests │ │ ├── .gitignore │ │ └── CMakeLists.txt │ └── lib │ ├── .gitignore │ ├── BUCK │ ├── README.md │ ├── common │ ├── bitstream.h │ ├── compiler.h │ ├── cpu.h │ ├── debug.c │ ├── debug.h │ ├── entropy_common.c │ ├── error_private.c │ ├── error_private.h │ ├── fse.h │ ├── fse_decompress.c │ ├── huf.h │ ├── mem.h │ ├── pool.c │ ├── pool.h │ ├── threading.c │ ├── threading.h │ ├── xxhash.c │ ├── xxhash.h │ ├── zstd_common.c │ ├── zstd_errors.h │ └── zstd_internal.h │ ├── compress │ ├── fse_compress.c │ ├── hist.c │ ├── hist.h │ ├── huf_compress.c │ ├── zstd_compress.c │ ├── zstd_compress_internal.h │ ├── zstd_double_fast.c │ ├── zstd_double_fast.h │ ├── zstd_fast.c │ ├── zstd_fast.h │ ├── zstd_lazy.c │ ├── zstd_lazy.h │ ├── zstd_ldm.c │ ├── zstd_ldm.h │ ├── zstd_opt.c │ ├── zstd_opt.h │ ├── zstdmt_compress.c │ └── zstdmt_compress.h │ ├── decompress │ ├── huf_decompress.c │ └── zstd_decompress.c │ ├── deprecated │ ├── zbuff.h │ ├── zbuff_common.c │ ├── zbuff_compress.c │ └── zbuff_decompress.c │ ├── dictBuilder │ ├── cover.c │ ├── cover.h │ ├── divsufsort.c │ ├── divsufsort.h │ ├── fastcover.c │ ├── zdict.c │ └── zdict.h │ ├── dll │ ├── example │ │ ├── Makefile │ │ ├── README.md │ │ ├── build_package.bat │ │ ├── fullbench-dll.sln │ │ └── fullbench-dll.vcxproj │ └── libzstd.def │ ├── legacy │ ├── zstd_legacy.h 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