Files in seqminer

Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

configure

MD5

ChangeLog

README.md

NAMESPACE

configure.ac

DESCRIPTION

LICENSE

configure.win

cleanup

R/genMakefile.R R/seqminer.R

src/BGenFile.cpp

src/Makevars.win

src/AnnotationString.h

src/SimpleMatrix.cpp

src/VCFOutputFile.h

src/AnnotationResult.h

src/PatternMatch.h

src/vcf2genoLoader.h

src/Gene.h

src/VCFIndividual.h

src/VCFFunction.h

src/GeneLoader.h

src/PlinkOutputFile.h

src/kstring.h

src/VCFBuffer.h

src/VCFInputFile.h

src/Utils.cpp

src/CommonFunction.h

src/VCFHeader.h

src/OrderedMap.h

src/TabixReader.h

src/FileIO.cpp

src/BCFReader.cpp

src/SingleChromosomeVCFIndex.h

src/AnnotationOutput.h

src/Exception.h

src/Priority.h

src/bcf.c

src/AnnotationOutputFile.h

src/htslib-1.16.tar.bz2

src/TimeUtil.h

src/SimpleMatrix.h

src/AnnotationResultCollection.h

src/PlinkOutputFile.cpp

src/FileIO.h

src/VCFConstant.h

src/VCFRecord.h

src/PatternMatch.cpp

src/SingleChromosomeVCFIndex.cpp

src/kstring.c

src/Common.h

src/tabixLoader.cpp

src/bgen2genoLoader.h

src/VCFUtil.h

src/BGenIndex.h

src/GenomeScore.h

src/GeneFormat.h

src/bcf_index.c

src/Range.h

src/SequenceUtil.h

src/BCFReader.h

src/bam_endian.h

src/FreqTable.h

src/scbcf2genoLoader.h

src/AnnotationController.h

src/StringTemplate.h

src/VCFHeader.cpp

src/LogFile.h

src/bedidx.c

src/PeopleSet.cpp

src/scbcf2genoLoader.cpp

src/ksort.h

src/RangeList.h

src/vcf2genoLoader.cpp

src/bcfutils.c

src/MmapFile.h

src/VCFIndividual.cpp

src/StringUtil.h

src/PeopleSet.h

src/knetfile.h

src/R_CPP_interface.h

src/plink2genoLoader.cpp

src/RangeList.cpp

src/GeneLoader.cpp

src/bgzf.h

src/Utils.h

src/VCFInfo.cpp

src/BGenVariant.cpp

src/VCFValue.h

src/tabix.h

src/Maximum.h

src/bcf.h

src/TypeConversion.h

src/SimpleTimer.h

src/rvMetaLoader.h

src/Indexer.h

src/Rannotation.h

src/PlinkInputFile.cpp

src/VCFUtil.cpp

src/VCFExtractor.h

src/plink2genoLoader.h

src/GeneAnnotation.h

src/TabixData.h

src/BCFHeader.h

src/HiCExtract.h

src/BGenVariant.h

src/Profiler.h

src/Type.h

src/scvcf2genoLoader.h

src/TypeConversion.cpp

src/tabix_index.c

src/khash.h

src/Profiler.cpp

src/tabixLoader.h

src/Makevars.in

src/bgen2genoLoader.cpp

src/scvcf2genoLoader.cpp

src/SingleChromosomeBCFIndex.cpp

src/VCFFilter.h

src/VCFInfo.h

src/Exception.cpp

src/config.h.in

src/rvMetaLoader.cpp

src/PlinkInputFile.h

src/BGenFile.h

src/ModelParser.h

src/SingleChromosomeBCFIndex.h

src/bgzf.c

src/BGenIndex.cpp

src/VCFInputFile.cpp

src/AnnotationInputFile.h

src/vcf.c

src/GenomeSequence.h

src/MmapFile.cpp

src/Rannotation.cpp

src/knetfile.c

src/FileFormat.h

src/seqForStat.c

src/seqminer_init.c

src/BedReader.h

src/R_CPP_interface.cpp

src/Codon.h

src/kseq.h

src/seqminer.c

src/BitReader.h

src/zstd/CONTRIBUTING.md src/zstd/README.md src/zstd/CODE_OF_CONDUCT.md

src/zstd/LICENSE

src/zstd/COPYING

src/zstd/appveyor.yml

src/zstd/TESTING.md

src/zstd/Makefile

src/zstd/build/README.md

src/zstd/build/VS2010/zstd.sln

src/zstd/build/VS2010/CompileAsCpp.props

src/zstd/build/VS2010/zstd/zstd.vcxproj

src/zstd/build/VS2010/zstd/zstd.rc

src/zstd/build/VS2010/datagen/datagen.vcxproj

src/zstd/build/VS2010/fullbench-dll/fullbench-dll.vcxproj

src/zstd/build/VS2010/libzstd/libzstd.vcxproj

src/zstd/build/VS2010/fuzzer/fuzzer.vcxproj

src/zstd/build/VS2010/libzstd-dll/libzstd-dll.vcxproj

src/zstd/build/VS2010/libzstd-dll/libzstd-dll.rc

src/zstd/build/VS2010/fullbench/fullbench.vcxproj

src/zstd/build/VS_scripts/build.VS2015.cmd

src/zstd/build/VS_scripts/build.VS2017Professional.cmd

src/zstd/build/VS_scripts/build.generic.cmd

src/zstd/build/VS_scripts/build.VS2017Enterprise.cmd

src/zstd/build/VS_scripts/README.md

src/zstd/build/VS_scripts/build.VS2012.cmd

src/zstd/build/VS_scripts/build.VS2010.cmd

src/zstd/build/VS_scripts/build.VS2017.cmd

src/zstd/build/VS_scripts/build.VS2017Community.cmd

src/zstd/build/VS_scripts/build.VS2013.cmd

src/zstd/build/VS2008/zstd.sln

src/zstd/build/VS2008/zstd/zstd.vcproj

src/zstd/build/VS2008/fuzzer/fuzzer.vcproj

src/zstd/build/VS2008/fullbench/fullbench.vcproj

src/zstd/build/VS2008/zstdlib/zstdlib.vcproj

src/zstd/build/cmake/CMakeLists.txt

src/zstd/build/cmake/contrib/CMakeLists.txt

src/zstd/build/cmake/contrib/pzstd/CMakeLists.txt

src/zstd/build/cmake/contrib/gen_html/CMakeLists.txt

src/zstd/build/cmake/tests/CMakeLists.txt

src/zstd/build/cmake/lib/CMakeLists.txt

src/zstd/build/cmake/lib/pkgconfig.cmake

src/zstd/build/cmake/lib/cmake_uninstall.cmake.in

src/zstd/build/cmake/programs/CMakeLists.txt

src/zstd/build/cmake/CMakeModules/GetZstdLibraryVersion.cmake

src/zstd/build/cmake/CMakeModules/AddZstdCompilationFlags.cmake

src/zstd/lib/libzstd.pc.in

src/zstd/lib/BUCK

src/zstd/lib/README.md

src/zstd/lib/zstd.h

src/zstd/lib/legacy/zstd_v02.c

src/zstd/lib/legacy/zstd_v07.c

src/zstd/lib/legacy/zstd_v01.h

src/zstd/lib/legacy/zstd_v03.h

src/zstd/lib/legacy/zstd_v01.c

src/zstd/lib/legacy/zstd_v05.c

src/zstd/lib/legacy/zstd_v05.h

src/zstd/lib/legacy/zstd_v06.c

src/zstd/lib/legacy/zstd_v06.h

src/zstd/lib/legacy/zstd_v04.c

src/zstd/lib/legacy/zstd_v07.h

src/zstd/lib/legacy/zstd_v03.c

src/zstd/lib/legacy/zstd_v04.h

src/zstd/lib/legacy/zstd_legacy.h

src/zstd/lib/legacy/zstd_v02.h

src/zstd/lib/dictBuilder/divsufsort.h

src/zstd/lib/dictBuilder/zdict.h

src/zstd/lib/dictBuilder/cover.h

src/zstd/lib/dictBuilder/zdict.c

src/zstd/lib/dictBuilder/divsufsort.c

src/zstd/lib/dictBuilder/cover.c

src/zstd/lib/dictBuilder/fastcover.c

src/zstd/lib/deprecated/zbuff_common.c

src/zstd/lib/deprecated/zbuff_compress.c

src/zstd/lib/deprecated/zbuff.h

src/zstd/lib/deprecated/zbuff_decompress.c

src/zstd/lib/decompress/huf_decompress.c

src/zstd/lib/decompress/zstd_decompress.c

src/zstd/lib/dll/libzstd.def

src/zstd/lib/dll/example/build_package.bat

src/zstd/lib/dll/example/README.md

src/zstd/lib/dll/example/fullbench-dll.vcxproj

src/zstd/lib/dll/example/fullbench-dll.sln

src/zstd/lib/dll/example/Makefile

src/zstd/lib/common/zstd_errors.h

src/zstd/lib/common/xxhash.h

src/zstd/lib/common/huf.h

src/zstd/lib/common/error_private.h

src/zstd/lib/common/bitstream.h

src/zstd/lib/common/threading.c

src/zstd/lib/common/xxhash.c

src/zstd/lib/common/entropy_common.c

src/zstd/lib/common/mem.h

src/zstd/lib/common/pool.h

src/zstd/lib/common/debug.c

src/zstd/lib/common/fse.h

src/zstd/lib/common/debug.h

src/zstd/lib/common/threading.h

src/zstd/lib/common/zstd_common.c

src/zstd/lib/common/zstd_internal.h

src/zstd/lib/common/compiler.h

src/zstd/lib/common/pool.c

src/zstd/lib/common/cpu.h

src/zstd/lib/common/fse_decompress.c

src/zstd/lib/common/error_private.c

src/zstd/lib/compress/huf_compress.c

src/zstd/lib/compress/zstdmt_compress.c

src/zstd/lib/compress/zstd_double_fast.c

src/zstd/lib/compress/zstd_compress.c

src/zstd/lib/compress/hist.c

src/zstd/lib/compress/zstd_opt.c

src/zstd/lib/compress/zstd_ldm.h

src/zstd/lib/compress/zstd_compress_internal.h

src/zstd/lib/compress/zstd_opt.h

src/zstd/lib/compress/zstd_lazy.c

src/zstd/lib/compress/zstd_double_fast.h

src/zstd/lib/compress/zstd_ldm.c

src/zstd/lib/compress/zstd_fast.c

src/zstd/lib/compress/zstd_lazy.h

src/zstd/lib/compress/zstdmt_compress.h

src/zstd/lib/compress/zstd_fast.h

src/zstd/lib/compress/fse_compress.c

src/zstd/lib/compress/hist.h

src/sqlite/sqlite3.c

src/sqlite/shell.c

src/sqlite/sqlite3ext.h

src/sqlite/sqlite3.h

inst/CITATION

inst/vcf/all.anno.filtered.extract.vcf.gz.scIdx

inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz

inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi

inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz.scIdx

inst/vcf/all.anno.filtered.extract.vcf.gz

inst/vcf/all.anno.filtered.extract.bcf.gz

inst/vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz

inst/vcf/all.anno.filtered.extract.vcf.gz.tbi

inst/vcf/all.anno.filtered.extract.headerFixed.vcf.gz

inst/vcf/refFlat_hg19_6col.txt.gz

inst/vcf/all.anno.filtered.extract.bcf.gz.bci

inst/tests/correct.Rdata

inst/bgen/all.anno.filtered.extract.bgen

inst/bgen/all.anno.filtered.extract.bgen.bgi

inst/plink/all.anno.filtered.extract.bed

inst/plink/all.anno.filtered.extract.bim

inst/plink/all.anno.filtered.extract.fam

inst/tabanno/test.fa.fai

inst/tabanno/input.test.plain.txt

inst/tabanno/input.demo.vcf

inst/tabanno/test.dbNSFP.gz.tbi

inst/tabanno/codon.txt

inst/tabanno/test.bed

inst/tabanno/priority.epact.txt

inst/tabanno/test.gene.txt

inst/tabanno/test.dbNSFP.gz

inst/tabanno/priority.txt

inst/tabanno/input.test.vcf

inst/tabanno/tmp.vcf

inst/tabanno/test.fa

inst/tabanno/input.100.vcf.gz

inst/benchmark/output.png

inst/benchmark/seqminer2_benchmark_script.txt

inst/test-triallelic/test2.study1.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study2.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study3.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaCov.assoc.gz.tbi

inst/test-triallelic/bi.MetaCov.assoc.gz.tbi

inst/test-triallelic/tri.MetaCov.assoc.gz.tbi

inst/test-triallelic/bi.MetaScore.assoc.gz

inst/test-triallelic/tri.MetaCov.assoc.gz

inst/test-triallelic/bi.MetaScore.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaCov.assoc.gz

inst/test-triallelic/tri.MetaScore.assoc.gz.tbi

inst/test-triallelic/tri.MetaScore.assoc.gz

inst/test-triallelic/test2.study3.MetaCov.assoc.gz

inst/test-triallelic/test2.study2.MetaScore.assoc.gz

inst/test-triallelic/bi.MetaCov.assoc.gz

inst/test-triallelic/test2.study3.MetaScore.assoc.gz

inst/test-triallelic/test2.study3.MetaCov.assoc.gz.tbi

inst/test-triallelic/test2.study2.MetaCov.assoc.gz

inst/test-triallelic/test2.study2.MetaCov.assoc.gz.tbi

inst/test-triallelic/test2.study1.MetaScore.assoc.gz

inst/rvtests/rvtest.MetaCov.assoc.gz.tbi

inst/rvtests/rvtest.MetaScore.assoc.anno.gz.tbi

inst/rvtests/rvtest.MetaSkew.assoc.gz.tbi

inst/rvtests/rvtest.MetaCov.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.gz.tbi

inst/rvtests/rvtest.MetaSkew.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.gz

inst/rvtests/rvtest.MetaScore.assoc.anno.gz

inst/rvtests/cfh.refFlat.txt

demo/meta.workflow.R

demo/00Index

demo/vcf.workflow.R demo/annotate.R tests/testthat.R tests/testthat/test-vcf.R tests/testthat/test-triallelic.R man/verifyFilename.Rd man/createSingleChromosomeBCFIndex.Rd man/createSingleChromosomeVCFIndex.Rd man/sub-.PlinkFile.Rd man/tabix.createIndex.Rd man/readVCFToListByRange.Rd man/isDirWritable.Rd man/getCovPair.Rd man/readBGENToListByRange.Rd man/download.annotation.resource.Rd man/writeWorkflow.Rd man/readVCFToListByGene.Rd man/isInRange.Rd man/getRefBase.Rd man/readVCFToMatrixByGene.Rd man/rvmeta.readNullModel.Rd man/newJob.Rd man/annotateVcf.Rd man/validateAnnotationParameter.Rd man/annotatePlain.Rd man/annotateGene.Rd man/tabix.read.Rd man/addJob.Rd man/readSingleChromosomeBCFToMatrixByRange.Rd man/readBGENToListByGene.Rd man/rvmeta.readCovByRange.Rd man/rvmeta.writeScoreData.Rd man/tabix.read.header.Rd man/tabix.read.table.Rd man/rvmeta.readSkewByRange.Rd man/tabix.createIndex.vcf.Rd man/readVCFToMatrixByRange.Rd man/readPlinkToMatrixByIndex.Rd man/isURL.Rd man/openPlink.Rd man/hasIndex.Rd man/readBGENToMatrixByGene.Rd man/newWorkflow.Rd man/readBGENToMatrixByRange.Rd man/rvmeta.writeCovData.Rd man/SEQMINER.Rd man/makeAnnotationParameter.Rd man/rvmeta.readScoreByRange.Rd man/rvmeta.readDataByRange.Rd man/readSingleChromosomeVCFToMatrixByRange.Rd man/rvmeta.readDataByGene.Rd man/isTabixRange.Rd man/tabix.createIndex.meta.Rd

seqminer documentation built on Sept. 2, 2023, 9:08 a.m.