Files in PacificBiosciences/pbbamr
Interface R with PacBio BAM File Formats

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R R/gff.R R/utils.R README.md
ci/Dockerfile
ci/buildAndTest.sh
ci/withDocker.sh
circle.yml
clean.sh
deploy/deploy.sh
inst/.gitignore
inst/extdata/All4Mer.V2.11.fna
inst/extdata/All4Mer.V2.11.fna.fai
inst/extdata/bam_mapping_1.bam
inst/extdata/bam_mapping_1.bam.bai
inst/extdata/bam_mapping_1.bam.pbi
inst/extdata/internalsample.bam
inst/extdata/internalsample.bam.pbi
inst/extdata/lambdaNEB.fa
inst/extdata/lambdaNEB.fa.fai
inst/include/boost/algorithm/string.hpp
inst/include/boost/algorithm/string/case_conv.hpp
inst/include/boost/algorithm/string/classification.hpp
inst/include/boost/algorithm/string/compare.hpp
inst/include/boost/algorithm/string/concept.hpp
inst/include/boost/algorithm/string/config.hpp
inst/include/boost/algorithm/string/constants.hpp
inst/include/boost/algorithm/string/detail/case_conv.hpp
inst/include/boost/algorithm/string/detail/classification.hpp
inst/include/boost/algorithm/string/detail/find_format.hpp
inst/include/boost/algorithm/string/detail/find_format_all.hpp
inst/include/boost/algorithm/string/detail/find_format_store.hpp
inst/include/boost/algorithm/string/detail/find_iterator.hpp
inst/include/boost/algorithm/string/detail/finder.hpp
inst/include/boost/algorithm/string/detail/formatter.hpp
inst/include/boost/algorithm/string/detail/predicate.hpp
inst/include/boost/algorithm/string/detail/replace_storage.hpp
inst/include/boost/algorithm/string/detail/sequence.hpp
inst/include/boost/algorithm/string/detail/trim.hpp
inst/include/boost/algorithm/string/detail/util.hpp
inst/include/boost/algorithm/string/erase.hpp
inst/include/boost/algorithm/string/find.hpp
inst/include/boost/algorithm/string/find_format.hpp
inst/include/boost/algorithm/string/find_iterator.hpp
inst/include/boost/algorithm/string/finder.hpp
inst/include/boost/algorithm/string/formatter.hpp
inst/include/boost/algorithm/string/iter_find.hpp
inst/include/boost/algorithm/string/join.hpp
inst/include/boost/algorithm/string/predicate.hpp
inst/include/boost/algorithm/string/predicate_facade.hpp
inst/include/boost/algorithm/string/replace.hpp
inst/include/boost/algorithm/string/sequence_traits.hpp
inst/include/boost/algorithm/string/split.hpp
inst/include/boost/algorithm/string/std/list_traits.hpp
inst/include/boost/algorithm/string/std/slist_traits.hpp
inst/include/boost/algorithm/string/std/string_traits.hpp
inst/include/boost/algorithm/string/std_containers_traits.hpp
inst/include/boost/algorithm/string/trim.hpp
inst/include/boost/algorithm/string/yes_no_type.hpp
inst/include/boost/aligned_storage.hpp
inst/include/boost/array.hpp
inst/include/boost/assert.hpp
inst/include/boost/bind/mem_fn.hpp
inst/include/boost/bind/mem_fn_cc.hpp
inst/include/boost/bind/mem_fn_template.hpp
inst/include/boost/bind/mem_fn_vw.hpp
inst/include/boost/blank.hpp
inst/include/boost/blank_fwd.hpp
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inst/include/boost/concept/usage.hpp
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inst/include/boost/config/abi/borland_suffix.hpp
inst/include/boost/config/abi/msvc_prefix.hpp
inst/include/boost/config/abi/msvc_suffix.hpp
inst/include/boost/config/abi_prefix.hpp
inst/include/boost/config/abi_suffix.hpp
inst/include/boost/config/auto_link.hpp
inst/include/boost/config/compiler/borland.hpp
inst/include/boost/config/compiler/clang.hpp
inst/include/boost/config/compiler/codegear.hpp
inst/include/boost/config/compiler/comeau.hpp
inst/include/boost/config/compiler/common_edg.hpp
inst/include/boost/config/compiler/compaq_cxx.hpp
inst/include/boost/config/compiler/cray.hpp
inst/include/boost/config/compiler/digitalmars.hpp
inst/include/boost/config/compiler/gcc.hpp
inst/include/boost/config/compiler/gcc_xml.hpp
inst/include/boost/config/compiler/greenhills.hpp
inst/include/boost/config/compiler/hp_acc.hpp
inst/include/boost/config/compiler/intel.hpp
inst/include/boost/config/compiler/kai.hpp
inst/include/boost/config/compiler/metrowerks.hpp
inst/include/boost/config/compiler/mpw.hpp
inst/include/boost/config/compiler/nvcc.hpp
inst/include/boost/config/compiler/pathscale.hpp
inst/include/boost/config/compiler/pgi.hpp
inst/include/boost/config/compiler/sgi_mipspro.hpp
inst/include/boost/config/compiler/sunpro_cc.hpp
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inst/include/boost/config/platform/haiku.hpp
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inst/include/boost/config/platform/irix.hpp
inst/include/boost/config/platform/linux.hpp
inst/include/boost/config/platform/macos.hpp
inst/include/boost/config/platform/qnxnto.hpp
inst/include/boost/config/platform/solaris.hpp
inst/include/boost/config/platform/symbian.hpp
inst/include/boost/config/platform/vms.hpp
inst/include/boost/config/platform/vxworks.hpp
inst/include/boost/config/platform/win32.hpp
inst/include/boost/config/posix_features.hpp
inst/include/boost/config/requires_threads.hpp
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inst/include/boost/config/stdlib/libcomo.hpp
inst/include/boost/config/stdlib/libcpp.hpp
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inst/include/boost/config/stdlib/modena.hpp
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inst/include/boost/config/stdlib/roguewave.hpp
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inst/include/boost/detail/lightweight_mutex.hpp
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inst/include/boost/detail/reference_content.hpp
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inst/include/boost/dynamic_bitset/dynamic_bitset.hpp
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inst/include/boost/function/detail/gen_maybe_include.pl
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inst/include/boost/function/detail/prologue.hpp
inst/include/boost/function/function0.hpp
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inst/include/boost/function/function10.hpp
inst/include/boost/function/function2.hpp
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inst/include/boost/function/function6.hpp
inst/include/boost/function/function7.hpp
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inst/include/boost/function_equal.hpp
inst/include/boost/functional/hash/hash_fwd.hpp
inst/include/boost/functional/hash_fwd.hpp
inst/include/boost/get_pointer.hpp
inst/include/boost/icl/concept/interval.hpp
inst/include/boost/icl/concept/interval_bounds.hpp
inst/include/boost/icl/detail/concept_check.hpp
inst/include/boost/icl/detail/design_config.hpp
inst/include/boost/icl/discrete_interval.hpp
inst/include/boost/icl/dynamic_interval_traits.hpp
inst/include/boost/icl/interval_bounds.hpp
inst/include/boost/icl/interval_traits.hpp
inst/include/boost/icl/type_traits/difference_type_of.hpp
inst/include/boost/icl/type_traits/domain_type_of.hpp
inst/include/boost/icl/type_traits/identity_element.hpp
inst/include/boost/icl/type_traits/infinity.hpp
inst/include/boost/icl/type_traits/is_asymmetric_interval.hpp
inst/include/boost/icl/type_traits/is_continuous.hpp
inst/include/boost/icl/type_traits/is_continuous_interval.hpp
inst/include/boost/icl/type_traits/is_discrete.hpp
inst/include/boost/icl/type_traits/is_discrete_interval.hpp
inst/include/boost/icl/type_traits/is_increasing.hpp
inst/include/boost/icl/type_traits/is_interval.hpp
inst/include/boost/icl/type_traits/is_numeric.hpp
inst/include/boost/icl/type_traits/no_type.hpp
inst/include/boost/icl/type_traits/rep_type_of.hpp
inst/include/boost/icl/type_traits/size_type_of.hpp
inst/include/boost/icl/type_traits/succ_pred.hpp
inst/include/boost/icl/type_traits/type_to_string.hpp
inst/include/boost/icl/type_traits/unit_element.hpp
inst/include/boost/icl/type_traits/value_size.hpp
inst/include/boost/integer.hpp
inst/include/boost/integer/integer_log2.hpp
inst/include/boost/integer/integer_mask.hpp
inst/include/boost/integer/static_log2.hpp
inst/include/boost/integer_fwd.hpp
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inst/include/boost/io/ios_state.hpp
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inst/include/boost/iterator/interoperable.hpp
inst/include/boost/iterator/iterator_adaptor.hpp
inst/include/boost/iterator/iterator_categories.hpp
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inst/include/boost/iterator/reverse_iterator.hpp
inst/include/boost/iterator/transform_iterator.hpp
inst/include/boost/lexical_cast.hpp
inst/include/boost/lexical_cast/bad_lexical_cast.hpp
inst/include/boost/lexical_cast/detail/converter_lexical.hpp
inst/include/boost/lexical_cast/detail/converter_lexical_streams.hpp
inst/include/boost/lexical_cast/detail/converter_numeric.hpp
inst/include/boost/lexical_cast/detail/inf_nan.hpp
inst/include/boost/lexical_cast/detail/is_character.hpp
inst/include/boost/lexical_cast/detail/lcast_char_constants.hpp
inst/include/boost/lexical_cast/detail/lcast_unsigned_converters.hpp
inst/include/boost/lexical_cast/detail/widest_char.hpp
inst/include/boost/lexical_cast/try_lexical_convert.hpp
inst/include/boost/limits.hpp
inst/include/boost/math/common_factor_ct.hpp
inst/include/boost/math/policies/policy.hpp
inst/include/boost/math/special_functions/detail/fp_traits.hpp
inst/include/boost/math/special_functions/detail/round_fwd.hpp
inst/include/boost/math/special_functions/fpclassify.hpp
inst/include/boost/math/special_functions/math_fwd.hpp
inst/include/boost/math/special_functions/sign.hpp
inst/include/boost/math/tools/config.hpp
inst/include/boost/math/tools/promotion.hpp
inst/include/boost/math/tools/real_cast.hpp
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inst/include/boost/move/adl_move_swap.hpp
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inst/include/boost/move/iterator.hpp
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inst/include/pbbam/exception/InvalidSequencingChemistryException.h
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inst/include/pbbam/internal/DataSetElement.h
inst/include/pbbam/internal/DataSetElement.inl
inst/include/pbbam/internal/DataSetListElement.h
inst/include/pbbam/internal/DataSetListElement.inl
inst/include/pbbam/internal/DataSetTypes.inl
inst/include/pbbam/internal/FastaSequence.inl
inst/include/pbbam/internal/Frames.inl
inst/include/pbbam/internal/GenomicInterval.inl
inst/include/pbbam/internal/Interval.inl
inst/include/pbbam/internal/PbiBasicTypes.inl
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inst/include/pbbam/internal/PbiIndex.inl
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inst/include/pbbam/virtual/VirtualPolymeraseBamRecord.h
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inst/include/pbbam/virtual/WhitelistedZmwReadStitcher.h
inst/include/pbbam/virtual/ZmwReadStitcher.h
inst/include/pbbam/virtual/ZmwWhitelistVirtualReader.h
man/chkClass.Rd man/combineConditions.Rd man/fromPhred.Rd man/getBAMNamesFromDatasetFile.Rd man/getFastaFileNameFromDatasetFile.Rd man/getHoleX.Rd man/getHoleY.Rd man/getReadReport.Rd man/getReferencePath.Rd man/hello.Rd man/loadAlnsFromIndex.Rd man/loadDataAtOffsets.Rd man/loadHMMfromBAM.Rd man/loadHeader.Rd man/loadPBI.Rd man/loadReadsFromIndex.Rd man/loadReferenceWindow.Rd man/loadRegionsTable.Rd man/loadSingleZmwHMMfromBAM.Rd man/loadSubreadsAtOffsets.Rd man/toPhred.Rd
pbbamr.Rproj
src/DatasetAccessors.cpp
src/LoadData.cpp
src/LoadPBI.cpp
src/Makevars
src/RcppExports.cpp
src/ReadProfiling.cpp
src/htslib/.gitignore
src/htslib/INSTALL
src/htslib/LICENSE
src/htslib/Makefile
src/htslib/README
src/htslib/README.md
src/htslib/bgzf.c
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src/htslib/htslib/knetfile.h
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src/htslib/htslib/ksort.h
src/htslib/htslib/kstring.h
src/htslib/htslib/regidx.h
src/htslib/htslib/sam.h
src/htslib/htslib/synced_bcf_reader.h
src/htslib/htslib/tbx.h
src/htslib/htslib/vcf.h
src/htslib/htslib/vcf_sweep.h
src/htslib/htslib/vcfutils.h
src/htslib/htslibConfig.cmake
src/htslib/htslib_vars.mk
src/htslib/kfunc.c
src/htslib/knetfile.c
src/htslib/kstring.c
src/htslib/regidx.c
src/htslib/sam.5
src/htslib/sam.c
src/htslib/synced_bcf_reader.c
src/htslib/tabix.1
src/htslib/tabix.c
src/htslib/tbx.c
src/htslib/vcf.5
src/htslib/vcf.c
src/htslib/vcf_sweep.c
src/htslib/vcfutils.c
src/htslib/version.h
src/pbbam/Accuracy.cpp
src/pbbam/AlignmentPrinter.cpp
src/pbbam/AssertUtils.cpp
src/pbbam/AssertUtils.h
src/pbbam/BaiIndexedBamReader.cpp
src/pbbam/BamFile.cpp
src/pbbam/BamHeader.cpp
src/pbbam/BamReader.cpp
src/pbbam/BamRecord.cpp
src/pbbam/BamRecordBuilder.cpp
src/pbbam/BamRecordImpl.cpp
src/pbbam/BamRecordTags.cpp
src/pbbam/BamRecordTags.h
src/pbbam/BamTagCodec.cpp
src/pbbam/BamWriter.cpp
src/pbbam/BarcodeQuery.cpp
src/pbbam/CMakeLists.txt
src/pbbam/ChemistryTable.cpp
src/pbbam/ChemistryTable.h
src/pbbam/Cigar.cpp
src/pbbam/CigarOperation.cpp
src/pbbam/Compare.cpp
src/pbbam/Config.cpp
src/pbbam/DataSet.cpp
src/pbbam/DataSetBaseTypes.cpp
src/pbbam/DataSetElement.cpp
src/pbbam/DataSetIO.cpp
src/pbbam/DataSetIO.h
src/pbbam/DataSetTypes.cpp
src/pbbam/DataSetUtils.h
src/pbbam/DataSetXsd.cpp
src/pbbam/EntireFileQuery.cpp
src/pbbam/EnumClassHash.h
src/pbbam/FastaReader.cpp
src/pbbam/FileProducer.cpp
src/pbbam/FileProducer.h
src/pbbam/FileUtils.cpp
src/pbbam/FileUtils.h
src/pbbam/FofnReader.cpp
src/pbbam/FofnReader.h
src/pbbam/Frames.cpp
src/pbbam/GenomicInterval.cpp
src/pbbam/GenomicIntervalQuery.cpp
src/pbbam/IRecordWriter.cpp
src/pbbam/IndexedFastaReader.cpp
src/pbbam/MD5.cpp
src/pbbam/Makefile
src/pbbam/MemoryUtils.cpp
src/pbbam/MemoryUtils.h
src/pbbam/PbiBuilder.cpp
src/pbbam/PbiFile.cpp
src/pbbam/PbiFilter.cpp
src/pbbam/PbiFilterQuery.cpp
src/pbbam/PbiFilterTypes.cpp
src/pbbam/PbiIndex.cpp
src/pbbam/PbiIndexIO.cpp
src/pbbam/PbiIndexIO.h
src/pbbam/PbiIndexedBamReader.cpp
src/pbbam/PbiRawData.cpp
src/pbbam/ProgramInfo.cpp
src/pbbam/Pulse2BaseCache.h
src/pbbam/QNameQuery.cpp
src/pbbam/QualityValue.cpp
src/pbbam/ReadAccuracyQuery.cpp
src/pbbam/ReadGroupInfo.cpp
src/pbbam/SamTagCodec.cpp
src/pbbam/SamWriter.cpp
src/pbbam/SequenceInfo.cpp
src/pbbam/SequenceUtils.h
src/pbbam/StringUtils.h
src/pbbam/SubreadLengthQuery.cpp
src/pbbam/Tag.cpp
src/pbbam/TagCollection.cpp
src/pbbam/TimeUtils.h
src/pbbam/UnmappedReadsQuery.cpp
src/pbbam/ValidationErrors.cpp
src/pbbam/ValidationErrors.h
src/pbbam/ValidationException.cpp
src/pbbam/Validator.cpp
src/pbbam/Version.cpp
src/pbbam/Version.h
src/pbbam/VirtualRegionTypeMap.cpp
src/pbbam/VirtualZmwBamRecord.cpp
src/pbbam/VirtualZmwCompositeReader.cpp
src/pbbam/VirtualZmwCompositeReader.h
src/pbbam/VirtualZmwReader.cpp
src/pbbam/VirtualZmwReader.h
src/pbbam/WhitelistedZmwReadStitcher.cpp
src/pbbam/XmlReader.cpp
src/pbbam/XmlReader.h
src/pbbam/XmlWriter.cpp
src/pbbam/XmlWriter.h
src/pbbam/ZmwGroupQuery.cpp
src/pbbam/ZmwQuery.cpp
src/pbbam/ZmwReadStitcher.cpp
src/pbbam/ZmwTypeMap.cpp
src/pbbam/files.cmake
src/pbbam/pugixml/pugiconfig.hpp
src/pbbam/pugixml/pugixml.cpp
src/pbbam/pugixml/pugixml.hpp
src/utils.h
tests/testthat.R
tests/testthat/AlignmentSet/m54006_160504_020705.alignmentset.xml
tests/testthat/AlignmentSet/m54006_160504_020705.tiny_mapped.1.subreads.bam
tests/testthat/AlignmentSet/m54006_160504_020705.tiny_mapped.1.subreads.bam.pbi
tests/testthat/AlignmentSet/m54006_160504_020705.tiny_mapped.2.subreads.bam
tests/testthat/AlignmentSet/m54006_160504_020705.tiny_mapped.2.subreads.bam.pbi
tests/testthat/All4mers_circular_72x_l50256.fasta
tests/testthat/All4mers_circular_72x_l50256.fasta.fai
tests/testthat/ReferenceSet/lambdaNEB/reference.info.xml
tests/testthat/ReferenceSet/lambdaNEB/referenceset.xml
tests/testthat/ReferenceSet/lambdaNEB/sequence/lambdaNEB.fasta
tests/testthat/ReferenceSet/lambdaNEB/sequence/lambdaNEB.fasta.contig.index
tests/testthat/ReferenceSet/lambdaNEB/sequence/lambdaNEB.fasta.fai
tests/testthat/ReferenceSet/lambdaNEB/sequence/lambdaNEB.fasta.index
tests/testthat/ReferenceSet/lambdaNEB/sequence/lambdaNEB.fasta.sa
tests/testthat/SubreadSet/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam
tests/testthat/SubreadSet/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.bai
tests/testthat/SubreadSet/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi
tests/testthat/SubreadSet/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreadset.xml
tests/testthat/SubreadSet/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0_filtered.subreadset.xml
tests/testthat/SubreadSet/m54006_160504_020705.sts.xml
tests/testthat/SubreadSet/m54006_160504_020705.tiny.scraps.bam
tests/testthat/SubreadSet/m54006_160504_020705.tiny.scraps.bam.pbi
tests/testthat/SubreadSet/m54006_160504_020705.tiny.subreads.bam
tests/testthat/SubreadSet/m54006_160504_020705.tiny.subreads.bam.pbi
tests/testthat/SubreadSet/m54006_160504_020705.tiny.subreadset.xml
tests/testthat/goat.bam
tests/testthat/goat.bam.pbi
tests/testthat/goat.values.R
tests/testthat/lambdaNEB.fa
tests/testthat/lambdaNEB.fa.fai
tests/testthat/loadedAln.Rd
tests/testthat/referenceset.xml
tests/testthat/test.aligned.bam
tests/testthat/test.aligned.bam.bai
tests/testthat/test.aligned.bam.pbi
tests/testthat/test.load.R tests/testthat/test.readReports.R tests/testthat/test.utils.R
update_pbbam.sh
vignettes/pbbamr.R vignettes/pbbamr.Rmd
vignettes/pbbamr.html
vignettes/pbbamrUpdates.Rmd
PacificBiosciences/pbbamr documentation built on Oct. 4, 2017, 12:07 a.m.