/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/ |
H A D | VcfHeader.h | 15 namespace PacBio { 73 VcfHeader& AddGeneralDefinition(PacBio::VCF::GeneralDefinition def); 77 VcfHeader& AddContigDefinition(PacBio::VCF::ContigDefinition def); 82 VcfHeader& AddInfoDefinition(PacBio::VCF::InfoDefinition info); 87 VcfHeader& AddFilterDefinition(PacBio::VCF::FilterDefinition filter); 101 std::vector<PacBio::VCF::GeneralDefinition> generalDefinitions_; 102 std::vector<PacBio::VCF::ContigDefinition> contigDefinitions_; 103 std::vector<PacBio::VCF::InfoDefinition> infoDefinitions_; 104 std::vector<PacBio::VCF::FilterDefinition> filterDefinitions_; 105 std::vector<PacBio::VCF::FormatDefinition> formatDefinitions_; [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/sra/ |
H A D | pacbio.vschema | 37 * NCBI:SRA:PacBio 80 * NCBI:SRA:PacBio:smrt:db 100 const PacBio:hole:status PacBio:hole:SEQUENCING = 0; 101 const PacBio:hole:status PacBio:hole:ANTIHOLE = 1; 102 const PacBio:hole:status PacBio:hole:FIDUCIAL = 2; 103 const PacBio:hole:status PacBio:hole:SUSPECT = 3; 104 const PacBio:hole:status PacBio:hole:ANTIMIRROR = 4; 105 const PacBio:hole:status PacBio:hole:FDZMW = 5; 106 const PacBio:hole:status PacBio:hole:FBZMW = 6; 107 const PacBio:hole:status PacBio:hole:ANTIBEAMLET = 7; [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/sra/ |
H A D | pacbio.vschema | 37 * NCBI:SRA:PacBio 80 * NCBI:SRA:PacBio:smrt:db 100 const PacBio:hole:status PacBio:hole:SEQUENCING = 0; 101 const PacBio:hole:status PacBio:hole:ANTIHOLE = 1; 102 const PacBio:hole:status PacBio:hole:FIDUCIAL = 2; 103 const PacBio:hole:status PacBio:hole:SUSPECT = 3; 104 const PacBio:hole:status PacBio:hole:ANTIMIRROR = 4; 105 const PacBio:hole:status PacBio:hole:FDZMW = 5; 106 const PacBio:hole:status PacBio:hole:FBZMW = 6; 107 const PacBio:hole:status PacBio:hole:ANTIBEAMLET = 7; [all …]
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/dports/biology/pbbam/pbbam-0.18.0/tools/pbbamify/src/ |
H A D | main.cpp | 16 namespace PacBio { namespace 92 parser.version(PacBio::BAM::pbbamify::Version); in main() 124 const PacBio::BAM::pbbamify::Settings settings = in main() 125 PacBio::BAM::pbbamify::Settings::FromCommandLine(parser, argc, argv); in main() 139 PacBio::BAM::ProgramInfo pbbamifyProgram; in main() 142 .Version(PacBio::BAM::pbbamify::Version); in main() 144 PacBio::BAM::DataSet dataset = PacBio::BAM::DataSet(settings.pbbamFilename_); in main() 145 PacBio::BAM::BamReader inputBamReader(settings.inputFilename_); in main() 146 PacBio::BAM::BamHeader newHeader; in main() 155 std::shared_ptr<PacBio::BAM::pbbamify::QueryLookup> queryLookup = in main() [all …]
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H A D | PbBamify.h | 14 namespace PacBio { 29 static PacBio::BAM::BamHeader ComposeHeader(const PacBio::BAM::DataSet& dataset, 30 PacBio::BAM::FastaReader& refReader, 31 const PacBio::BAM::BamReader& input); 40 const PacBio::BAM::IndexedFastaReader& indexedRefReader, 41 PacBio::BAM::BamReader& input, PacBio::BAM::BamWriter& writer, 52 const PacBio::BAM::IndexedFastaReader& indexedRefReader, 86 static Cigar BasicToExtendedCigar(const PacBio::BAM::IndexedFastaReader& indexedRefReader,
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H A D | PbBamify.cpp | 16 namespace PacBio { namespace 34 PacBio::BAM::BamHeader Pbbamify::ComposeHeader(const PacBio::BAM::DataSet& dataset, in ComposeHeader() 35 PacBio::BAM::FastaReader& refReader, in ComposeHeader() 36 const PacBio::BAM::BamReader& input) in ComposeHeader() 39 PacBio::BAM::BamHeader retHeader; in ComposeHeader() 61 PacBio::BAM::FastaSequence record; in ComposeHeader() 74 PacBio::BAM::SequenceInfo seq(header, ossLength.str()); in ComposeHeader() 75 auto hash = PacBio::BAM::MD5Hash(record.Bases()); in ComposeHeader() 222 PacBio::BAM::BamReader& input, PacBio::BAM::BamWriter& writer, in AugmentAlignments() 296 const PacBio::BAM::IndexedFastaReader& indexedRefReader, in AugmentAlignment() [all …]
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H A D | QueryLookup.h | 15 namespace PacBio { 26 std::unique_ptr<QueryLookup> CreateQueryLookup(const PacBio::BAM::DataSet& dataset); 49 friend std::unique_ptr<QueryLookup> CreateQueryLookup(const PacBio::BAM::DataSet& dataset); 70 QueryLookup(const PacBio::BAM::DataSet& dataset); 72 const PacBio::BAM::DataSet& dataset_; 73 std::vector<std::shared_ptr<PacBio::BAM::BamReader>> readers_;
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/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/ |
H A D | DataSetTypes.h | 16 namespace PacBio { 72 const PacBio::BAM::Provenance& Provenance() const; 102 PacBio::BAM::Provenance& Provenance(); 195 PacBio::BAM::ExternalResources& ExternalResources(); 308 const PacBio::BAM::Properties& Properties() const; 317 PacBio::BAM::Properties& Properties(); 546 PacBio::BAM::ParentTool& ParentTool(); 646 const PacBio::BAM::Filters& Filters() const; 682 PacBio::BAM::Filters& Filters(); 690 PacBio::BAM::DataSetMetadata& Metadata(); [all …]
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H A D | DataSet.h | 19 namespace PacBio { 270 PacBio::BAM::DataSet::TypeEnum Type() const; 289 const PacBio::BAM::Extensions& Extensions() const; 302 const PacBio::BAM::Filters& Filters() const; 308 const PacBio::BAM::DataSetMetadata& Metadata() const; 314 const PacBio::BAM::SubDataSets& SubDataSets() const; 654 PacBio::BAM::Extensions& Extensions(); 662 PacBio::BAM::ExternalResources& ExternalResources(); 670 PacBio::BAM::Filters& Filters(); 678 PacBio::BAM::DataSetMetadata& Metadata(); [all …]
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H A D | BamRecord.h | 34 namespace PacBio { 94 PacBio::BAM::LocalContextFlags LocalContextFlags() const; 764 BamRecord& QueryEnd(const PacBio::BAM::Position pos); 773 BamRecord& QueryStart(const PacBio::BAM::Position pos); 1112 const PacBio::BAM::Position start, const PacBio::BAM::Position end); 1121 const PacBio::BAM::Position end); 1125 const PacBio::BAM::Position end) const; 1165 BamRecord& ClipToQuery(const PacBio::BAM::Position start, const PacBio::BAM::Position end); 1166 BamRecord& ClipToReference(const PacBio::BAM::Position start, const PacBio::BAM::Position end); 1168 const PacBio::BAM::Position end); [all …]
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H A D | BamTagCodec.h | 15 namespace PacBio { 42 static std::vector<uint8_t> Encode(const PacBio::BAM::TagCollection& tags); 58 static uint8_t TagTypeCode(const PacBio::BAM::Tag& tag, 73 const PacBio::BAM::Tag& tag, const TagModifier& additionalModifier = TagModifier::NONE); 82 static PacBio::BAM::Tag FromRawData(uint8_t* rawData);
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/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/ |
H A D | VcfHeader.inl | 6 namespace PacBio { namespace 9 inline VcfHeader& VcfHeader::AddContigDefinition(PacBio::VCF::ContigDefinition contig) 22 inline VcfHeader& VcfHeader::AddFilterDefinition(PacBio::VCF::FilterDefinition filter) 35 inline VcfHeader& VcfHeader::AddFormatDefinition(PacBio::VCF::FormatDefinition format) 48 inline VcfHeader& VcfHeader::AddGeneralDefinition(PacBio::VCF::GeneralDefinition def) 61 inline VcfHeader& VcfHeader::AddInfoDefinition(PacBio::VCF::InfoDefinition info) 87 inline const std::vector<PacBio::VCF::ContigDefinition>& VcfHeader::ContigDefinitions() const 117 inline const std::vector<PacBio::VCF::FilterDefinition>& VcfHeader::FilterDefinitions() const 174 inline const std::vector<PacBio::VCF::InfoDefinition>& VcfHeader::InfoDefinitions() const 184 inline VcfHeader& VcfHeader::InfoDefinitions(std::vector<PacBio::VCF::InfoDefinition> defs) [all …]
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/dports/biology/pbbam/pbbam-0.18.0/src/ |
H A D | DataSetUtils.h | 10 namespace PacBio { 24 inline const PacBio::BAM::DataSetMetadata& NullObject() in NullObject() 26 static const PacBio::BAM::DataSetMetadata empty("", ""); in NullObject() 44 const PacBio::BAM::Type& Class::Method() const \ 47 return Child<PacBio::BAM::Type>(#Type); \ 49 return internal::NullObject<PacBio::BAM::Type>(); \ 57 PacBio::BAM::Type& Class::Method() \ 59 if (!HasChild(#Type)) AddChild(internal::NullObject<PacBio::BAM::Type>()); \ 60 return Child<PacBio::BAM::Type>(#Type); \
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H A D | DataSetTypes.cpp | 19 namespace PacBio { namespace 88 DataSetBase& DataSetBase::Filters(const PacBio::BAM::Filters& filters) in DEFINE_ACCESSORS() 96 DataSetBase& DataSetBase::Metadata(const PacBio::BAM::DataSetMetadata& metadata) in DEFINE_ACCESSORS() 102 const PacBio::BAM::SubDataSets& DataSetBase::SubDataSets() const in SubDataSets() 105 return Child<PacBio::BAM::SubDataSets>("DataSets"); in SubDataSets() 107 return internal::NullObject<PacBio::BAM::SubDataSets>(); in SubDataSets() 111 PacBio::BAM::SubDataSets& DataSetBase::SubDataSets() in SubDataSets() 114 return Child<PacBio::BAM::SubDataSets>("DataSets"); in SubDataSets() 117 DataSetBase& DataSetBase::SubDataSets(const PacBio::BAM::SubDataSets& subdatasets) in SubDataSets() 227 const PacBio::BAM::ExternalResources& resources) in DEFINE_ACCESSORS() [all …]
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/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/ |
H A D | DataSet.inl | 9 namespace PacBio { namespace 30 inline const PacBio::BAM::Extensions& DataSet::Extensions() const 33 inline PacBio::BAM::Extensions& DataSet::Extensions() 42 inline PacBio::BAM::ExternalResources& DataSet::ExternalResources() 48 inline const PacBio::BAM::Filters& DataSet::Filters() const 51 inline PacBio::BAM::Filters& DataSet::Filters() 66 inline const PacBio::BAM::DataSetMetadata& DataSet::Metadata() const 69 inline PacBio::BAM::DataSetMetadata& DataSet::Metadata() 114 inline PacBio::BAM::SubDataSets& DataSet::SubDataSets() 138 inline PacBio::BAM::DataSet::TypeEnum DataSet::Type() const [all …]
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H A D | BamRecord.inl | 9 namespace PacBio { namespace 14 const PacBio::BAM::Position start, 15 const PacBio::BAM::Position end) 21 const PacBio::BAM::Position start, 22 const PacBio::BAM::Position end) const 51 } // namespace PacBio
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/dports/biology/pbbam/pbbam-0.18.0/docs/source/api/ |
H A D | ReadGroupInfo.rst | 8 .. doxygenenum:: PacBio::BAM::BaseFeature 10 .. doxygenenum:: PacBio::BAM::FrameCodec 12 .. doxygenenum:: PacBio::BAM::BarcodeModeType 14 .. doxygenenum:: PacBio::BAM::BarcodeQualityType 16 .. doxygenclass:: PacBio::BAM::ReadGroupInfo 21 .. doxygenfunction:: PacBio::BAM::MakeReadGroupId
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H A D | PbiFile.rst | 8 .. doxygenenum:: PacBio::BAM::PbiFile::Section 10 .. doxygentypedef:: PacBio::BAM::PbiFile::Sections 12 .. doxygenenum:: PacBio::BAM::PbiFile::VersionEnum 14 .. doxygenfunction:: PacBio::BAM::PbiFile::CreateFrom
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/dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
H A D | test_LongCigar.cpp | 13 using BamReader = PacBio::BAM::BamReader; 14 using BamRecord = PacBio::BAM::BamRecord; 15 using BamWriter = PacBio::BAM::BamWriter; 16 using Cigar = PacBio::BAM::Cigar; 17 using CigarOp = PacBio::BAM::CigarOperation; 18 using PacBio::BAM::CigarOperationType; 19 using Tag = PacBio::BAM::Tag; 24 static const std::string LongCigarBam = PacBio::BAM::PbbamTestsConfig::Data_Dir + "/long-cigar.bam"; 27 PacBio::BAM::PbbamTestsConfig::GeneratedData_Dir + "/long-cigar-generated.bam";
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H A D | test_VcfWriter.cpp | 13 using VcfFile = PacBio::VCF::VcfFile; 14 using VcfFormat = PacBio::VCF::VcfFormat; 15 using VcfQuery = PacBio::VCF::VcfQuery; 16 using VcfWriter = PacBio::VCF::VcfWriter; 20 static const std::string VcfFn{PacBio::BAM::PbbamTestsConfig::Data_Dir + 28 const std::string newFn{PacBio::BAM::PbbamTestsConfig::GeneratedData_Dir + "/temp.vcf"}; in TEST()
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H A D | test_VcfSort.cpp | 12 using VcfFile = PacBio::VCF::VcfFile; 13 using VcfQuery = PacBio::VCF::VcfQuery; 19 static const std::string inputFn = PacBio::BAM::PbbamTestsConfig::Data_Dir + 21 static const std::string outputFn = PacBio::BAM::PbbamTestsConfig::GeneratedData_Dir + "/sorted.vcf… 28 PacBio::VCF::SortFile(file, VcfSortTests::outputFn); in TEST()
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H A D | test_StringUtils.cpp | 9 using PacBio::BAM::Split; in TEST() 21 using PacBio::BAM::Split; in TEST() 33 using PacBio::BAM::Split; in TEST() 42 using PacBio::BAM::Split; in TEST() 55 using PacBio::BAM::RemoveAllWhitespace; in TEST() 70 using PacBio::BAM::RemoveAllWhitespace; in TEST()
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/dports/biology/pbbam/pbbam-0.18.0/docs/specs/ |
H A D | pbbam.rst | 76 | (2) | `PacBio BAM`_ | PacBio BAM specification | 78 | (3) | `PacBio BAM index`_ | PacBio BAM index specification | 156 `PacBio BAM`_ (2) or `DataSet XML`_ (4) specifications. 163 Output PacBio BAMs will be compatible with the `PacBio BAM`_ specification (2) 203 PacBio BAM format - see `PacBio BAM`_ specification (2) for more detail. 275 * a `PacBio BAM index`_ (.pbi) for each source BAM file 306 5.3. Write PacBio BAM data 341 5.4. Create PacBio BAM index file 347 Much of PacBio BAM data processing relies on the presence of a `PacBio BAM index`_ 353 `PacBio BAM`_ file [all …]
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H A D | pbbam_updated_release3_2.rst | 80 | (2) | `PacBio BAM`_ | PacBio BAM specification | 82 | (3) | `PacBio BAM index`_ | PacBio BAM index specification | 160 `PacBio BAM`_ (2) or `DataSet XML`_ (4) specifications. 167 Output PacBio BAMs will be compatible with the `PacBio BAM`_ specification (2) 207 PacBio BAM format - see `PacBio BAM`_ specification (2) for more detail. 274 * a `PacBio BAM index`_ (.pbi) for each source BAM file 301 5.3. Write PacBio BAM data 331 5.4. Create PacBio BAM index file 337 Much of PacBio BAM data processing relies on the presence of a `PacBio BAM index`_ 343 `PacBio BAM`_ file [all …]
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/dports/biology/pbbam/pbbam-0.18.0/tools/common/ |
H A D | BamFileMerger.h | 12 namespace PacBio { 31 static void Merge(const PacBio::BAM::DataSet& dataset, const std::string& outputFilename, 32 const PacBio::BAM::ProgramInfo& mergeProgram = PacBio::BAM::ProgramInfo(),
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