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/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/
H A DVcfHeader.h15 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_;
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/sra/
H A Dpacbio.vschema37 * 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;
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/sra/
H A Dpacbio.vschema37 * 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;
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/dports/biology/pbbam/pbbam-0.18.0/tools/pbbamify/src/
H A Dmain.cpp16 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()
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H A DPbBamify.h14 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,
H A DPbBamify.cpp16 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()
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H A DQueryLookup.h15 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_;
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/
H A DDataSetTypes.h16 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();
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H A DDataSet.h19 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();
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H A DBamRecord.h34 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);
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H A DBamTagCodec.h15 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);
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/vcf/internal/
H A DVcfHeader.inl6 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)
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/dports/biology/pbbam/pbbam-0.18.0/src/
H A DDataSetUtils.h10 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); \
H A DDataSetTypes.cpp19 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()
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/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/
H A DDataSet.inl9 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
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H A DBamRecord.inl9 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
/dports/biology/pbbam/pbbam-0.18.0/docs/source/api/
H A DReadGroupInfo.rst8 .. 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
H A DPbiFile.rst8 .. doxygenenum:: PacBio::BAM::PbiFile::Section
10 .. doxygentypedef:: PacBio::BAM::PbiFile::Sections
12 .. doxygenenum:: PacBio::BAM::PbiFile::VersionEnum
14 .. doxygenfunction:: PacBio::BAM::PbiFile::CreateFrom
/dports/biology/pbbam/pbbam-0.18.0/tests/src/
H A Dtest_LongCigar.cpp13 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";
H A Dtest_VcfWriter.cpp13 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()
H A Dtest_VcfSort.cpp12 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()
H A Dtest_StringUtils.cpp9 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()
/dports/biology/pbbam/pbbam-0.18.0/docs/specs/
H A Dpbbam.rst76 | (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
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H A Dpbbam_updated_release3_2.rst80 | (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
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/dports/biology/pbbam/pbbam-0.18.0/tools/common/
H A DBamFileMerger.h12 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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