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/dports/biology/pbbam/pbbam-0.18.0/tools/pbbamify/src/
H A Dmain.cpp17 namespace BAM { 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.h15 namespace BAM {
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.cpp17 namespace BAM { 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.h16 namespace BAM {
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.h17 namespace BAM {
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.h20 namespace BAM {
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.h35 namespace BAM {
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.h16 namespace BAM {
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/docs/specs/
H A Dpbbam.rst74 | (1) | `BAM format`_ | General SAM/BAM specification |
76 | (2) | `PacBio BAM`_ | PacBio BAM specification |
88 .. _PacBio BAM: http://pacbiofileformats.readthedocs.org/en/3.0/BAM.html
114 `PacBio BAM`_ specification (2). BAM records must be editable e.g. adding
203 PacBio BAM format - see `PacBio BAM`_ specification (2) for more detail.
275 * a `PacBio BAM index`_ (.pbi) for each source BAM file
319 * BAM records
334 BAM file conforming to the `PacBio BAM`_ specification.
353 `PacBio BAM`_ file
364 `PacBio BAM index`_ file
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H A Dpbbam_updated_release3_2.rst78 | (1) | `BAM format`_ | General SAM/BAM specification |
80 | (2) | `PacBio BAM`_ | PacBio BAM specification |
92 .. _PacBio BAM: http://pacbiofileformats.readthedocs.org/en/3.0/BAM.html
118 `PacBio BAM`_ specification (2). BAM records must be editable e.g. adding
207 PacBio BAM format - see `PacBio BAM`_ specification (2) for more detail.
274 * a `PacBio BAM index`_ (.pbi) for each source BAM file
314 * BAM records
329 BAM file conforming to the `PacBio BAM`_ specification.
343 `PacBio BAM`_ file
354 `PacBio BAM index`_ file
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/dports/biology/pbbam/pbbam-0.18.0/src/
H A DDataSetUtils.h11 namespace BAM {
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.cpp20 namespace BAM { 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/bedtools/bedtools2-2.30.0/docs/content/tools/
H A Dbamtobed.rst7 in BAM format into BED, BED12, and/or BEDPE records.
15 bedtools bamtobed [OPTIONS] -i <BAM>
20 bamToBed [OPTIONS] -i <BAM>
78 ``-tag`` Set the score field based on BAM tags
82 option to select the BAM edit distance (the `NM` tag) as the score
94 ``-bedpe`` Set the score field based on BAM tags
99 the BAM alignment reported will be the one where the BAM insert size is greater
107 When using this option, it is required that the BAM
113 using BAM. bamToBed will fail if an aligner does not report
144 ``-split`` Creating BED12 features from "spliced" BAM entries.
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H A Dbamtofastq.rst7 from sequence alignments in BAM format.
24 bedtools bamtofastq [OPTIONS] -i <BAM> -fq <FASTQ>
29 bamToFastq [OPTIONS] -i <BAM> -fq <FASTQ>
38 **-fq2** FASTQ for second end. Used if BAM contains paired-end data.
39 BAM should be sorted by query name
42 **-tags** Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
49 By default, each alignment in the BAM file is converted to a FASTQ record
51 follows the order of the records in the BAM input file.
72 If your BAM alignments are from paired-end sequence data, one can use the
78 When using this option, it is required that the BAM
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H A Dbedtobam.rst6 **bedToBam** converts features in a feature file to BAM format. This is useful as an efficient mean…
16 bedToBam [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> > <BAM>
22 **-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
23 … will convert blocked BED features (e.g., gene annotations) into "spliced" BAM alignments by creat…
54 Creating "spliced" BAM entries from "blocked" BED features
56 Optionally, **bedToBam** will create spliced BAM entries from "blocked" BED features by using the
57 -bed12 option. This will create CIGAR strings in the BAM output that will be displayed as "spliced"
58 alignments. The image illustrates this behavior, as the top track is a BAM representation (using
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/
H A DDataSet.inl10 namespace BAM { 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.inl10 namespace BAM { 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
50 } // namespace BAM
/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
H A DBamRecord.rst8 .. doxygenenum:: PacBio::BAM::ClipType
10 .. doxygenenum:: PacBio::BAM::RecordType
12 .. doxygenenum:: PacBio::BAM::FrameEncodingType
14 .. doxygenclass:: PacBio::BAM::BamRecord
/dports/devel/hs-haskell-language-server/haskell-language-server-1.4.0/_cabal_deps/algebraic-graphs-0.5/src/Algebra/Graph/Bipartite/Undirected/
H A DAdjacencyMap.hs153 data AdjacencyMap a b = BAM { constructor
190 BAM lr1 rl1 == BAM lr2 rl2 = lr1 == lr2 && Map.keysSet rl1 == Map.keysSet rl2 function
237 empty = BAM Map.empty Map.empty
251 leftVertex x = BAM (Map.singleton x Set.empty) Map.empty
305 overlay (BAM lr1 rl1) (BAM lr2 rl2) =
331 connect (BAM lr1 rl1) (BAM lr2 rl2) = BAM lr rl
411 swap (BAM lr rl) = BAM rl lr
463 fromBipartite (BAM lr rl) = AM.fromAdjacencySets $
492 isEmpty (BAM lr rl) = Map.null lr && Map.null rl
503 hasLeftVertex x (BAM lr _) = Map.member x lr
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/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_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/seqan-apps/seqan-seqan-v2.4.0/apps/samcat/
H A DREADME.md4 Concatenate and convert SAM/BAM files quickly.
11 This tool reads one or many SAM/BAM files and outputs their concatenation as a SAM/BAM file.
19 Input and output formats can be arbitrary, i.e. to convert a SAM into a BAM file use:
25 …put file name is omitted the result is written to stdout in SAM format, use ```-b``` to select BAM.
35 As the BAM format is more compact than SAM and faster to parse the best performance will be reached…
/dports/biology/pbbam/pbbam-0.18.0/tools/common/
H A DBamFileMerger.h13 namespace BAM {
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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