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Searched refs:FastaRecord (Results 1 – 25 of 40) sorted by relevance

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/dports/biology/abyss/abyss-2.3.1/Sealer/
H A Dsealer.cc533 FastaRecord &record, in insertIntoScaffold()
567 std::pair<FastaRecord, FastaRecord>
570 std::pair<FastaRecord, FastaRecord> scaftigs; in makePseudoReads()
591 map<FastaRecord, map<FastaRecord, Gap> > &flanks, in kRun() argument
597 map<FastaRecord, map<FastaRecord, Gap> >::iterator read1_it; in kRun()
621 vector<map<FastaRecord, map<FastaRecord, Gap> >::iterator> flanks_closed; in kRun()
697 bool operator<(const FastaRecord& a, const FastaRecord& b) in operator <()
708 map<FastaRecord, map<FastaRecord, Gap> > &flanks) in findFlanks() argument
735 std::pair<FastaRecord, FastaRecord> scaftigs = in findFlanks()
966 map<FastaRecord, map<FastaRecord, Gap> > flanks; in main()
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/
H A Dpostnuc_main.cc160 class FastaRecord class
170 FastaRecord() = default;
171 FastaRecord(const std::string& Id, const std::string& seq) in FastaRecord() function in FastaRecord
175 FastaRecord(std::string&& Id, std::string&& seq) in FastaRecord() function in FastaRecord
179 …FastaRecord(FastaRecord&& rhs) noexcept : m_Id(std::move(rhs.m_Id)), m_seq(std::move(rhs.m_seq)) {… in FastaRecord() function in FastaRecord
193 typedef Synteny<FastaRecord> synteny_type; in main()
195 std::vector<FastaRecord> Af; // array of all the reference sequences in main()
199 FastaRecord Bf; // Query sequence information in main()
235 const FastaRecord& Af, const FastaRecord& Bf) { in main()
238 auto print_clusters = [&](const synteny_list_type& Syntenys, const FastaRecord& Bf) { in main()
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H A Dpostpro.cc77 struct FastaRecord struct
155 const FastaRecord * A, const FastaRecord * B, FILE * DeltaFile);
160 const FastaRecord * Af, const FastaRecord * Bf,
185 const FastaRecord * Af, const FastaRecord *Bf);
211 const FastaRecord * Af, const FastaRecord * Bf);
335 Af = (FastaRecord *) Safe_malloc ( sizeof(FastaRecord) * Ac ); in main()
347 Af = (FastaRecord *) Safe_realloc ( Af, sizeof(FastaRecord) * Ac ); in main()
754 const FastaRecord * Af, const FastaRecord * Bf, FILE * DeltaFile) in extendClusters()
946 const FastaRecord * Af, const FastaRecord * Bf, in flushAlignments()
1284 const FastaRecord * Af, const FastaRecord *Bf) in parseDelta()
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/dports/biology/abyss/abyss-2.3.1/DataLayer/
H A DFastaReader.h123 struct FastaRecord struct
134 FastaRecord() : anchor(0) { } in FastaRecord() argument
135 FastaRecord(const std::string& id, const std::string& comment, in FastaRecord() argument
141 FastaRecord& operator=(const std::string& s) argument
149 friend FastaReader& operator >>(FastaReader& in, FastaRecord& o) argument
157 const FastaRecord& o) argument
167 struct FastqRecord : FastaRecord
175 : FastaRecord(id, comment, seq), qual(qual) in FastqRecord()
190 return out << static_cast<const FastaRecord&>(o);
H A Dabyss-tofastq.cc183 F convertFasta = convert<FastaRecord>; in main()
197 interleave<FastaRecord>(argv + optind, argv + argc); in main()
/dports/biology/abyss/abyss-2.3.1/Unittest/Konnector/
H A DkonnectorTest.cpp17 FastaRecord read("2", "", "ACGTACGT"); in TEST()
23 read = FastaRecord("2", "", "ACGTACGTA"); in TEST()
33 FastaRecord read("2", "", "ACGTACGT"); in TEST()
51 FastaRecord read1, read2; in TEST()
63 vector<FastaRecord> mergedSeqs; in TEST()
H A DDBGBloomAlgorithmsTest.cpp35 FastaRecord testRead;
137 FastaRecord correctRead;
138 FastaRecord singleErrorRead;
163 FastaRecord read = singleErrorRead; in TEST_F()
178 FastaRecord read = singleErrorRead; in TEST_F()
193 FastaRecord read = singleErrorRead; in TEST_F()
206 FastaRecord read = singleErrorRead; in TEST_F()
/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/include/mummer/
H A Dpostnuc.hh49 template<typename FastaRecord>
53 const FastaRecord* AfP; // a pointer to the reference sequence record
56 Synteny(const FastaRecord* Af) : AfP(Af) { } in Synteny()
269 template<typename FastaRecord>
271 const FastaRecord& Af, const FastaRecord& Bf, in printDeltaAlignments()
285 template<typename FastaRecord>
286 void printSyntenys(const std::vector<Synteny<FastaRecord> >& Syntenys, const FastaRecord& Bf, std::…
382 template<typename FastaRecord>
383 void printSyntenys(const std::vector<Synteny<FastaRecord> > & Syntenys, const FastaRecord& Bf, std:… in printSyntenys()
/dports/biology/abyss/abyss-2.3.1/KAligner/
H A DKAligner.cpp218 static PipeMux<FastaRecord> g_pipeMux(1);
268 Pipe<FastaRecord>& out;
269 WorkerArg(FastaReader& in, Pipe<FastaRecord>& out) in WorkerArg()
444 for (FastaRecord rec; in >> rec;) { in readContigsIntoDB()
478 static void readFile(FastaReader& in, Pipe<FastaRecord>& pipe) in readFile()
480 for (FastaRecord rec; in >> rec;) in readFile()
515 for (pair<FastaRecord, size_t> recPair = g_pipeMux.nextValue(); in alignReadsToDB()
517 const FastaRecord& rec = recPair.first; in alignReadsToDB()
/dports/biology/abyss/abyss-2.3.1/Konnector/
H A Dkonnector.h33 std::vector<FastaRecord> mergedSeqs;
40 FastaRecord consensusSeq;
196 const FastaRecord& read1, in writeDot()
197 const FastaRecord& read2, in writeDot()
237 const FastaRecord& read1, in connectPairs()
238 const FastaRecord& read2, in connectPairs()
267 const FastaRecord* pRead1 = &read1; in connectPairs()
269 FastaRecord correctedRead1; in connectPairs()
270 FastaRecord correctedRead2; in connectPairs()
371 FastaRecord mergedSeq; in connectPairs()
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H A DDBGBloomAlgorithms.h128 FastaRecord& read, size_t& correctedPos, bool rc = false)
183 static inline unsigned maskNew(const FastaRecord& read1,
184 const FastaRecord& read2, FastaRecord& merged, int mask = 0)
/dports/biology/abyss/abyss-2.3.1/GapFiller/
H A Dgapfill.h15 FastaRecord rec;
18 Scaffold(FastaRecord rec) : rec(rec) in Scaffold()
H A Dgapfill.cpp82 FastaRecord rec; in readScaffolds()
288 FastaRecord rec; in printFixedContigs()
/dports/biology/pyfasta/pyfasta-0.5.2/
H A DREADME.rst111 * FastaRecord, which uses using fseek/fread
123 >>> from pyfasta import FastaRecord # default is NpyFastaRecord
124 >>> f = Fasta('tests/data/three_chrs.fasta', record_class=FastaRecord)
126 FastaRecord('tests/data/three_chrs.fasta.flat', 0..80)
130 it's possible to create your own using a sub-class of FastaRecord. see the source
H A DPKG-INFO119 * FastaRecord, which uses using fseek/fread
131 >>> from pyfasta import FastaRecord # default is NpyFastaRecord
132 >>> f = Fasta('tests/data/three_chrs.fasta', record_class=FastaRecord)
134 FastaRecord('tests/data/three_chrs.fasta.flat', 0..80)
138 it's possible to create your own using a sub-class of FastaRecord. see the source
/dports/biology/abyss/abyss-2.3.1/Overlap/
H A DOverlap.cpp200 static FastaRecord newContig(const Graph& g, in newContig()
208 return FastaRecord(createContigName(), comment.str(), seq); in newContig()
240 static FastaRecord createGapContig(const Graph& g, in createGapContig()
358 for (FastaRecord rec; in >> rec;) in readContigs()
566 FastaRecord contig = createGapContig(graph, in main()
/dports/biology/pyfasta/pyfasta-0.5.2/pyfasta.egg-info/
H A DPKG-INFO119 * FastaRecord, which uses using fseek/fread
131 >>> from pyfasta import FastaRecord # default is NpyFastaRecord
132 >>> f = Fasta('tests/data/three_chrs.fasta', record_class=FastaRecord)
134 FastaRecord('tests/data/three_chrs.fasta.flat', 0..80)
138 it's possible to create your own using a sub-class of FastaRecord. see the source
/dports/biology/abyss/abyss-2.3.1/Assembly/
H A DLoadAlgorithm.h18 for (FastaRecord rec; in >> rec;) { in loadKmer()
100 for (FastaRecord rec; reader >> rec;) { in loadSequences()
/dports/biology/pyfasta/pyfasta-0.5.2/pyfasta/
H A Drecords.py19 class FastaRecord(object): class
173 class NpyFastaRecord(FastaRecord):
221 class MemoryRecord(FastaRecord):
/dports/biology/abyss/abyss-2.3.1/BloomDBG/
H A Dbloom-dbg.h465 FastaRecord contig; in printContig()
782 const FastaRecord& rec, in processRead()
1011 for (std::vector<FastaRecord> buffer;;) { in assemble()
1018 FastaRecord rec; in assemble()
1030 for (std::vector<FastaRecord>::iterator it = buffer.begin(); it != buffer.end(); ++it) { in assemble()
1204 for (FastaRecord rec;;) { in outputGraph()
1296 for (FastaRecord rec; ref >> rec;) { in writeCovTrack()
/dports/biology/pyfasta/pyfasta-0.5.2/tests/
H A Dtest_all.py2 from pyfasta.records import NpyFastaRecord, MemoryRecord, FastaRecord
3 record_classes = [NpyFastaRecord, MemoryRecord, FastaRecord]
/dports/biology/abyss/abyss-2.3.1/RResolver/
H A DContigs.cpp113 for (FastaRecord rec; in >> rec;) { in loadContigs()
161 FastaRecord rec; in storeContigs()
/dports/biology/abyss/abyss-2.3.1/Parallel/
H A DparallelAbyss.cpp43 for (FastaRecord rec; reader >> rec;) { in mergeFastaFiles()
/dports/biology/abyss/abyss-2.3.1/Align/
H A Dalign.cc116 FastaRecord fa; in alignFile()
/dports/biology/abyss/abyss-2.3.1/Consensus/
H A DConsensus.cpp112 for (FastaRecord rec; contigsFile >> rec;) { in readContigs()
415 outFile << FastaRecord( in consensus()

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