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/dports/biology/canu/canu-2.2/src/bogart/
H A DAS_BAT_Unitig_PlaceReadUsingEdges.C67 readId, in placeRead_contained()
71 fMax = fMin + RI->readLength(readId); in placeRead_contained()
80 read.ident = readId; in placeRead_contained()
92 readId, in placeRead_contained()
182 readId, in placeRead_dovetail()
208 read.ident = readId; in placeRead_dovetail()
240 assert(readId > 0); in placeRead()
241 assert(readId <= RI->numReads()); in placeRead()
243 read.ident = readId; in placeRead()
257 assert(edge->readId() != 0); in placeRead()
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H A DAS_BAT_PopulateUnitig.C34 if ((bestnext == NULL) || (bestnext->readId() == 0)) { in populateUnitig()
52 while ((bestnext->readId() != 0) && in populateUnitig()
53 (unitig->inUnitig(bestnext->readId()) == 0)) { in populateUnitig()
77 (OG->isSpur(bestnext->readId()) == true) ? "spur" : "read", in populateUnitig()
78 bestnext->readId(), in populateUnitig()
100 if (bestnext->readId() == 0) in populateUnitig()
104 bestnext->readId(), in populateUnitig()
105 unitig->inUnitig(bestnext->readId())); in populateUnitig()
154 bool edgeTo5 = ((backedge5->readId() == fi) && (backedge5->read3p() == false)); in populateUnitig()
204 if (bestedge3->readId()) { in populateUnitig()
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H A DAS_BAT_BestOverlapGraph_implementation.H21 return((readId() == that.readId()) && (read3p() == that.read3p()));
27 return((readId() != that.readId()) || (read3p() != that.read3p()));
33 if (readId() != that.readId())
34 return readId() < that.readId();
81 BestEdgeOverlap::setReverse(BestEdgeOverlap *that, uint32 readId, bool read3p) { in setReverse() argument
82 _id = readId; in setReverse()
H A DAS_BAT_ChunkGraph.C41 _chunkLength[fid].readId = fid; in ChunkGraph()
80 … return((a.pathLen > b.pathLen) || ((a.pathLen == b.pathLen) && (a.readId < b.readId))); in ChunkGraph()
109 return(e.readId() * 2 + e.read3p()); in getIndex()
117 assert(firstEnd.readId() != 0); in countFullWidth()
122 firstEnd.readId(), in countFullWidth()
136 while ((lastEnd.readId() != 0) && in countFullWidth()
153 if (lastEnd.readId() == 0) { in countFullWidth()
211 firstEnd.readId(), in countFullWidth()
215 while ((currEnd.readId() != 0) && in countFullWidth()
224 currEnd.readId(), in countFullWidth()
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H A DAS_BAT_BestOverlapGraph.C560 …int32 back5ovlLen = RI->overlapLength(this5->readId(), back5->readId(), back5->ahang(), back5->bh… in removeLopsidedEdges()
561 …int32 back3ovlLen = RI->overlapLength(this3->readId(), back3->readId(), back3->ahang(), back3->bh… in removeLopsidedEdges()
585 if ((this5->readId() > 0) && in removeLopsidedEdges()
586 (this3->readId() > 0)) in removeLopsidedEdges()
592 else if (this5->readId() > 0) in removeLopsidedEdges()
597 else if (this3->readId() > 0) in removeLopsidedEdges()
654 uint32 inid = edge->readId(); in spurDistance()
1358 used.insert(bestedge5->readId()); in reportBestEdges()
1359 used.insert(bestedge3->readId()); in reportBestEdges()
1393 bestedge3->readId(), in reportBestEdges()
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H A DAS_BAT_TigVector.H45 void registerRead(uint32 readId, uint32 tigid=0, uint32 ufpathidx=UINT32_MAX) {
46 _inUnitig[readId] = tigid;
47 _ufpathIdx[readId] = ufpathidx;
50 uint32 inUnitig(uint32 readId) { return(_inUnitig[readId]); }; in inUnitig() argument
51 uint32 ufpathIdx(uint32 readId) { return(_ufpathIdx[readId]); }; in ufpathIdx() argument
/dports/biology/seqan1/seqan-1.3.1/apps/rabema/
H A Dintervals.h60 size_t readId; member
88 : readName(_readName), flags(_flags), readId(0), distance(_distance), in WitRecord()
94 if (readId < other.readId)
96 if (readId == other.readId && distance < other.distance)
98 if (readId == other.readId && distance == other.distance &&
101 if (readId == other.readId && distance == other.distance &&
104 if (readId == other.readId && distance == other.distance &&
117 if (a.contigId == b.contigId && a.readId < b.readId) in operator()
119 if (a.contigId == b.contigId && a.readId == b.readId && a.lastPos < b.lastPos) in operator()
H A Dwit_store.h44 size_t readId; member
124 return a.readId < b.readId;
312 record.readId = length(value(store.readNames));
320 mateElem.readId[mateNo] = record.readId;
331 record.readId = fragments.matePairStore[matePairId].readId[mateNo];
332 if (record.readId == TMatePairElement::INVALID_ID) {
339 fragments.matePairStore[matePairId].readId[mateNo] = record.readId;
346 …record.readId = fragments.matePairStore[fragments.readStore[record.readId].matePairId].readId[mate…
401 …if (thisInterval.readId != it->readId || thisInterval.contigId != it->contigId || thisInterval.las…
439 …if (thisInterval.readId != it->readId || thisInterval.contigId != it->contigId || thisInterval.las…
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H A Dbuild_gold_standard.h64 size_t readId = it->first; in intervalizeErrorCurves() local
123 int mateNo = getMateNo(fragments, readId); in intervalizeErrorCurves()
151 size_t readId, in buildErrorCurvePoints() argument
209 if (ENABLE && (ALL || readId == READID)) { in buildErrorCurvePoints()
210 …std::cerr << "**************** read id = " << readId << " readname = " << readNames[readId] << " r… in buildErrorCurvePoints()
241 if (ENABLE && (ALL || readId == READID)) { in buildErrorCurvePoints()
262 if (ENABLE && (ALL || readId == READID)) { in buildErrorCurvePoints()
298 if (ENABLE && (ALL || readId == READID)) { in buildErrorCurvePoints()
371 if (ENABLE && (ALL || readId == READID)) { in buildErrorCurvePoints()
550 TReadId readId = alignedRead.readId; in matchesToErrorFunction() local
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H A Devaluation.h174 TReadSeq read = readSeqs[alignedRead.readId]; in bestScoreForAligned()
238 size_t const & readId, in compareAlignedReadsToReferenceOnContigForOneRead() argument
302 SEQAN_ASSERT_EQ(it->readId, readId); in compareAlignedReadsToReferenceOnContigForOneRead()
318 if (endPos < length(fragments.readSeqStore[it->readId])) in compareAlignedReadsToReferenceOnContigForOneRead()
413 Dna5String rcRead(fragments.readSeqStore[it->readId]); in compareAlignedReadsToReferenceOnContigForOneRead()
503 size_t readId = _min(alignedReadsBeginForRead->readId, witRecordsBeginForRead->readId); in compareAlignedReadsToReferenceOnContig() local
505 … while (alignedReadsEndForRead != alignedReadsEnd && alignedReadsEndForRead->readId <= readId) in compareAlignedReadsToReferenceOnContig()
508 while (witRecordsEndForRead != witRecordsEnd && witRecordsEndForRead->readId <= readId) in compareAlignedReadsToReferenceOnContig()
628 << "\", \"read_id\": " << value(it).readId in evaluateFoundIntervals_compareToIntervals()
783 for (size_t readId = 0; readId < length(value(witStore.readNames)); ++readId) { in evaluateFoundIntervals() local
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/
H A Dbits_context.h118 return ctx.minErrors[readId]; in getMinErrors()
128 if (errors < getMinErrors(ctx,readId)) in setMinErrors()
129 assignValue(ctx.minErrors, readId, errors); in setMinErrors()
137 inline void setMapped(TReadsContext & ctx, TReadId readId) in setMapped() argument
139 assignValue(ctx.mapped, readId, true); in setMapped()
147 inline bool isMapped(TReadsContext const & ctx, TReadId readId) in isMapped() argument
149 return ctx.mapped[readId]; in isMapped()
157 inline void setPaired(TReadsContext & ctx, TReadId readId) in setPaired() argument
159 assignValue(ctx.paired, readId, true); in setPaired()
167 inline bool isPaired(TReadsContext const & ctx, TReadId readId) in isPaired() argument
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rabema/
H A Drabema_build_gold_standard.cpp259 size_t readId = it->first; in intervalizeAndDumpErrorCurves() local
332 SEQAN_ASSERT_EQ(readNameStore[readId][length(readNameStore[readId]) - 2], '/'); in intervalizeAndDumpErrorCurves()
389 size_t readId, in buildErrorCurvePoints() argument
444 if (ENABLE && (ALL || readId == READID)) in buildErrorCurvePoints()
446 std::cerr << "**************** read id = " << readId << " readname = " << readNames[readId] in buildErrorCurvePoints()
829 unsigned readId = 0; in matchesToErrorFunction() local
832 readId = length(readNameStore); in matchesToErrorFunction()
927 for (unsigned readId = 0; readId < length(readLengthStore); ++readId) in matchesToErrorFunction() local
934 std::sort(begin(errorCurves[readId], Standard()), end(errorCurves[readId], Standard())); in matchesToErrorFunction()
935 fillGaps(errorCurves[readId]); in matchesToErrorFunction()
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H A Dio_gsi.h75 size_t readId; member
100 …flags(0), readId(0), originalDistance(0), distance(0), contigId(0), isForward(0), firstPos(0), las… in GsiRecord()
111 … readName(_readName), flags(_flags), readId(0), originalDistance(_distance), distance(_distance), in GsiRecord()
118 if (readId < other.readId)
121 if (readId == other.readId && distance < other.distance)
124 if (readId == other.readId && distance == other.distance &&
128 if (readId == other.readId && distance == other.distance &&
132 if (readId == other.readId && distance == other.distance &&
158 record.readId = 0; in clear()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A Drazers_match_filter.h187 if (filter.hitCount[readId - filter.readOffset] == filter.matchThreshold) in registerRead()
190 histogramId = _createHistogram(filter, readId); in registerRead()
191 filter.readIdToHistogramId[readId] = histogramId; in registerRead()
197 TIterator it = filter.readIdToHistogramId.find(readId); in registerRead()
212 if (filter.hitCount[readId - filter.readOffset] < filter.matchThreshold) in processRead()
217 TIterator it = filter.readIdToHistogramId.find(readId); in processRead()
235 appendValue(filter.purgedReadIds, readId); in processRead()
245 appendValue(filter.purgedReadIds, readId); in processRead()
251 limitRead(value(filter.callback), readId, newLimit - 1); in processRead()
252 filter.options.errorCutOff[readId] = newLimit; in processRead()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/
H A Dstore_matepair.h85 …TId readId[2]; // refers to the two reads of a mate-pair, INVALID_ID if this is a single… member
90 readId[0] = INVALID_ID; in MatePairStoreElement()
91 readId[1] = INVALID_ID; in MatePairStoreElement()
96 return readId[0] == other.readId[0] &&
97 readId[1] == other.readId[1] &&
/dports/biology/seqan1/seqan-1.3.1/seqan/store/
H A Dstore_matepair.h85 …TId readId[2]; // refers to the two reads of a mate-pair, INVALID_ID if this is a singleton fragm… member
90 readId[0] = INVALID_ID; in MatePairStoreElement()
91 readId[1] = INVALID_ID; in MatePairStoreElement()
96 return readId[0] == other.readId[0] &&
97 readId[1] == other.readId[1] &&
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/
H A Dstore_matepair.h85 …TId readId[2]; // refers to the two reads of a mate-pair, INVALID_ID if this is a single… member
90 readId[0] = INVALID_ID; in MatePairStoreElement()
91 readId[1] = INVALID_ID; in MatePairStoreElement()
96 return readId[0] == other.readId[0] &&
97 readId[1] == other.readId[1] &&
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/
H A Dstore_matepair.h85 …TId readId[2]; // refers to the two reads of a mate-pair, INVALID_ID if this is a single… member
90 readId[0] = INVALID_ID; in MatePairStoreElement()
91 readId[1] = INVALID_ID; in MatePairStoreElement()
96 return readId[0] == other.readId[0] &&
97 readId[1] == other.readId[1] &&
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sra/
H A Dreader-abi.c278 if( readId > 0 ) {
291 if( readId > 0 && read_label_sz > 0 ) {
297 if( readId > 0 && read_label_sz > 0 ) {
330 if( readId > 0 ) {
349 data[0] = (*me->cs_key)[readId];
365 if( readId > 0 ) {
415 if( readId > 0 ) {
457 return AbsolidReaderSignal(self, readId, 0, data, dsize, written);
462 return AbsolidReaderSignal(self, readId, 1, data, dsize, written);
467 return AbsolidReaderSignal(self, readId, 2, data, dsize, written);
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sra/
H A Dreader-abi.c278 if( readId > 0 ) {
291 if( readId > 0 && read_label_sz > 0 ) {
297 if( readId > 0 && read_label_sz > 0 ) {
330 if( readId > 0 ) {
349 data[0] = (*me->cs_key)[readId];
365 if( readId > 0 ) {
415 if( readId > 0 ) {
457 return AbsolidReaderSignal(self, readId, 0, data, dsize, written);
462 return AbsolidReaderSignal(self, readId, 1, data, dsize, written);
467 return AbsolidReaderSignal(self, readId, 2, data, dsize, written);
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A Drazers.h564 if (a.readId < b.readId) return true;
565 if (a.readId > b.readId) return false;
588 if (a.readId < b.readId) return true;
589 if (a.readId > b.readId) return false;
613 if (a.readId < b.readId) return true;
662 if (a.readId < b.readId) return true;
713 if (a.readId < b.readId) return true;
733 if (a.readId < b.readId) return true;
789 readId = (*it).readId;
815 readId = (*it).readId;
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/sra/
H A Dabi.h112 SRA_RD_EXTERN rc_t CC AbsolidReader_SpotReadInfo(const AbsolidReader* self, uint32_t readId, SRARea…
134 SRA_RD_EXTERN rc_t CC AbsolidReaderHeader(const AbsolidReader* self, uint32_t readId,
141 SRA_RD_EXTERN rc_t CC AbsolidReaderBase(const AbsolidReader* self, uint32_t readId,
148 SRA_RD_EXTERN rc_t CC AbsolidReaderQuality(const AbsolidReader* self, uint32_t readId,
155 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalFTC(const AbsolidReader* self, uint32_t readId,
157 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY3(const AbsolidReader* self, uint32_t readId,
159 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalTXR(const AbsolidReader* self, uint32_t readId,
161 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY5(const AbsolidReader* self, uint32_t readId,
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/sra/
H A Dabi.h112 SRA_RD_EXTERN rc_t CC AbsolidReader_SpotReadInfo(const AbsolidReader* self, uint32_t readId, SRARea…
134 SRA_RD_EXTERN rc_t CC AbsolidReaderHeader(const AbsolidReader* self, uint32_t readId,
141 SRA_RD_EXTERN rc_t CC AbsolidReaderBase(const AbsolidReader* self, uint32_t readId,
148 SRA_RD_EXTERN rc_t CC AbsolidReaderQuality(const AbsolidReader* self, uint32_t readId,
155 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalFTC(const AbsolidReader* self, uint32_t readId,
157 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY3(const AbsolidReader* self, uint32_t readId,
159 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalTXR(const AbsolidReader* self, uint32_t readId,
161 SRA_RD_EXTERN rc_t CC AbsolidReaderSignalCY5(const AbsolidReader* self, uint32_t readId,
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rep_sep/
H A Dassembly_parser.h122 …cout << debug_alignIt->readId << " (" << fragStore.readNameStore[debug_alignIt->readId] << ")" << … in parseContig()
142 …cout << "-> will remove: " << end_erase->readId << " (" << fragStore.readNameStore[end_erase->read… in parseContig()
157 … cout << alignIt->readId << " (" << fragStore.readNameStore[alignIt->readId] << ")" << endl; in parseContig()
163 cout << alignIt->readId << " (" << fragStore.readNameStore[alignIt->readId] << ")" << endl; in parseContig()
177 … cout << iter_cr->readId << " (" << fragStore.readNameStore[iter_cr->readId] << ")" << endl; in parseContig()
186 String<Dna5Q> ungapped_seq = fragStore.readSeqStore[iter_cr->readId]; in parseContig()
197 … TAssignedReadChar(_sequenceCharacter(gapped_read[p - offset]), iter_cr->readId, _positionInRead(g… in parseContig()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-dump/
H A Dabi.c65 uint32_t q, readId; in Absolid2BioFilter_GetKey() local
70 for(q = 0, readId = 0; rc == 0 && readId < num_reads && q < 2; readId++) { in Absolid2BioFilter_GetKey()
177 uint32_t readId, q; in AbsolidLabelerFilter_GetKeySet() local
187 for(q = 0, readId = 0; rc == 0 && readId < num_reads; readId++) { in AbsolidLabelerFilter_GetKeySet()
330 uint32_t readId; in AbsolidReadLenFilter_GetKey() local
335 for(readId = 0; rc == 0 && readId < num_reads; readId++) { in AbsolidReadLenFilter_GetKey()
341 set_readmask(new_mask, readId); in AbsolidReadLenFilter_GetKey()
448 uint32_t readId; in AbsolidQFilter_GetKey() local
455 for(readId = 0; rc == 0 && readId < num_reads; readId++) { in AbsolidQFilter_GetKey()
570 uint32_t num_reads, readId; in AbsolidFormatterSplitter_Dump() local
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