/dports/biology/canu/canu-2.2/src/bogart/ |
H A D | AS_BAT_Unitig_PlaceReadUsingEdges.C | 67 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() [all …]
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H A D | AS_BAT_PopulateUnitig.C | 34 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() [all …]
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H A D | AS_BAT_BestOverlapGraph_implementation.H | 21 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()
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H A D | AS_BAT_ChunkGraph.C | 41 _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() [all …]
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H A D | AS_BAT_BestOverlapGraph.C | 560 …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() [all …]
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H A D | AS_BAT_TigVector.H | 45 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
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/dports/biology/seqan1/seqan-1.3.1/apps/rabema/ |
H A D | intervals.h | 60 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()
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H A D | wit_store.h | 44 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… [all …]
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H A D | build_gold_standard.h | 64 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 [all …]
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H A D | evaluation.h | 174 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 [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/ |
H A D | bits_context.h | 118 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 [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rabema/ |
H A D | rabema_build_gold_standard.cpp | 259 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() [all …]
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H A D | io_gsi.h | 75 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
H A D | razers_match_filter.h | 187 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() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
H A D | store_matepair.h | 85 …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] &&
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/dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
H A D | store_matepair.h | 85 …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] &&
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/ |
H A D | store_matepair.h | 85 …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] &&
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/ |
H A D | store_matepair.h | 85 …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] &&
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sra/ |
H A D | reader-abi.c | 278 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); [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sra/ |
H A D | reader-abi.c | 278 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); [all …]
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | razers.h | 564 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; [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/sra/ |
H A D | abi.h | 112 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,
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/sra/ |
H A D | abi.h | 112 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,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rep_sep/ |
H A D | assembly_parser.h | 122 …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()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-dump/ |
H A D | abi.c | 65 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 [all …]
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