/dports/biology/canu/canu-2.2/src/correction/ |
H A D | computeGlobalScore.C | 25 globalScore::compute(uint32 ovlLen, in compute() argument 36 resizeArray(hist, histLen, histMax, ovlLen, _raAct::doNothing); in compute() 38 for (uint32 oo=0; oo<ovlLen; oo++) { in compute() 70 for (uint32 oo=0; oo<ovlLen; oo++) { in compute() 128 ovl[0].a_iid, ovlLen, histLen, 0, histLen); in compute() 140 globalScore::estimate(uint32 ovlLen, in estimate() argument 144 stats->totalOverlaps += ovlLen; in estimate() 146 if (ovlLen < expectedCoverage) { in estimate() 147 stats->retained += ovlLen; in estimate() 150 fractionFiltered = (double)(ovlLen - expectedCoverage) / ovlLen; in estimate() [all …]
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H A D | generateCorrectionLayouts.C | 73 uint32 ovlLen, in generateLayout() argument 78 layout->allocateChildren(ovlLen); in generateLayout() 82 layout->_tigID, layout->_layoutLen, ovlLen); in generateLayout() 86 for (uint32 oo=0; oo<ovlLen; oo++) { in generateLayout() 323 uint32 ovlLen = ovlStore->loadOverlapsForRead(rr, ovl, ovlMax); in main() local 325 if (ovlLen > 0) { in main() 334 ovl, ovlLen, in main()
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H A D | filterCorrectionOverlaps.C | 189 uint32 ovlLen = 0; in main() local 227 ovlLen = ovlStore->loadOverlapsForRead(id, ovl, ovlMax); in main() 229 if (ovlLen > 0) { in main() 230 assert(ovlLen == numOlaps[id]); in main() 233 scores[id] = scoreExact = gs->compute(ovlLen, ovl, expectedCoverage, 0, NULL); in main()
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H A D | computeGlobalScore.H | 87 uint16 compute(uint32 ovlLen, 93 void estimate(uint32 ovlLen,
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/dports/biology/canu/canu-2.2/src/stores/ |
H A D | ovStore.C | 108 uint32 ovlLen = 0; in testStore() local 122 ovlLen = loadOverlapsForRead(tid, ovl, ovlMax); in testStore() 124 if (ovlLen != nopr[tid]) { in testStore() 126 tid, nopr[tid], ovlLen); in testStore() 211 uint32 ovlLen = 0; in loadBlockOfOverlaps() local 225 while ((ovlLen + _index[_curID]._numOlaps < ovlMax) && in loadBlockOfOverlaps() 250 if (_bof->readOverlap(ovl + ovlLen) == false) { in loadBlockOfOverlaps() 255 ovl[ovlLen].a_iid = _curID; in loadBlockOfOverlaps() 261 ovl[ovlLen].evalue(_evalues[_index[_curID]._overlapID++]); in loadBlockOfOverlaps() 263 ovlLen++; in loadBlockOfOverlaps() [all …]
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H A D | ovStoreDump.C | 943 uint32 ovlLen = 0; in main() local 990 ovlLen = ovlStore->loadBlockOfOverlaps(ovl, ovlMax); in main() 992 while (ovlLen > 0) { in main() 993 for (uint32 oo=0; oo<ovlLen; oo++) { in main() 1020 ovlLen = ovlStore->loadBlockOfOverlaps(ovl, ovlMax); in main() 1022 while (ovlLen > 0) { in main() 1023 for (uint32 oo=0; oo<ovlLen; oo++) { in main() 1140 ovlLen = ovlStore->loadBlockOfOverlaps(ovl, ovlMax); in main() 1142 while (ovlLen > 0) { in main() 1143 for (uint32 oo=0; oo<ovlLen; oo++) { in main() [all …]
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/dports/biology/canu/canu-2.2/src/bogart/ |
H A D | AS_BAT_FindCircular.C | 30 ovlLen = 0; in init() 31 ovl = OC->getOverlaps(read->ident, ovlLen); in init() 36 uint32 ovlLen; variable 174 uint32 ovlLen = rc[ai].ovlLen; in isCircularizingEdge() local 186 for (uint32 oo=0; (oo<ovlLen) && (ovl[oo].b_iid <= rdBid) && (found == false); oo++) { in isCircularizingEdge() 241 uint32 ovlLen = 0; in findCircularContigs() local 242 BAToverlap *ovl = OC->getOverlaps(lRead->ident, ovlLen); in findCircularContigs() 244 for (uint32 oo=0; oo<ovlLen; oo++) { in findCircularContigs()
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H A D | AS_BAT_Unitig.C | 178 uint32 ovlLen = 0; in computeErrorProfile() local 179 BAToverlap *ovl = OC->getOverlaps(rdA->ident, ovlLen); in computeErrorProfile() 181 for (uint32 oi=0; oi<ovlLen; oi++) { in computeErrorProfile() 209 uint32 ovlLen = 0; in computeErrorProfile() local 210 BAToverlap *ovl = OC->getOverlaps(rdA->ident, ovlLen); in computeErrorProfile() 212 for (uint32 oi=0; oi<ovlLen; oi++) { in computeErrorProfile()
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H A D | AS_BAT_PlaceReadUsingOverlaps.C | 38 uint32 ovlLen, in placeRead_fromOverlaps() argument 44 writeLog("pRUO()-- placements for read %u with %u overlaps\n", fid, ovlLen); in placeRead_fromOverlaps() 46 for (uint32 oo=0; oo<ovlLen; oo++) { in placeRead_fromOverlaps() 551 uint32 ovlLen = 0; in placeReadUsingOverlaps() local 552 BAToverlap *ovl = OC->getOverlaps(fid, ovlLen); in placeReadUsingOverlaps() 562 overlapPlacement *ovlPlace = new overlapPlacement [ovlLen]; in placeReadUsingOverlaps() 564 placeRead_fromOverlaps(tigs, target, fid, flags, errorLimit, ovlLen, ovl, ovlPlaceLen, ovlPlace); in placeReadUsingOverlaps()
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H A D | AS_BAT_OptimizePositions.C | 227 uint32 ovlLen = 0; in optimize_initPlace() local 228 BAToverlap *ovl = OC->getOverlaps(iid, ovlLen); in optimize_initPlace() 230 for (uint32 oo=0; oo<ovlLen; oo++) { in optimize_initPlace() 305 uint32 ovlLen = 0; in optimize_recompute() local 306 BAToverlap *ovl = OC->getOverlaps(iid, ovlLen); in optimize_recompute() 319 for (uint32 oo=0; oo<ovlLen; oo++) { in optimize_recompute()
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H A D | AS_BAT_OverlapCache.C | 590 searchForOverlap(BAToverlap *ovl, uint32 ovlLen, uint32 bID, bool flipped) { in searchForOverlap() argument 592 int32 L = ovlLen - 1; in searchForOverlap() 598 for (uint32 ss=0; ss<ovlLen; ss++) in searchForOverlap()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/consensus/ |
H A D | overlap_info_computation.h | 248 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildGlobalAlignmentOverlapInfos() local 264 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildGlobalAlignmentOverlapInfos() 295 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildPositionBasedOverlapInfos() local 296 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildPositionBasedOverlapInfos() 302 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 311 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 394 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildAllToAllOverlapInfos() local 395 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildAllToAllOverlapInfos() 401 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildAllToAllOverlapInfos()
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H A D | overlapper.h | 376 int ovlLen = overlap.length(); in computeOverlap() local 377 bool ok = ((options.overlapMinLength < 0 || ovlLen >= options.overlapMinLength) && in computeOverlap() 378 ((options.overlapErrorRate < 0 || ovlLen == 0) in computeOverlap() 379 || (1.0 * overlap.errors / ovlLen) <= options.overlapErrorRate + 0.00001)); in computeOverlap()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/ |
H A D | overlap_info_computation.h | 248 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildGlobalAlignmentOverlapInfos() local 264 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildGlobalAlignmentOverlapInfos() 295 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildPositionBasedOverlapInfos() local 296 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildPositionBasedOverlapInfos() 302 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 311 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 394 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildAllToAllOverlapInfos() local 395 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildAllToAllOverlapInfos() 401 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildAllToAllOverlapInfos()
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H A D | overlapper.h | 376 int ovlLen = overlap.length(); in computeOverlap() local 377 bool ok = ((options.overlapMinLength < 0 || ovlLen >= options.overlapMinLength) && in computeOverlap() 378 ((options.overlapErrorRate < 0 || ovlLen == 0) in computeOverlap() 379 || (1.0 * overlap.errors / ovlLen) <= options.overlapErrorRate + 0.00001)); in computeOverlap()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/ |
H A D | overlap_info_computation.h | 248 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildGlobalAlignmentOverlapInfos() local 264 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildGlobalAlignmentOverlapInfos() 295 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildPositionBasedOverlapInfos() local 296 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildPositionBasedOverlapInfos() 302 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 311 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildPositionBasedOverlapInfos() 394 int ovlLen = length(store.readSeqStore[info.seq0]) - info.pos1; in buildAllToAllOverlapInfos() local 395 …if (ovlLen < options.overlapMinLength || 100.0 * info.numErrors / ovlLen > options.overlapMaxError… in buildAllToAllOverlapInfos() 401 << "\tnumErrors=" << info.numErrors << "\tovlLen=" << ovlLen << "\n"; in buildAllToAllOverlapInfos()
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H A D | overlapper.h | 376 int ovlLen = overlap.length(); in computeOverlap() local 377 bool ok = ((options.overlapMinLength < 0 || ovlLen >= options.overlapMinLength) && in computeOverlap() 378 ((options.overlapErrorRate < 0 || ovlLen == 0) in computeOverlap() 379 || (1.0 * overlap.errors / ovlLen) <= options.overlapErrorRate + 0.00001)); in computeOverlap()
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/dports/biology/canu/canu-2.2/src/overlapBasedTrimming/ |
H A D | splitReads-workUnit.C | 27 ovOverlap *ovl, uint32 ovlLen) { in addAndFilterOverlaps() argument 29 if (adjMax < ovlLen) { in addAndFilterOverlaps() 32 adjMax = ovlLen; in addAndFilterOverlaps() 38 for (uint32 oo=0; oo<ovlLen; oo++) { in addAndFilterOverlaps()
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H A D | trimReads.C | 235 uint32 ovlLen = 0; in main() local 295 ovlLen = ovs->loadOverlapsForRead(id, ovl, ovlMax); in main() 300 if (ovlLen == 0) { in main() 307 assert(ovlLen > 0); in main() 310 isGood = largestCovered(ovl, ovlLen, in main() 325 assert(ovlLen > 0); in main() 328 isGood = bestEdge(ovl, ovlLen, in main() 363 if (ovlLen == 0) { in main()
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H A D | trimReads-bestEdge.C | 31 uint32 ovlLen, in bestEdge() argument 49 assert(ovlLen > 0); in bestEdge() 59 …if (largestCovered(ovl, ovlLen, readID, readLen, ibgn, iend, lbgn, lend, logMsg, errorValue, minOv… in bestEdge() 78 for (uint32 i=0; i<ovlLen; i++) { in bestEdge() 188 for (uint32 i=0; i < ovlLen; i++) { in bestEdge() 261 for (uint32 i=0; i < ovlLen; i++) { in bestEdge()
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H A D | trimReads.H | 45 uint32 ovlLen, 60 uint32 ovlLen,
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H A D | trimReads-largestCovered.C | 25 uint32 ovlLen, in largestCovered() argument 43 assert(ovlLen > 0); in largestCovered() 52 for (uint32 i=0; i<ovlLen; i++) { in largestCovered()
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H A D | splitReads.C | 194 uint32 ovlLen = 0; in main() local 233 ovlLen = ovs->loadOverlapsForRead(id, ovl, ovlMax); in main() 237 if (ovlLen == 0) { in main() 244 w->addAndFilterOverlaps(seq, finClr, errorRate, ovl, ovlLen); in main()
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H A D | splitReads.H | 169 ovOverlap *ovl, uint32 ovlLen);
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/dports/biology/canu/canu-2.2/src/overlapInCore/ |
H A D | overlapInCore-Process_String_Overlaps.C | 22 uint64 computeExpected(uint64 kmerSize, double ovlLen, double erate) { in computeExpected() argument 23 if (ovlLen < kmerSize) return 0; in computeExpected() 24 return int(floor(exp(-1.0 * (double)kmerSize * erate) * (ovlLen - kmerSize + 1))); in computeExpected() 28 uint64 computeMinimumKmers(uint64 kmerSize, double ovlLen, double erate) { in computeMinimumKmers() argument 31 ovlLen = (ovlLen < 0 ? ovlLen*-1.0 : ovlLen); in computeMinimumKmers() 32 return std::max(G.Filter_By_Kmer_Count, computeExpected(kmerSize, ovlLen, erate)); in computeMinimumKmers()
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