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Searched refs:ovlLen (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/canu/canu-2.2/src/correction/
H A DcomputeGlobalScore.C25 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()
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H A DgenerateCorrectionLayouts.C73 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()
H A DfilterCorrectionOverlaps.C189 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()
H A DcomputeGlobalScore.H87 uint16 compute(uint32 ovlLen,
93 void estimate(uint32 ovlLen,
/dports/biology/canu/canu-2.2/src/stores/
H A DovStore.C108 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()
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H A DovStoreDump.C943 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 …]
/dports/biology/canu/canu-2.2/src/bogart/
H A DAS_BAT_FindCircular.C30 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()
H A DAS_BAT_Unitig.C178 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()
H A DAS_BAT_PlaceReadUsingOverlaps.C38 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()
H A DAS_BAT_OptimizePositions.C227 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()
H A DAS_BAT_OverlapCache.C590 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/consensus/
H A Doverlap_info_computation.h248 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()
H A Doverlapper.h376 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/
H A Doverlap_info_computation.h248 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()
H A Doverlapper.h376 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/
H A Doverlap_info_computation.h248 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()
H A Doverlapper.h376 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()
/dports/biology/canu/canu-2.2/src/overlapBasedTrimming/
H A DsplitReads-workUnit.C27 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()
H A DtrimReads.C235 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()
H A DtrimReads-bestEdge.C31 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()
H A DtrimReads.H45 uint32 ovlLen,
60 uint32 ovlLen,
H A DtrimReads-largestCovered.C25 uint32 ovlLen, in largestCovered() argument
43 assert(ovlLen > 0); in largestCovered()
52 for (uint32 i=0; i<ovlLen; i++) { in largestCovered()
H A DsplitReads.C194 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()
H A DsplitReads.H169 ovOverlap *ovl, uint32 ovlLen);
/dports/biology/canu/canu-2.2/src/overlapInCore/
H A DoverlapInCore-Process_String_Overlaps.C22 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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