Home
last modified time | relevance | path

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

12

/dports/biology/seqan1/seqan-1.3.1/apps/razers/
H A Drazers_spliced.h524 m.gSeedLen = m.gEnd - m.gBegin; in matchVerify()
795 m.gEnd = m.gBegin + bestHitLength; in matchVerify()
913 m.gBegin = m.gEnd - bestHitLength; in matchVerify()
1074 mR.gBegin = mL.gEnd; in combineLeftRight()
1107 if(mL.gEnd == mR.gBegin) in combineLeftRight()
1144 if (mR.gSeedLen < (int)mR.gEnd - mL.gEnd) rowPosR2 = mR.gEnd - mL.gEnd - mR.gSeedLen; in combineLeftRight()
1376 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1377 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
1397 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1398 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
[all …]
H A DoutputFormat.h168 genome = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in getErrorDistribution()
761 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
762 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
766 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
912 file << _sep_ << (*it).gEnd << _sep_ << 'R' << _sep_ << ".."; in dumpMatches()
916 gInf = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in dumpMatches()
1052 assignSource(row(align, 1), infix(currGenome, (*it).gBegin, (*it).gEnd)); in dumpMatches()
1074 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
1075 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
1079 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
[all …]
H A Drazers_matepairs.h745 …while (!empty(fifo) && front(fifo).i2.gEnd + maxDistance + (TSignedGPos)doubleParWidth < (TSignedG…
759 while (empty(fifo) || back(fifo).i2.gEnd + minDistance < (TSignedGPos)(rEndPos + doubleParWidth))
772 fL.i2.gEnd = gPair.i2;
797 (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd),
823 int libSizeError = options.libraryLength - (int)((__int64)mR.gEnd - (__int64)(*it).i2.gBegin);
861 __int64 dist = (__int64)mR.gEnd - (__int64)(*bestLeft).i2.gBegin;
875 fL.i2.gBegin = gLength - fL.i2.gEnd;
876 fL.i2.gEnd = gLength - temp;
878 mR.gBegin = gLength - mR.gEnd;
879 mR.gEnd = gLength - temp;
H A Drazers.h728 if (a.gEnd < b.gEnd) return true;
729 if (a.gEnd > b.gEnd) return false;
829 typename TMatch::TGPos gEnd = -1;
842 if (gEnd == (*it).gEnd && orientation == (*it).orientation &&
850 gEnd = (*it).gEnd;
1270 m.gEnd = m.gBegin + bestHitLength;
1350 m.gEnd = m.gBegin + ndlLength;
1426 m.gBegin = m.gEnd - (position(myersFinderRev) + 1);
1536 m.gEnd = m.gBegin + ndlLength;
1652 m.gBegin = gLength - m.gEnd;
[all …]
H A Drazers_parallel.h167 m.gBegin = gLength - m.gEnd; in operator()
168 m.gEnd = gLength - temp; in operator()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/
H A Drazers_spliced.h526 m.gSeedLen = m.gEnd - m.gBegin; in matchVerify()
797 m.gEnd = m.gBegin + bestHitLength; in matchVerify()
915 m.gBegin = m.gEnd - bestHitLength; in matchVerify()
1076 mR.gBegin = mL.gEnd; in combineLeftRight()
1109 if(mL.gEnd == mR.gBegin) in combineLeftRight()
1146 if (mR.gSeedLen < (int)mR.gEnd - mL.gEnd) rowPosR2 = mR.gEnd - mL.gEnd - mR.gSeedLen; in combineLeftRight()
1378 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1379 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
1399 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1400 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
[all …]
H A DoutputFormat.h172 genome = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in getErrorDistribution()
767 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
768 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
772 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
918 file << _sep_ << (*it).gEnd << _sep_ << 'R' << _sep_ << ".."; in dumpMatches()
922 gInf = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in dumpMatches()
1063 assignSource(row(align, 1), infix(currGenome, (*it).gBegin, (*it).gEnd)); in dumpMatches()
1085 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
1086 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
1090 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
[all …]
H A Drazers_matepairs.h435 …while (!empty(fifo) && (TSignedGPos)front(fifo).i2.gEnd + maxDistance + (TSignedGPos)doubleParWidt…
449 …while (empty(fifo) || (TSignedGPos)back(fifo).i2.gEnd + minDistance < (TSignedGPos)(rEndPos + doub…
462 fL.i2.gEnd = gPair.i2;
490 if ((TSignedGPos)(*it).i2.gEnd + minDistance < (TSignedGPos)(rEndPos + doubleParWidth))
493 (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd),
543 … int libSizeError = options.libraryLength - (int)((int64_t)mR.gEnd - (int64_t)(*it).i2.gBegin);
582 int64_t dist = (int64_t)mR.gEnd - (int64_t)(*bestLeft).i2.gBegin;
596 fL.i2.gBegin = gLength - fL.i2.gEnd;
597 fL.i2.gEnd = gLength - temp;
599 mR.gBegin = gLength - mR.gEnd;
[all …]
H A Drazers.h745 if (a.gEnd < b.gEnd) return true;
746 if (a.gEnd > b.gEnd) return false;
862 typename TMatch::TGPos gEnd = -1;
876 if (gEnd == (*it).gEnd && orientation == (*it).orientation &&
885 gEnd = (*it).gEnd;
1323 m.gEnd = m.gBegin + bestHitLength;
1403 m.gEnd = m.gBegin + ndlLength;
1479 m.gBegin = m.gEnd - (position(myersFinderRev) + 1);
1589 m.gEnd = m.gBegin + ndlLength;
1723 m.gBegin = gLength - m.gEnd;
[all …]
/dports/biology/seqan1/seqan-1.3.1/apps/splazers/
H A Drazers_spliced.h537 m.gSeedLen = m.gEnd - m.gBegin; in matchVerify()
782 m.gEnd = m.gBegin + bestHitLength; in matchVerify()
902 m.gBegin = m.gEnd - bestHitLength; in matchVerify()
1088 mR.gBegin = mL.gEnd; in combineLeftRight()
1121 if(mL.gEnd == mR.gBegin) in combineLeftRight()
1155 if (mR.gSeedLen < (int)mR.gEnd - mL.gEnd) rowPosR2 = mR.gEnd - mL.gEnd - mR.gSeedLen; in combineLeftRight()
1413 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1414 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
1438 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1439 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
[all …]
H A DoutputFormat.h168 genome = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in getErrorDistribution()
865 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
866 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
870 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
1016 file << _sep_ << (*it).gEnd << _sep_ << 'R' << _sep_ << ".."; in dumpMatches()
1139 (*it).gBegin = (*it).gEnd - _min((TGPos)(genomePosReadLast + 1),(*it).gEnd); in dumpMatches()
1140 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
1209 gInf = infix(currGenome, (*it).gBegin, (*it).gEnd); in dumpMatches()
1370 if(mL.gEnd != mR.gBegin) indelLen = mR.gBegin - mL.gEnd; in dumpMatches()
1407 gInfL = infix(currGenome, mL.gBegin, mL.gEnd); in dumpMatches()
[all …]
H A Drazers_matepairs.h724 …while (!empty(fifo) && front(fifo).i2.gEnd + maxDistance + (TSignedGPos)doubleParWidth < (TSignedG…
738 while (empty(fifo) || back(fifo).i2.gEnd + minDistance < (TSignedGPos)(rEndPos + doubleParWidth))
751 fL.i2.gEnd = gPair.i2;
776 (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd),
802 int libSizeError = options.libraryLength - (int)((__int64)mR.gEnd - (__int64)(*it).i2.gBegin);
840 __int64 dist = (__int64)mR.gEnd - (__int64)(*bestLeft).i2.gBegin;
854 fL.i2.gBegin = gLength - fL.i2.gEnd;
855 fL.i2.gEnd = gLength - temp;
857 mR.gBegin = gLength - mR.gEnd;
858 mR.gEnd = gLength - temp;
H A Drazers.h727 if (a.gEnd < b.gEnd) return true;
728 if (a.gEnd > b.gEnd) return false;
850 typename TMatch::TGPos gEnd = -1;
863 if (gEnd == (*it).gEnd && orientation == (*it).orientation &&
871 gEnd = (*it).gEnd;
1291 m.gEnd = m.gBegin + bestHitLength;
1371 m.gEnd = m.gBegin + ndlLength;
1447 m.gBegin = m.gEnd - (position(myersFinderRev) + 1);
1557 m.gEnd = m.gBegin + ndlLength;
1673 m.gBegin = gLength - m.gEnd;
[all …]
H A Drazers_parallel.h167 m.gBegin = gLength - m.gEnd; in operator()
168 m.gEnd = gLength - temp; in operator()
/dports/biology/star/STAR-2.7.9a/source/
H A DTranscript_convertGenomeCigar.cpp20 uint64 gEnd=gStart;//gEnd is end+1 in convertGenomeCigar() local
28 uint64 gStart1=gEnd; in convertGenomeCigar()
29 gEnd += cc[1]; in convertGenomeCigar()
31 …while (( bE=coBl[icB][0]+coBl[icB][1] ) <= gEnd) {//MDN-block ends at the c-block end, or goes past in convertGenomeCigar()
48 if (gEnd>gStart1) in convertGenomeCigar()
49 A.cigar.push_back({ cc[0], (uint32) (gEnd-gStart1) }); in convertGenomeCigar()
57 if (gEnd<coBl[icB][0]) //step back in convertGenomeCigar()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/
H A Drazers_spliced.h693 m.gSeedLen = m.gEnd - m.gBegin; in matchVerify()
961 m.gEnd = m.gBegin + bestHitLength; in matchVerify()
1081 m.gBegin = m.gEnd - bestHitLength; in matchVerify()
1575 mR.gBegin = mL.gEnd; in combineLeftRight()
1608 if(mL.gEnd == mR.gBegin) in combineLeftRight()
1642 if (mR.gSeedLen < (int)mR.gEnd - mL.gEnd) rowPosR2 = mR.gEnd - mL.gEnd - mR.gSeedLen; in combineLeftRight()
1901 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1902 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
1926 mR.gBegin = mR.gEnd - mR.mScore; in combineLeftRight()
1927 mL.gEnd = mL.gBegin + mL.mScore; in combineLeftRight()
[all …]
H A DoutputFormat.h945 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
946 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
950 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
1224 (*it).gBegin = (*it).gEnd - _min((TGPos)(genomePosReadLast + 1),(*it).gEnd); in dumpMatches()
1225 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
1458 if(mL.gEnd != mR.gBegin) indelLen = mR.gBegin - mL.gEnd; in dumpMatches()
1488 gInfL = infix(currGenome, mL.gBegin, mL.gEnd); in dumpMatches()
1499 gInfR = infix(currGenome, mR.gBegin, mR.gEnd); in dumpMatches()
1702 if(mL.gEnd != mR.gBegin) indelLen = mR.gBegin - mL.gEnd; in dumpMatches()
1750 gInfL = infix(currGenome, mL.gBegin, mL.gEnd); in dumpMatches()
[all …]
H A Drazers_matepairs.h712 …while (!empty(fifo) && front(fifo).i2.gEnd + maxDistance + (TSignedGPos)doubleParWidth < (TSignedG…
726 while (empty(fifo) || back(fifo).i2.gEnd + minDistance < (TSignedGPos)(rEndPos + doubleParWidth))
739 fL.i2.gEnd = gPair.i2;
764 (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd),
790 int libSizeError = options.libraryLength - (int)((int64_t)mR.gEnd - (int64_t)(*it).i2.gBegin);
828 int64_t dist = (int64_t)mR.gEnd - (int64_t)(*bestLeft).i2.gBegin;
842 fL.i2.gBegin = gLength - fL.i2.gEnd;
843 fL.i2.gEnd = gLength - temp;
845 mR.gBegin = gLength - mR.gEnd;
846 mR.gEnd = gLength - temp;
H A Drazers.h715 if (a.gEnd < b.gEnd) return true;
716 if (a.gEnd > b.gEnd) return false;
841 typename TMatch::TGPos gEnd = -1;
854 if (gEnd == (*it).gEnd && orientation == (*it).orientation &&
862 gEnd = (*it).gEnd;
1282 m.gEnd = m.gBegin + bestHitLength;
1362 m.gEnd = m.gBegin + ndlLength;
1438 m.gBegin = m.gEnd - (position(myersFinderRev) + 1);
1548 m.gEnd = m.gBegin + ndlLength;
1664 m.gBegin = gLength - m.gEnd;
[all …]
H A Drazers_parallel.h167 m.gBegin = gLength - m.gEnd; in operator()
168 m.gEnd = gLength - temp; in operator()
/dports/graphics/blend2d/blend2d-592d1ba52672bbf6365aba476bfe26b7bd2dfab8/src/blend2d/opentype/
H A Dotglyf.cpp303 if (BL_UNLIKELY(gPtr == gEnd)) in getGlyphOutlines()
324 if (BL_UNLIKELY(gPtr == gEnd)) in getGlyphOutlines()
349 remainingSize = (size_t)(gEnd - gPtr); in getGlyphOutlines()
411 BL_ASSERT(gPtr <= gEnd - 1); in getGlyphOutlines()
418 BL_ASSERT(gPtr <= gEnd - 2); in getGlyphOutlines()
424 BL_ASSERT(yPtr <= gEnd - 1); in getGlyphOutlines()
431 BL_ASSERT(yPtr <= gEnd - 2); in getGlyphOutlines()
463 BL_ASSERT(gPtr <= gEnd - 1); in getGlyphOutlines()
472 BL_ASSERT(gPtr <= gEnd - 2); in getGlyphOutlines()
480 BL_ASSERT(yPtr <= gEnd - 1); in getGlyphOutlines()
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/micro_razers/
H A DoutputFormat.h168 genome = infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd); in getErrorDistribution()
212 assignSource(row(align, 1), infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd)); in getErrorDistribution()
456 assignSource(row(align, 1), infix(genomes[(*it).gseqNo], (*it).gBegin, (*it).gEnd)); in dumpMatches()
470 (*it).gBegin = (*it).gEnd - (genomePosReadLast + 1); in dumpMatches()
471 (*it).gEnd -= genomePosReadFirst; in dumpMatches()
475 (*it).gEnd = (*it).gBegin + (genomePosReadLast + 1); in dumpMatches()
480 …file << _sep_ << ((*it).gBegin + options.positionFormat) << _sep_ << (*it).gEnd << _sep_ << ::std:… in dumpMatches()
/dports/math/singular/Singular-Release-4-2-1/Singular/dyn_modules/gfanlib/
H A DppinitialReduction.cc61 pNext(g) = NULL; poly gEnd = g; in pReduce() local
106 pNext(gEnd)=toBeChecked; in pReduce()
107 pIter(gEnd); pIter(toBeChecked); in pReduce()
108 pNext(gEnd)=NULL; in pReduce()
139 pNext(g) = NULL; poly gEnd = g; in pReduceInhomogeneous() local
184 pNext(gEnd)=toBeChecked; in pReduceInhomogeneous()
185 pIter(gEnd); pIter(toBeChecked); in pReduceInhomogeneous()
186 pNext(gEnd)=NULL; in pReduceInhomogeneous()
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A Drazers_parallel.h167 m.gBegin = gLength - m.gEnd; in operator()
168 m.gEnd = gLength - temp; in operator()
/dports/games/trenchbroom/TrenchBroom-ed46601/common/src/View/
H A DTextureBrowserView.cpp119 Assets::TextureManager::GroupList::const_iterator gIt, gEnd; in doReloadLayout() local
120 for (gIt = groups.begin(), gEnd = groups.end(); gIt != gEnd; ++gIt) { in doReloadLayout()

12