/dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
H A D | razers_spliced.h | 524 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 …]
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H A D | outputFormat.h | 168 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 …]
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H A D | razers_matepairs.h | 745 …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;
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H A D | razers.h | 728 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 …]
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H A D | razers_parallel.h | 167 m.gBegin = gLength - m.gEnd; in operator() 168 m.gEnd = gLength - temp; in operator()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
H A D | razers_spliced.h | 526 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 …]
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H A D | outputFormat.h | 172 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 …]
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H A D | razers_matepairs.h | 435 …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 …]
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H A D | razers.h | 745 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 …]
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
H A D | razers_spliced.h | 537 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 …]
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H A D | outputFormat.h | 168 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 …]
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H A D | razers_matepairs.h | 724 …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;
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H A D | razers.h | 727 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 …]
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H A D | razers_parallel.h | 167 m.gBegin = gLength - m.gEnd; in operator() 168 m.gEnd = gLength - temp; in operator()
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/dports/biology/star/STAR-2.7.9a/source/ |
H A D | Transcript_convertGenomeCigar.cpp | 20 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
H A D | razers_spliced.h | 693 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 …]
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H A D | outputFormat.h | 945 (*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 …]
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H A D | razers_matepairs.h | 712 …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;
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H A D | razers.h | 715 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 …]
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H A D | razers_parallel.h | 167 m.gBegin = gLength - m.gEnd; in operator() 168 m.gEnd = gLength - temp; in operator()
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/dports/graphics/blend2d/blend2d-592d1ba52672bbf6365aba476bfe26b7bd2dfab8/src/blend2d/opentype/ |
H A D | otglyf.cpp | 303 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 …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/micro_razers/ |
H A D | outputFormat.h | 168 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()
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/dports/math/singular/Singular-Release-4-2-1/Singular/dyn_modules/gfanlib/ |
H A D | ppinitialReduction.cc | 61 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()
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | razers_parallel.h | 167 m.gBegin = gLength - m.gEnd; in operator() 168 m.gEnd = gLength - temp; in operator()
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/dports/games/trenchbroom/TrenchBroom-ed46601/common/src/View/ |
H A D | TextureBrowserView.cpp | 119 Assets::TextureManager::GroupList::const_iterator gIt, gEnd; in doReloadLayout() local 120 for (gIt = groups.begin(), gEnd = groups.end(); gIt != gEnd; ++gIt) { in doReloadLayout()
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