| /dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
| H A D | razers_spliced.h | 703 SwiftSemiGlobalHamming, // HammingDistance in matchVerify() argument
812 SwiftSemiGlobalHamming, in matchVerify() argument
1323 SwiftSemiGlobalHamming) in combineLeftRight() argument
1475 SwiftSemiGlobalHamming) in findBestSplitPosition() argument
2421 …matches, genomeSet, readSet, cnts, options, ungappedL, ungappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
2423 …atches, genomeSet, readSet, cnts, options, ungappedL, onegappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
2425 …s(matches, genomeSet, readSet, cnts, options, ungappedL, gappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
2435 …(matches, genomeSet, readSet, cnts, options, onegappedL, gappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
2441 …s(matches, genomeSet, readSet, cnts, options, gappedL, ungappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
2443 …(matches, genomeSet, readSet, cnts, options, gappedL, onegappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
[all …]
|
| H A D | razers.h | 1318 SwiftSemiGlobalHamming) // Hamming only
2201 …ist, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2204 …st, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2207 …eList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
2251 …rn mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2254 …n mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2257 …return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>(…
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
| H A D | razers_spliced.h | 882 SwiftSemiGlobalHamming, // HammingDistance in matchVerify() argument
991 SwiftSemiGlobalHamming, in matchVerify() argument
1811 SwiftSemiGlobalHamming) in combineLeftRight() argument
1963 SwiftSemiGlobalHamming) in findBestSplitPosition() argument
3132 …meSet, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
3134 …eSet, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
3136 …nomeSet, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
3146 …omeSet, readSet, readRegions, cnts, options, onegappedL, gappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
3152 …nomeSet, readSet, readRegions, cnts, options, gappedL, ungappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
3154 …omeSet, readSet, readRegions, cnts, options, gappedL, onegappedR, Swift<SwiftSemiGlobalHamming>()); in mapSplicedReads()
[all …]
|
| H A D | razers.h | 1309 SwiftSemiGlobalHamming) // Hamming only
2184 …ist, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2187 …st, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2190 …eList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
2239 …rn mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2242 …n mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2245 …return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>(…
|
| /dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
| H A D | razers.h | 1297 SwiftSemiGlobalHamming) // Hamming only
2192 …ist, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2195 …st, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2198 …eList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
2233 …rn mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2236 …n mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2239 …return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>(…
|
| H A D | razers_spliced.h | 718 SwiftSemiGlobalHamming, // HammingDistance in matchVerify() argument
825 SwiftSemiGlobalHamming, in matchVerify() argument
1286 SwiftSemiGlobalHamming) in combineLeftRight() argument
1374 …meInf,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation, SwiftSemiGlobalHamming()); in combineLeftRight()
1393 …f,read,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation,SwiftSemiGlobalHamming()); in combineLeftRight()
1431 SwiftSemiGlobalHamming) in findBestSplitPosition() argument
|
| /dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
| H A D | razers.h | 1219 SwiftSemiGlobalHamming) // Hamming only
2156 …store, genomeFileNameList, gnoToFileMap, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2159 …tore, genomeFileNameList, gnoToFileMap, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2162 …s(store, genomeFileNameList, gnoToFileMap, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
2197 …rn mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2200 …n mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2203 …return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>(…
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
| H A D | razers.h | 1350 SwiftSemiGlobalHamming) // Hamming only
2265 …ist, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2268 …st, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2271 …eList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>());
2306 …rn mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift<SwiftSemiGlobalHamming>());
2309 …n mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift<SwiftSemiGlobalHamming>());
2312 …return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift<SwiftSemiGlobalHamming>(…
|
| H A D | razers_spliced.h | 720 SwiftSemiGlobalHamming, // HammingDistance in matchVerify() argument
827 SwiftSemiGlobalHamming, in matchVerify() argument
1288 SwiftSemiGlobalHamming) in combineLeftRight() argument
1376 …meInf,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation, SwiftSemiGlobalHamming()); in combineLeftRight()
1395 …f,read,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation,SwiftSemiGlobalHamming()); in combineLeftRight()
1433 SwiftSemiGlobalHamming) in findBestSplitPosition() argument
|
| /dports/biology/seqan1/seqan-1.3.1/seqan/index/ |
| H A D | find_swift.h | 101 typedef Tag<SwiftSemiGlobal_<Hamming_> > SwiftSemiGlobalHamming; typedef
117 struct Swift<SwiftSemiGlobalHamming> {
|
| H A D | index_generated_forwards.h | 1341 typedef Tag<SwiftSemiGlobal_<Hamming_> > SwiftSemiGlobalHamming; // "seqan-1.3.1/seqan/index… typedef
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/ |
| H A D | find_swift.h | 152 typedef Tag<SwiftSemiGlobal_<Hamming_> > SwiftSemiGlobalHamming; typedef
168 struct Swift<SwiftSemiGlobalHamming> {
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
| H A D | find_swift.h | 152 typedef Tag<SwiftSemiGlobal_<Hamming_> > SwiftSemiGlobalHamming; typedef
168 struct Swift<SwiftSemiGlobalHamming> {
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/ |
| H A D | find_swift.h | 152 typedef Tag<SwiftSemiGlobal_<Hamming_> > SwiftSemiGlobalHamming; typedef
168 struct Swift<SwiftSemiGlobalHamming> {
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | razers_parallel.h | 1196 …typename If<IsSameType<TGapMode, RazerSGapped>, SwiftSemiGlobal, SwiftSemiGlobalHamming>::Type TSw… in _mapSingleReadsParallel()
|
| H A D | razers.h | 3215 …typename If<IsSameType<TGapMode, RazerSGapped>, SwiftSemiGlobal, SwiftSemiGlobalHamming>::Type TSw…
3246 …typename If<IsSameType<TGapMode, RazerSGapped>, SwiftSemiGlobal, SwiftSemiGlobalHamming>::Type TSw…
|
| H A D | razers_matepairs_parallel.h | 1656 …typename If<IsSameType<TGapMode, RazerSGapped>, SwiftSemiGlobal, SwiftSemiGlobalHamming>::Type TSw… in _mapMatePairReadsParallel()
|