Searched refs:maxSeedErrors (Results 1 – 7 of 7) sorted by relevance
| /dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
| H A D | outputFormat.h | 283 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
284 resize(cooc,maxSeedErrors+1,0); in countCoocurrences()
285 for (int i = 0; i < maxSeedErrors+1; ++i) in countCoocurrences()
300 if(dist > maxSeedErrors) continue; in countCoocurrences()
421 int maxSeedErrors = (int)(options.errorRate*options.artSeedLength)+1; in assignMappingQuality() local
456 if((bestQualSum==secondBestQualSum) || (kPrime>maxSeedErrors)) in assignMappingQuality()
472 qualTerm2 = kPrimeLoss + cooc[maxSeedErrors-kPrime]; in assignMappingQuality()
483 if(avgSeedQual>14) qualTerm2 += (int)((maxSeedErrors-kPrime)*(avgSeedQual-14)); in assignMappingQuality()
540 …int maxSeedErrors = (int)(options.errorRate * options.artSeedLength); //without + 1 here, used to … in dumpMatches() local
951 if(options.maqMapping && options.noBelowIdentity && (*it).seedEditDist > maxSeedErrors) in dumpMatches()
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| /dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
| H A D | outputFormat.h | 326 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
327 resize(cooc,maxSeedErrors+1,0); in countCoocurrences()
328 for (int i = 0; i < maxSeedErrors+1; ++i) in countCoocurrences()
343 if(dist > maxSeedErrors) continue; in countCoocurrences()
449 int maxSeedErrors = (int)(options.errorRate*options.artSeedLength)+1; in assignMappingQuality() local
484 if((bestQualSum==secondBestQualSum) || (kPrime>maxSeedErrors)) in assignMappingQuality()
500 qualTerm2 = kPrimeLoss + cooc[maxSeedErrors-kPrime]; in assignMappingQuality()
511 if(avgSeedQual>14) qualTerm2 += (int)((maxSeedErrors-kPrime)*(avgSeedQual-14)); in assignMappingQuality()
570 …int maxSeedErrors = (int)(options.errorRate * options.artSeedLength); //without + 1 here, used to … in dumpMatches() local
964 if(options.maqMapping && options.noBelowIdentity && (*it).seedEditDist > maxSeedErrors) in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
| H A D | outputFormat.h | 289 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
290 resize(cooc,maxSeedErrors+1,0); in countCoocurrences()
291 for (int i = 0; i < maxSeedErrors+1; ++i) in countCoocurrences()
306 if(dist > maxSeedErrors) continue; in countCoocurrences()
427 int maxSeedErrors = (int)(options.errorRate*options.artSeedLength)+1; in assignMappingQuality() local
462 if((bestQualSum==secondBestQualSum) || (kPrime>maxSeedErrors)) in assignMappingQuality()
478 qualTerm2 = kPrimeLoss + cooc[maxSeedErrors-kPrime]; in assignMappingQuality()
489 if(avgSeedQual>14) qualTerm2 += (int)((maxSeedErrors-kPrime)*(avgSeedQual-14)); in assignMappingQuality()
546 …int maxSeedErrors = (int)(options.errorRate * options.artSeedLength); //without + 1 here, used to … in dumpMatches() local
962 if(options.maqMapping && options.noBelowIdentity && (*it).seedEditDist > maxSeedErrors) in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/searchjoin/ |
| H A D | db.h | 715 TSeedLength maxSeedErrors = 0;
733 maxSeedErrors = _max(maxSeedErrors, seedErrors);
736 resize(seedCounts, maxSeedErrors + 1);
865 TErrors maxSeedErrors = length(seedCounts);
866 for (TErrors seedErrors = 0; seedErrors < maxSeedErrors; ++seedErrors)
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| /dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
| H A D | outputFormat.h | 283 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
284 resize(cooc,maxSeedErrors+1,0); in countCoocurrences()
285 for (int i = 0; i < maxSeedErrors+1; ++i) in countCoocurrences()
300 if(dist > maxSeedErrors) continue; in countCoocurrences()
494 int maxSeedErrors = (int)(options.errorRate*options.artSeedLength)+1; in assignMappingQuality() local
529 if((bestQualSum==secondBestQualSum) || (kPrime>maxSeedErrors)) in assignMappingQuality()
545 qualTerm2 = kPrimeLoss + cooc[maxSeedErrors-kPrime]; in assignMappingQuality()
556 if(avgSeedQual>14) qualTerm2 += (int)((maxSeedErrors-kPrime)*(avgSeedQual-14)); in assignMappingQuality()
649 …int maxSeedErrors = (int)(options.errorRate * options.artSeedLength); //without + 1 here, used to … in dumpMatches() local
1055 if(options.maqMapping && options.noBelowIdentity && (*it).seedEditDist > maxSeedErrors) in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
| H A D | outputFormat.h | 285 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
286 resize(cooc,maxSeedErrors+1,0); in countCoocurrences()
287 for (int i = 0; i < maxSeedErrors+1; ++i) in countCoocurrences()
302 if(dist > maxSeedErrors) continue; in countCoocurrences()
496 int maxSeedErrors = (int)(options.errorRate*options.artSeedLength)+1; in assignMappingQuality() local
531 if((bestQualSum==secondBestQualSum) || (kPrime>maxSeedErrors)) in assignMappingQuality()
547 qualTerm2 = kPrimeLoss + cooc[maxSeedErrors-kPrime]; in assignMappingQuality()
558 if(avgSeedQual>14) qualTerm2 += (int)((maxSeedErrors-kPrime)*(avgSeedQual-14)); in assignMappingQuality()
731 …int maxSeedErrors = (int)(options.errorRate * options.artSeedLength); //without + 1 here, used to … in dumpMatches() local
1140 if(options.maqMapping && options.noBelowIdentity && (*it).seedEditDist > maxSeedErrors) in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | outputFormat.h | 346 int maxSeedErrors = (int)(options.errorRate * options.artSeedLength) + 1; in countCoocurrences() local
347 resize(cooc, maxSeedErrors + 1, 0); in countCoocurrences()
348 for (int i = 0; i < maxSeedErrors + 1; ++i) in countCoocurrences()
365 if (dist > maxSeedErrors) in countCoocurrences()
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