Searched refs:BBaseMap (Results 1 – 4 of 4) sorted by relevance
71 BBaseMap.clear(); in traceBack()91 if (createBaseMap) { BBaseMap[row] = count; } in traceBack()106 BBaseMap[row] = count; in traceBack()132 for (map<int, int>::iterator it = BBaseMap.begin(); it != BBaseMap.end(); it++) { in traceBack()136 BBaseMap = newBMap; in traceBack()214 return BBaseMap; in getSeqBAlnBaseMap()
87 for (int i = 0; i < bLength; i++) { BBaseMap[i+numGaps] = i; } in align()92 for (int i = 0; i < bLength; i++) { BBaseMap[i] = i; } in align()
55 map<int, int> BBaseMap; member in Alignment
1278 map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap(); in assembleFragments() local1308 …ength(); i++) { if ((seq2[i] != '.') && (seq2[i] != '-')) { if (scores2[BBaseMap[i]] == 2) { seq2F… in assembleFragments()1311 … i >= 0; i--) { if ((seq2[i] != '.') && (seq2[i] != '-')) { if (scores2[BBaseMap[i]] == 2) { seq2l… in assembleFragments()1319 …ck(qual_match_simple_bayesian[PHREDCLAMP(scores1[ABaseMap[i]])][PHREDCLAMP(scores2[BBaseMap[i]])]); in assembleFragments()1323 if (scores2[BBaseMap[i]] <= insert) { } // in assembleFragments()1326 contigScores.push_back(scores2[BBaseMap[i]]); in assembleFragments()1339 …if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scor… in assembleFragments()1341 if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; } in assembleFragments()1344 …qual_mismatch_simple_bayesian[PHREDCLAMP(scores1[ABaseMap[i]])][PHREDCLAMP(scores2[BBaseMap[i]])]); in assembleFragments()1347 else { contigScores.push_back(scores2[BBaseMap[i]]); } in assembleFragments()[all …]