void ppSanger(char *databaseDir, char *pairFileName) /* ppSanger - Analyse paired plasmid reads from Sanger and make pairs file.. */ { char readFile[512], insertFile[512], rangeFile[512]; struct hash *rangeHash = newHash(7); struct hash *pairHash = newHash(19); struct sangPair *pairList, *pair; struct sangRange *rangeList, *range; struct sangRead *readList, *read; sprintf(readFile, "%s/TBL_INSERT_FILE", databaseDir); sprintf(insertFile, "%s/TBL_INSERT_LENGTH", databaseDir); sprintf(rangeFile, "%s/TBL_LENGTH_RANGE", databaseDir); rangeList = readRanges(rangeFile, rangeHash); pairList = readPairs(insertFile, pairHash, rangeHash); readList = readReads(readFile, pairHash); writePairs(pairList, pairFileName); }
KmerHash::KmerHash(int K, string genomePath, string exonBoundaryPath, string readPath) { this -> K = K; this -> readLength = -1; mask = 0; for(int i = 0; i < K; i++) { mask = (mask << 2) + 3; } NW = 0; NG = 0; NE.clear(); kmerCount.clear(); kmerTable.clear(); geneBoundary.clear(); readReads(readPath); readGenome(exonBoundaryPath); buildKmerTable(genomePath); mergeKmerTable(); }