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();
}
