bool run ( Data& d ) {
LINFO ( "instancing " << d.grammar->patterns.size() <<
" patterns over this sentence:" << d.sentence );
d.stats->setTimeStart ("instantiate-patterns");
instantiatePatternsHash ( d );
d.stats->setTimeEnd ("instantiate-patterns");
writeHashToFile ( d );
LINFO ( "Finished!" );
return false;
};
void findCounts(struct cutter *cutters, struct dnaSeq *seqs, char *outputFile)
/* Go through each sequence, and each time add the counts of the enzymes */
/* encountered to the hash of counts. */
{
struct dnaSeq *seq;
struct hash *countHash = initCutterCountHash(cutters);
for (seq = seqs; seq != NULL; seq = seq->next)
{
struct bed *bedList = matchEnzymes(cutters, seq, 0);
if (bedList)
{
addCountsToHash(countHash, bedList);
bedFreeList(&bedList);
}
}
writeHashToFile(countHash, outputFile);
}
void consolidateTheCounts(char *inputFile, char *outputFile)
/* Read the cat'ed file in, and either make a new hash item for each enzyme */
/* encountered on each line, or add to an existing one. Then output the hash. */
{
struct lineFile *lf = lineFileOpen(inputFile, TRUE);
struct hash *countHash = newHash(12);
char *words[2];
while (lineFileRow(lf, words))
{
char *name = words[0];
int count = lineFileNeedFullNum(lf, words, 1);
struct hashEl *el = hashLookup(countHash, name);
if (!el)
hashAddInt(countHash, name, count);
else
el->val = intToPt(ptToInt(el->val) + count);
}
writeHashToFile(countHash, outputFile);
freeHash(&countHash);
}
