void pslRecalcMatch(char *inName, char *targetName, char *queryName,
char *outName)
/* pslRecalcMatch - Recalculate match,mismatch,repMatch columns in psl file.
* This can be useful if the psl went through pslMap, or if you've added
* lower-case repeat masking after the fact. */
{
struct nibTwoCache *tCache = nibTwoCacheNew(targetName);
struct dnaSeq *qSeqList = dnaLoadAll(queryName);
struct hash *qHash = dnaSeqHash(qSeqList);
struct psl *psl;
struct lineFile *lf = pslFileOpen(inName);
FILE *f = mustOpen(outName, "w");
while ((psl = pslNext(lf)) != NULL)
{
int tSize;
struct dnaSeq *tSeqPart = nibTwoCacheSeqPart(tCache,
psl->tName, psl->tStart, psl->tEnd - psl->tStart, &tSize);
struct dnaSeq *qSeq = hashMustFindVal(qHash, getQName(psl->qName));
recalcMatches(psl, tSeqPart, psl->tStart, qSeq);
pslTabOut(psl, f);
dnaSeqFree(&tSeqPart);
}
carefulClose(&f);
lineFileClose(&lf);
}
void vgLoadNibb(char *sourceImageDir, char *parsedTab, char *probesFa,
char *nameTab, char *stageTab, char *outDir)
/* vgLoadNibb - Create .ra and .tab files for loading Xenopus images from NIBB
* into VisiGene. */
{
struct hash *nameHash = makeNameHash(nameTab);
struct hash *seqHash = dnaSeqHash(faReadAllDna(probesFa));
struct hash *stageHash = makeStageHash(stageTab);
char outPath[PATH_LEN];
verbose(1, "Got %d named probes\n", nameHash->elCount);
verbose(1, "Got %d probe sequences\n", seqHash->elCount);
verbose(1, "Got %d stages\n", stageHash->elCount);
/* Make output directory and ra file. */
makeDir(outDir);
safef(outPath, sizeof(outPath), "%s/%s", outDir, "nibb.ra");
writeRa(outPath);
/* Make tab separated file. */
safef(outPath, sizeof(outPath), "%s/%s", outDir, "nibb.tab");
writeTab(stageHash, seqHash, sourceImageDir, parsedTab, nameHash, outPath);
}
