void addTwoBit(char *file, struct hash *fileHash, struct hash *seqHash)
/* Add a 2bit file to hashes. */
{
struct twoBitFile *lf = twoBitOpen(file);
char *rFile = hashStoreName(fileHash, file);
struct slName *names = twoBitSeqNames(file);
struct slName *name;
for(name = names;name;name = name->next)
{
struct seqFilePos *sfp;
AllocVar(sfp);
hashAddSaveName(seqHash, name->name, sfp, &sfp->name);
sfp->file = rFile;
sfp->isTwoBit = TRUE;
sfp->pos = 0;
}
slFreeList(&names);
twoBitClose(&lf);
}
void nibTwoCacheFree(struct nibTwoCache **pNtc)
/* Free up resources associated with nibTwoCache. */
{
struct nibTwoCache *ntc = *pNtc;
if (ntc != NULL)
{
freez(&ntc->pathName);
if (ntc->isTwoBit)
twoBitClose(&ntc->tbf);
else
{
struct hashEl *el, *list = hashElListHash(ntc->nibHash);
struct nibInfo *nib;
for (el = list; el != NULL; el = el->next)
{
nib = el->val;
nibInfoFree(&nib);
}
hashElFreeList(&list);
hashFree(&ntc->nibHash);
}
freez(pNtc);
}
}
void searchOneIndex(int fileCount, char *files[], struct genoFind *gf, char *outName,
boolean isProt, struct hash *maskHash, FILE *outFile, boolean showStatus)
/* Search all sequences in all files against single genoFind index. */
{
int i;
char *fileName;
int count = 0;
long long totalSize = 0;
gfOutputHead(gvo, outFile);
for (i=0; i<fileCount; ++i)
{
fileName = files[i];
if (nibIsFile(fileName))
{
struct dnaSeq *seq;
if (isProt)
errAbort("%s: Can't use .nib files with -prot or d=prot option\n", fileName);
seq = nibLoadAllMasked(NIB_MASK_MIXED, fileName);
freez(&seq->name);
seq->name = cloneString(fileName);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
freeDnaSeq(&seq);
}
else if (twoBitIsSpec(fileName))
{
struct twoBitSpec *tbs = twoBitSpecNew(fileName);
struct twoBitFile *tbf = twoBitOpen(tbs->fileName);
if (isProt)
errAbort("%s is a two bit file, which doesn't work for proteins.",
fileName);
if (tbs->seqs != NULL)
{
struct twoBitSeqSpec *ss = NULL;
for (ss = tbs->seqs; ss != NULL; ss = ss->next)
{
struct dnaSeq *seq = twoBitReadSeqFrag(tbf, ss->name,
ss->start, ss->end);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
dnaSeqFree(&seq);
}
}
else
{
struct twoBitIndex *index = NULL;
for (index = tbf->indexList; index != NULL; index = index->next)
{
struct dnaSeq *seq = twoBitReadSeqFrag(tbf, index->name, 0, 0);
searchOneMaskTrim(seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
dnaSeqFree(&seq);
}
}
twoBitClose(&tbf);
}
else
{
static struct dnaSeq seq;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
searchOneMaskTrim(&seq, isProt, gf, outFile,
maskHash, &totalSize, &count);
}
lineFileClose(&lf);
}
}
carefulClose(&outFile);
if (showStatus)
printf("Searched %lld bases in %d sequences\n", totalSize, count);
}
