struct dnaSeq *gfiExpandAndLoadCached(struct gfRange *range,
struct hash *tFileCache, char *tSeqDir, int querySize,
int *retTotalSeqSize, boolean respectFrame, boolean isRc, int expansion)
/* Expand range to cover an additional expansion bases on either side.
* Load up target sequence and return. (Done together because don't
* know target size before loading.) */
{
struct dnaSeq *target = NULL;
char fileName[PATH_LEN+256];
safef(fileName, sizeof(fileName), "%s/%s", tSeqDir, range->tName);
if (nibIsFile(fileName))
{
struct nibInfo *nib = hashFindVal(tFileCache, fileName);
if (nib == NULL)
{
nib = nibInfoNew(fileName);
hashAdd(tFileCache, fileName, nib);
}
if (isRc)
reverseIntRange(&range->tStart, &range->tEnd, nib->size);
gfiExpandRange(range, querySize, nib->size, respectFrame, isRc, expansion);
target = nibLdPart(fileName, nib->f, nib->size,
range->tStart, range->tEnd - range->tStart);
if (isRc)
{
reverseComplement(target->dna, target->size);
reverseIntRange(&range->tStart, &range->tEnd, nib->size);
}
*retTotalSeqSize = nib->size;
}
else
{
struct twoBitFile *tbf = NULL;
char *tSeqName = strchr(fileName, ':');
int tSeqSize = 0;
if (tSeqName == NULL)
errAbort("No colon in .2bit response from gfServer");
*tSeqName++ = 0;
tbf = hashFindVal(tFileCache, fileName);
if (tbf == NULL)
{
tbf = twoBitOpen(fileName);
hashAdd(tFileCache, fileName, tbf);
}
tSeqSize = twoBitSeqSize(tbf, tSeqName);
if (isRc)
reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
gfiExpandRange(range, querySize, tSeqSize, respectFrame, isRc, expansion);
target = twoBitReadSeqFragLower(tbf, tSeqName, range->tStart, range->tEnd);
if (isRc)
{
reverseComplement(target->dna, target->size);
reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
}
*retTotalSeqSize = tSeqSize;
}
return target;
}
static struct ssBundle *gfClumpsToBundles(struct gfClump *clumpList,
boolean isRc, struct dnaSeq *seq, int minScore,
struct gfRange **retRangeList)
/* Convert gfClumps to an actual alignments (ssBundles) */
{
struct ssBundle *bun, *bunList = NULL;
struct gfRange *rangeList = NULL, *range;
struct dnaSeq *targetSeq;
rangeList = seqClumpToRangeList(clumpList, 0);
slSort(&rangeList, gfRangeCmpTarget);
rangeList = gfRangesBundle(rangeList, 2000);
for (range = rangeList; range != NULL; range = range->next)
{
targetSeq = range->tSeq;
gfiExpandRange(range, seq->size, targetSeq->size, FALSE, isRc,
usualExpansion);
range->tStart = 0;
range->tEnd = targetSeq->size;
AllocVar(bun);
bun->qSeq = seq;
bun->genoSeq = targetSeq;
alignComponents(range, bun, ffCdna);
ssStitch(bun, ffCdna, minScore, ssAliCount);
slAddHead(&bunList, bun);
}
slReverse(&bunList);
*retRangeList = rangeList;
return bunList;
}
