struct gapInfo *findLargeGaps(struct xaAli *xa, struct gapInfo *oldList)
/* Find large gaps in alignment and classify them. */
{
struct gdfGene *gdfList;
struct gapInfo *gapList = NULL, *gap;
int ceIx=0, cbIx=0, symIx=0;
int ceStart=0, cbStart=0, symStart=0;
int runSize = 0;
char sym, lastSym = 0;
int symCount = xa->symCount;
/* Fetch C. elegans region. */
gdfList = wormGdfGenesInRange(xa->target, xa->tStart, xa->tEnd, &wormSangerGdfCache);
/* Run a little state machine that does something at the end of each solid run
* of a symbol. */
for (symIx = 0; symIx <= symCount; ++symIx)
{
sym = xa->hSym[symIx];
if (sym != lastSym)
{
if (runSize > 32) /* Introns need to be at least this long. */
{
/* We're at end of a solid run. */
if (lastSym == 'Q' || lastSym == 'T')
{
int ceGapStart = xa->tStart + ceStart;
int ceGapEnd = xa->tStart + ceIx;
struct gdfGene *gdf;
char hBefore = xa->hSym[symStart-1];
char hAfter = sym;
char strand = '.';
AllocVar(gap);
gap->query = cloneString(xa->query);
gap->qStart = xa->qStart + cbStart;
gap->qEnd = xa->qStart + cbIx;
gap->target = cloneString(xa->target);
gap->tStart = ceGapStart;
gap->tEnd = ceGapEnd;
gap->name = cloneString(xa->name);
gap->size = runSize;
gap->hSym = lastSym;
if (uniqueGap(oldList, gap))
{
slAddHead(&gapList, gap);
classifyGap(gdfList, xa->target, ceGapStart, ceGapEnd, lastSym, &gap->type, &gdf);
if (gdf != NULL)
strand = gdf->strand;
gap->hasIntronEnds = isIntron(xa, symStart, symIx, lastSym, strand, &gap->slideCount, &gap->isRc);
if (gap->hasIntronEnds)
slideGap(gap, xa, lastSym, symStart, symIx);
if (isConserved(hBefore) && isConserved(hAfter))
gap->hasStrongHomology = TRUE;
if (gap->hasStrongHomology)
{
if (lastSym == 'T')
writeGap(gap, xa, symStart+gap->slideCount, symIx+gap->slideCount, strand, out);
}
}
}
}
runSize = 0;
ceStart = ceIx;
cbStart = cbIx;
symStart = symIx;
lastSym = sym;
}
++runSize;
if (xa->qSym[symIx] != '-')
++cbIx;
if (xa->tSym[symIx] != '-')
++ceIx;
}
gdfFreeGeneList(&gdfList);
slReverse(&gapList);
return gapList;
}
void outputCheck(struct psl *psl, struct dnaSeq *qSeq, int qOffset,
struct dnaSeq *tSeq, int tOffset, FILE *f)
/* Output quality check info to file */
{
int sizePolyA = 0;
int qSize = psl->qSize;
int i;
int missSmallStart = 0;
int missLargeStart = 0;
int missSmallEnd = 0;
int missLargeEnd = 0;
int missSmallMiddle = 0;
int missLargeMiddle = 0;
int weirdSplice = 0;
int doubleGap = 0;
int jumpBack = 0;
int diff;
int totalProblems = 0;
char strand = psl->strand[0];
if (strand == '+')
{
for (i=1; i<=qSize; ++i)
{
if (qSeq->dna[qSize - i - qOffset] == 'a')
++sizePolyA;
else
break;
}
}
else
{
for (i=0; i<qSize; ++i)
{
if (qSeq->dna[i - qOffset] == 't')
++sizePolyA;
else
break;
}
}
if (psl->qStart > tinySize)
{
if (psl->qStart <= smallSize)
{
missSmallStart = psl->qStart;
++totalProblems;
}
else
{
missLargeStart = psl->qStart;
++totalProblems;
}
}
diff = psl->qSize - psl->qEnd - sizePolyA;
if (diff > tinySize)
{
if (diff <= smallSize)
{
missSmallEnd = diff;
++totalProblems;
}
else
{
missLargeEnd = diff;
++totalProblems;
}
}
for (i=0; i<psl->blockCount-1; ++i)
{
int nextT = psl->tStarts[i+1];
int nextQ = psl->qStarts[i+1];
int sz = psl->blockSizes[i];
int t = psl->tStarts[i] + sz;
int q = psl->qStarts[i] + sz;
int dq = nextQ - q;
int dt = nextT - t;
if (dq < 0 || dt < 0)
{
++jumpBack;
++totalProblems;
}
else
{
if (dq > 0 && dt > 0)
{
++doubleGap;
++totalProblems;
}
if (dq > tinySize)
{
if (dq > smallSize)
{
++missLargeMiddle;
++totalProblems;
}
else
{
++missSmallMiddle;
++totalProblems;
}
}
if (dq == 0 && dt >=30)
{
char *dna = tSeq->dna - tOffset;
if (!isIntron(strand, dna + t, dna + nextT))
{
++weirdSplice;
++totalProblems;
}
}
}
}
fprintf(f, "%2d %9s %s ", totalProblems, psl->qName, psl->strand);
fprintf(f, "%4dS ", missLargeStart);
fprintf(f, "%2ds ", missSmallStart);
fprintf(f, "%4dE ", missLargeEnd);
fprintf(f, "%2de ", missSmallEnd);
fprintf(f, "%2dM ", missLargeMiddle);
fprintf(f, "%2dm ", missSmallMiddle);
fprintf(f, "%2dW ", weirdSplice);
fprintf(f, "%2dG ", doubleGap);
fprintf(f, "%2dJ ", jumpBack);
fprintf(f, "\n");
total_missSmallStart += boolify(missSmallStart);
total_missLargeStart += boolify(missLargeStart);
total_missSmallEnd += boolify(missSmallEnd);
total_missLargeEnd += boolify(missLargeEnd);
total_missSmallMiddle += boolify(missSmallMiddle);
total_missLargeMiddle += boolify(missLargeMiddle);
total_weirdSplice += boolify(weirdSplice);
total_doubleGap += boolify(doubleGap);
total_jumpBack += boolify(jumpBack);
++total_rnaCount;
if (totalProblems == 0)
++total_rnaPerfect;
}
