struct psl *filterPsls(struct psl *pslList, int chromStart, int chromEnd)
/** Filter pslList to get only "good" ones. */
{
struct psl *goodList = NULL, *psl = NULL, *pslNext = NULL;
for(psl = pslList; psl != NULL; psl = pslNext)
{
boolean notTooBig = FALSE;
pslNext = psl->next;
/* Figure out chromStart/chromEnd put us in the middle of a big
* intron or the like inside of another gene. If so ignore alignments
* from enclosing genes by setting notTooBig. */
int endFirstExon = psl->tStarts[0] + psl->blockSizes[0];
int startLastExon = psl->tStarts[psl->blockCount-1];
int pad=100;
notTooBig = (endFirstExon + pad >= chromStart && startLastExon -pad <= chromEnd);
#ifdef AFFYSPLICE
notTooBig = TRUE;
#endif
if(passFilters(psl) && notTooBig)
{
slSafeAddHead(&goodList, psl);
}
else
{
if(!useChromKeeper)
pslFree(&psl);
}
}
slReverse(&goodList);
return goodList;
}
static void condSelectReply(fr_t *fr, aobj *akey, void *rrow, long *card) {
uchar hit = 0;
if (fr->nowc) hit = 1;
else hit = passFilters(fr->btr, akey, rrow,
fr->w->flist, fr->w->tmatch);
if (hit) {
*card = *card + 1;
if (fr->cstar) return; /* just counting */
robj *r = outputRow(fr->btr, rrow, fr->qcols, fr->cmatchs,
akey, fr->w->tmatch, 0);
if (fr->q->qed) addRow2OBList(fr->ll, fr->w, fr->btr, r, fr->ofree,
rrow, akey);
else addReplyBulk(fr->c, r);
decrRefCount(r);
}
}
void processBestSingle(char *acc, struct psl *pslList, FILE *bestFile, FILE *repFile)
/* Find single best psl in list. */
{
struct psl *bestPsl = NULL, *psl;
int bestScore = 0, score, threshold;
for (psl = pslList; psl != NULL; psl = psl->next)
{
score = pslScore(psl);
if (score > bestScore)
{
bestScore = score;
bestPsl = psl;
}
}
threshold = round((1.0 - nearTop)*bestScore);
for (psl = pslList; psl != NULL; psl = psl->next)
{
if (pslScore(psl) >= threshold && passFilters(psl, NULL))
pslTabOut(psl, bestFile);
}
}
void processBestMulti(char *acc, struct psl *pslList, FILE *bestFile, FILE *repFile)
/* Find psl's that are best anywhere along their length. */
{
struct psl *psl;
int qSize;
int *repTrack = NULL;
int *scoreTrack = NULL;
int milliScore;
int goodAliCount = 0;
int bestAliCount = 0;
int milliMin = 1000*minAli;
if (pslList == NULL)
return;
qSize = pslList->qSize;
AllocArray(repTrack, qSize+1);
AllocArray(scoreTrack, qSize+1);
for (psl = pslList; psl != NULL; psl = psl->next)
{
int blockIx;
char strand = psl->strand[0];
milliScore = calcMilliScore(psl);
if (milliScore >= milliMin)
{
++goodAliCount;
milliScore += sizeFactor(psl);
for (blockIx = 0; blockIx < psl->blockCount; ++blockIx)
{
int start = psl->qStarts[blockIx];
int size = psl->blockSizes[blockIx];
int end = start+size;
int i;
if (strand == '-')
reverseIntRange(&start, &end, psl->qSize);
if (start < 0 || end > qSize)
{
warn("Odd: qName %s tName %s qSize %d psl->qSize %d start %d end %d",
psl->qName, psl->tName, qSize, psl->qSize, start, end);
if (start < 0)
start = 0;
if (end > qSize)
end = qSize;
}
for (i=start; i<end; ++i)
{
repTrack[i] += 1;
if (milliScore > scoreTrack[i])
scoreTrack[i] = milliScore;
}
}
}
}
/* Print out any alignments that are within 2% of top score. */
for (psl = pslList; psl != NULL; psl = psl->next)
{
if(passFilters(psl, scoreTrack))
{
pslTabOut(psl, bestFile);
++bestAliCount;
}
}
/* Print out run-length-encoded repeat info. */
{
int runVal = repTrack[0];
int curVal;
int runSize = 1;
int packetCount = 0;
int *packetSize = NULL;
int *packetVal = NULL;
int i;
AllocArray(packetSize, qSize);
AllocArray(packetVal, qSize);
repTrack[qSize] = -1; /* Sentinal value to simplify RLC loop. */
fprintf(repFile, "%s\t%d\t%d\t", acc, bestAliCount, goodAliCount);
for (i=1; i<=qSize; ++i)
{
if ((curVal = repTrack[i]) != runVal)
{
packetSize[packetCount] = runSize;
packetVal[packetCount] = runVal;
++packetCount;
runSize = 1;
runVal = curVal;
}
else
{
++runSize;
}
}
fprintf(repFile, "%d\t", packetCount);
for (i=0; i<packetCount; ++i)
fprintf(repFile, "%d,", packetSize[i]);
fprintf(repFile, "\t");
for (i=0; i<packetCount; ++i)
fprintf(repFile, "%d,", packetVal[i]);
fprintf(repFile, "\n");
freeMem(packetSize);
freeMem(packetVal);
}
freeMem(repTrack);
freeMem(scoreTrack);
}
