void writeClump(struct blockPos *first, struct blockPos *last,
char *cdnaName, char strand, char dir, DNA *cdna, int cdnaSize, struct cdnaAliList **pList)
/* Write hitOut one clump. */
{
struct dnaSeq *seq = first->seq;
char *bacName = seq->name;
int seqIx = first->seqIx;
int start = first->offset;
int end = last->offset+last->size;
struct ffAli *ff, *left, *right;
int extraAtEnds = minMatch*patSize;
struct cdnaAliList *cal;
start -= extraAtEnds;
if (start < 0)
start = 0;
end += extraAtEnds;
if (end >seq->size)
end = seq->size;
++ffSubmitted;
if (dumpMe)
fprintf(dumpOut, "%s %d %s %d-%d\n", cdnaName, cdnaSize, bacName, start, end);
ff = ffFind(cdna, cdna+cdnaSize, seq->dna+start, seq->dna+end, ffCdna);
if (dumpMe)
{
fprintf(dumpOut, "ffFind = %x\n", ff);
}
if (ff != NULL)
{
int ffScore = ffScoreCdna(ff);
++ffAccepted;
if (dumpMe) fprintf(dumpOut, "ffScore = %d\n", ffScore);
if (ffScore >= 22)
{
int hiStart, hiEnd;
int oldStart, oldEnd;
ffFindEnds(ff, &left, &right);
hiStart = oldStart = left->nStart - cdna;
hiEnd = oldEnd = right->nEnd - cdna;
++ffOkScore;
if (solidMatch(&left, &right, cdna, &hiStart, &hiEnd))
{
int solidSize = hiEnd - hiStart;
int solidScore;
int seqStart, seqEnd;
double cookedScore;
solidScore = scoreCdna(left, right);
cookedScore = (double)solidScore/solidSize;
if (cookedScore > 0.25)
{
++ffSolidMatch;
seqStart = left->hStart - seq->dna;
seqEnd = right->hEnd - seq->dna;
fprintf(hitOut, "%3.1f%% %c %s:%d-%d (old %d-%d) of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, strand, cdnaName,
hiStart, hiEnd, oldStart, oldEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
if (dumpMe)
{
fprintf(bigHtmlFile, "<A NAME=i%d>", htmlIx);
fprintf(bigHtmlFile, "<H2>%4.1f%% %4d %4d %c %s:%d-%d of %d at %s.%d:%d-%d</H2><BR>",
100.0 * cookedScore, solidScore, ffScore, strand, cdnaName,
hiStart, hiEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
fprintf(bigHtmlFile, "</A>");
ffShAli(bigHtmlFile, ff, cdnaName, cdna, cdnaSize, 0,
bacName, seq->dna+start, end-start, start, FALSE);
fprintf(bigHtmlFile, "<BR><BR>\n");
fprintf(littleHtmlFile, "<A HREF=\"patAli.html#i%d\">", htmlIx);
fprintf(littleHtmlFile, "%4.1f%% %4d %4d %c %s:%d-%d of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, solidScore, ffScore, strand, cdnaName,
hiStart, hiEnd, cdnaSize,
bacName, seqIx, seqStart, seqEnd);
fprintf(littleHtmlFile, "</A><BR>");
++htmlIx;
}
cal = newCal(first->bacIx, seqIx, hiStart, hiEnd, cdnaSize, strand, dir, cookedScore);
slAddHead(pList, cal);
}
}
}
ffFreeAli(&ff);
}
}
void glueFindOne(struct patSpace *ps, DNA *cdna, int cdnaSize,
char strand, char dir, char *cdnaName, struct cdnaAliList **pList)
/* Find occurrences of DNA in patSpace and print to hitOut. */
{
struct patClump *clumpList, *clump;
clumpList = patSpaceFindOne(ps, cdna, cdnaSize);
for (clump = clumpList; clump != NULL; clump = clump->next)
{
struct ffAli *ff;
struct dnaSeq *seq = clump->seq;
DNA *tStart = seq->dna + clump->start;
char *contigName = seq->name;
int seqIx = clump->seqIx;
int bacIx = clump->bacIx;
++ffSubmitted;
ff = ffFind(cdna, cdna+cdnaSize, tStart, tStart + clump->size, ffCdna);
if (ff != NULL)
{
int ffScore = ffScoreCdna(ff);
++ffAccepted;
if (ffScore >= 22)
{
int hiStart, hiEnd;
int oldStart, oldEnd;
struct ffAli *left, *right;
ffFindEnds(ff, &left, &right);
hiStart = oldStart = left->nStart - cdna;
hiEnd = oldEnd = right->nEnd - cdna;
++ffOkScore;
if (solidMatch(&left, &right, cdna, &hiStart, &hiEnd))
{
int solidSize = hiEnd - hiStart;
int solidScore;
int seqStart, seqEnd;
double cookedScore;
solidScore = scoreCdna(left, right);
cookedScore = (double)solidScore/solidSize;
if (cookedScore > 0.25)
{
struct cdnaAliList *cal;
++ffSolidMatch;
seqStart = left->hStart - seq->dna;
seqEnd = right->hEnd - seq->dna;
fprintf(hitOut, "%3.1f%% %c %s:%d-%d (old %d-%d) of %d at %s.%d:%d-%d\n",
100.0 * cookedScore, strand, cdnaName,
hiStart, hiEnd, oldStart, oldEnd, cdnaSize,
contigName, seqIx, seqStart, seqEnd);
cal = newCal(bacIx, seqIx, hiStart, hiEnd, cdnaSize, strand, dir, cookedScore);
slAddHead(pList, cal);
}
}
}
ffFreeAli(&ff);
}
}
slFreeList(&clumpList);
}