Beispiel #1
0
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);
}