static void dumpGeneInfo(char *desc, struct orgGenes *orgs)
/* dump information about genes */
{
FILE *fh = verboseLogFile();
int i;
struct orgGenes *genes;
struct gene *gene;
for (genes = orgs; genes != NULL; genes = genes->next)
{
fprintf(fh, "srcDb: %s\n", genes->srcDb);
for (gene = genes->genes; gene != NULL; gene = gene->next)
{
geneSortFramesOffTarget(gene);
fprintf(fh, "%s: ", desc);
geneDump(fh, gene);
}
for (i = 0; i < 90; i++)
fputc('-', fh);
fputc('\n', fh);
}
}
static void splitMultAlign(struct gene *gene, struct gene **geneRestRet)
/* Split based on portions of a gene being aligned multiple times. Opposite
* strand alignments must have been processed first. */
{
struct exonFrames *ef;
/* algorithm requires sorting by offset in gene */
geneSortFramesOffTarget(gene);
/* Check each exonFrame to see if the next one overlaps in gene, goes
* backwards in target space, or results in an absurdly large exon. If so,
* find the best continuation of this frame and move all intervening ones to
* the new gene */
for (ef = geneFirstExonFrames(gene); ef != NULL;)
{
struct exonFrames *nextEf = exonFramesNext(ef);
if (isNextConflicting(ef, nextEf))
ef = splitConflicting(ef, geneRestRet);
else
ef = nextEf;
}
}
