static void addAttrVals(struct gff3Ann *g3a, char *attr, char *valStr)
/* Add an attribute to the list of attributes. If attribute has already been
* specified, values are merged. Attribute name must already be unescaped,
* attribute values will be split and then unescaped. */
{
struct gff3AttrVals *attrVals = gff3AnnFindAttr(g3a, attr);
if (attrVals == NULL)
{
attrVals = gff3FileAlloc(g3a->file, sizeof(struct gff3AttrVals));
attrVals->attr = gff3FileCloneStr(g3a->file, attr);
slAddHead(&g3a->attrs, attrVals);
}
attrVals->vals = slCat(attrVals->vals, parseAttrVals(g3a, attr, valStr));
}
static void processMatchLine(FILE *pslF, struct gff3Ann *node,
struct hash *chromHash)
{
struct gff3Attr *attr = gff3AnnFindAttr(node, "Gap");
char *cigar = NULL;
if (!((attr == NULL) || (attr->vals == NULL) || (attr->vals->name == NULL)))
cigar = attr->vals->name;
struct nameAndSize *nsT = getNameAndSize(chromHash, node->targetId);
struct nameAndSize *nsQ = getNameAndSize(chromHash, node->seqid);
struct psl *psl = pslFromGff3Cigar(node->seqid, nsQ->size, node->start, node->end,
nsT->name, nsT->size, node->targetStart, node->targetEnd,
node->targetStrand, cigar);
pslOutput(psl, pslF, '\t' , '\n');
pslFree(&psl);
}
