struct psl *getParentAligns(struct sqlConnection *conn, struct mappingInfo *mi, char **table)
{
struct ucscRetroInfo *pg = mi->pg;
struct psl *pslList = NULL;
char query[512];
if (startsWith("August",mi->geneSet))
{
if (hTableExists(database, "augustusXAli"))
{
*table = cloneString( "augustusXAli");
pslList = loadPslRangeT(*table, mi->seqId, pg->gChrom, pg->gStart, pg->gEnd);
}
else if (hTableExists(database, "augustusX"))
{
struct sqlResult *sr;
char **row;
int targetSize = 0;
*table = cloneString( "augustusX");
sqlSafef(query, sizeof(query), "select * from augustusX where chrom = '%s' and txEnd > %d and txStart < %d and name like '%s%%'",
pg->gChrom, pg->gStart, pg->gEnd , mi->seqId );
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+1);
sqlSafef(query, sizeof(query),
"select size from chromInfo where chrom = '%s' " , gp->chrom);
sqlFreeResult(&sr);
targetSize = sqlNeedQuickNum(conn, query) ;
pslList = pslFromGenePred(gp, targetSize);
}
}
}
else if (hTableExists(database, "all_mrna"))
{
char parent[255];
char *dotPtr ;
*table = cloneString( "all_mrna");
safef(parent, sizeof(parent), "%s",pg->name);
/* strip off version and unique suffix when looking for parent gene*/
dotPtr = rStringIn(".",parent) ;
if (dotPtr != NULL)
*dotPtr = '\0';
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
if (pslList == NULL)
{
*table = cloneString( "refSeqAli");
pslList = loadPslRangeT(*table, mi->gbAcc, pg->gChrom, pg->gStart, pg->gEnd);
}
}
else
printf("no all_mrna table found<br>\n");
return pslList;
}
void pslListFromGenePred(char *chromSizesFile, struct genePred *gpList, FILE *out)
{
struct hash *chromSizes = getChromSizes(chromSizesFile);
struct genePred *gp = NULL;
struct psl *psl=NULL;
for(gp=gpList; gp != NULL; gp=gp->next)
{
int size = hashIntVal(chromSizes, gp->chrom);
psl = pslFromGenePred(gp, size);
pslTabOut(psl, out);
}
hashFree(&chromSizes);
}
