static void getAligns(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile)
/* get request alignments from database */
{
struct psl *psls = pslReaderLoadQuery(conn, "refSeqAli", NULL);
slSort(psls, pslCmpQuery);
FILE *fh = mustOpen(outFile, "w");
struct psl *psl;
for (psl = psls; psl != NULL; psl = psl->next)
processPsl(fh, refSeqVerInfoTbl, psl);
carefulClose(&fh);
pslFreeList(&psls);
}
static void processPslFile(struct sqlConnection *conn, struct gbSelect* select,
struct gbStatusTbl* statusTbl, char* pslPath)
/* Parse a psl file looking for accessions to add to the database. */
{
char* row[PSL_NUM_COLS];
struct lineFile *pslLf = gzLineFileOpen(pslPath);
while (lineFileNextRow(pslLf, row, PSL_NUM_COLS))
{
struct psl* psl = pslLoad(row);
processPsl(conn, select, statusTbl, psl, pslLf);
pslFree(&psl);
}
gzLineFileClose(&pslLf);
}
static void getAligns(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile)
/* get request alignments from database */
{
int off = hOffsetPastBin(sqlGetDatabase(conn), NULL, "refSeqAli");
struct sqlResult *sr = sqlGetResult(conn, "SELECT * FROM refSeqAli");
FILE *fh = mustOpen(outFile, "w");
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row+off);
processPsl(fh, refSeqVerInfoTbl, psl);
pslFree(&psl);
}
carefulClose(&fh);
sqlFreeResult(&sr);
}
