void readTableTask(char *db, char *table)
/* Implements the readTable task */
{
FILE *outFh = NULL;
struct sqlConnection *conn = sqlConnect(db);
struct pslReader* pr = pslReaderQuery(conn, table, gWhere);
struct psl* psl;
int numRows = 0;
if (gOutput != NULL)
outFh = mustOpen(gOutput, "w");
while ((numRows < gMaxRows) && ((psl = pslReaderNext(pr)) != NULL))
{
if (outFh != NULL)
pslTabOut(psl, outFh);
pslFree(&psl);
numRows++;
}
carefulClose(&outFh);
pslReaderFree(&pr);
sqlDisconnect(&conn);
checkNumRows(table, numRows);
}
struct psl *pslReaderAll(struct pslReader* pr)
/* Read the all of psls */
{
struct psl* pslList = NULL, *psl;
while ((psl = pslReaderNext(pr)) != NULL)
slAddHead(&pslList, psl);
slReverse(&pslList);
return pslList;
}
static void pslLiftSubrangeBlat(char *inPsl, char *outPsl, char *qSizesFile, char *tSizesFile)
/* pslLiftSubrangeBlat - lift PSLs from blat subrange alignments. */
{
struct hash *qSizes = (qSizesFile != NULL) ? loadSizes(qSizesFile) : NULL;
struct hash *tSizes = (tSizesFile != NULL) ? loadSizes(tSizesFile) : NULL;
struct pslReader *inRd = pslReaderFile(inPsl, NULL);
FILE *outFh = mustOpen(outPsl, "w");
struct psl *psl;
while ((psl = pslReaderNext(inRd)) != NULL)
{
liftIt(psl, qSizes, tSizes);
pslTabOut(psl, outFh);
pslFree(&psl);
}
carefulClose(&outFh);
pslReaderFree(&inRd);
}
void readFile(char *pslFile)
/* Implements the readFile task */
{
FILE *outFh = NULL;
struct pslReader* pr = pslReaderFile(pslFile, gChrom);
struct psl* psl;
int numRows = 0;
if (gOutput != NULL)
outFh = mustOpen(gOutput, "w");
while ((numRows < gMaxRows) && ((psl = pslReaderNext(pr)) != NULL))
{
if (outFh != NULL)
pslTabOut(psl, outFh);
pslFree(&psl);
numRows++;
}
carefulClose(&outFh);
pslReaderFree(&pr);
checkNumRows(pslFile, numRows);
}
