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 *pslReaderLoadFile(char* pslFile, char* chrom)
/* Function that encapsulates reading a psl file */
{
struct pslReader *pr = pslReaderFile(pslFile, chrom);
struct psl *pslList = pslReaderAll(pr);
pslReaderFree(&pr);
return pslList;
}
struct psl *pslReaderLoadQuery(struct sqlConnection* conn,
char* table, char* where)
/* Function that encapsulates doing a query and loading the results */
{
struct pslReader *pr = pslReaderQuery(conn, table, where);
struct psl *pslList = pslReaderAll(pr);
pslReaderFree(&pr);
return pslList;
}
struct psl *pslReaderLoadRangeQuery(struct sqlConnection* conn,
char* table, char* chrom,
int start, int end,
char* extraWhere)
/* Function that encapsulates doing a range query and loading the results */
{
struct pslReader *pr = pslReaderRangeQuery(conn, table, chrom,
start, end, extraWhere);
struct psl *pslList = pslReaderAll(pr);
pslReaderFree(&pr);
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);
}
