void roundNewViewLimitsInRa(char *input, char *output)
/* roundNewViewLimitsInRa - Filter though .ra file rounding the new_viewLimits and making them
* viewLimits.. */
{
struct lineFile *lf = lineFileOpen(input, TRUE);
FILE *f = mustOpen(output, "w");
struct slPair *el, *list;
while ((list = raNextRecordAsSlPairList(lf)) != NULL)
{
double mean = atof(mustFindVal(list, "new_mean", lf));
double std = atof(mustFindVal(list, "new_std", lf));
double minLimit = atof(mustFindVal(list, "new_minLimit", lf));
double maxLimit = atof(mustFindVal(list, "new_maxLimit", lf));
double minV = mean - 6*std;
if (minV < minLimit) minV = minLimit;
double maxV = mean + 6*std;
if (maxV > maxLimit) maxV = maxLimit;
double minRound, maxRound;
rangeRoundUp(minV, maxV, &minRound, &maxRound);
for (el = list; el != NULL; el = el->next)
{
fprintf(f, "%s %s\n", el->name, (char*)el->val);
}
fprintf(f, "round_viewLimits %g:%g\n\n", minRound, maxRound);
}
}
void findToFixBedGraphLimits(char *input, char *output)
/* findToFixBedGraphLimits - Scan through ra file of bedGraphs and calculate limits.. */
{
struct lineFile *lf = lineFileOpen(input, TRUE);
FILE *f = mustOpen(output, "w");
struct slPair *el, *list;
while ((list = raNextRecordAsSlPairList(lf)) != NULL)
{
/* Find required fields for calcs. */
char *db = mustFindVal(list, "db", lf);
char *track = mustFindVal(list, "track", lf);
char *type = cloneString(mustFindVal(list, "type", lf));
/* Parse out type value, which should be "bedGraph 4" and put the 4 or whatever other number
* in dataFieldIndex. */
char *typeWords[3];
int typeWordCount = chopLine(type, typeWords);
if (typeWordCount != 2 || !sameString(typeWords[0], "bedGraph"))
errAbort("Not well formed bedGraph type line %d of %s", lf->lineIx, lf->fileName);
int dataFieldIndex = sqlUnsigned(typeWords[1]);
/* Figure out field corresponding to dataFieldIndex. */
struct sqlConnection *conn = sqlConnect(db);
struct slName *fieldList = sqlFieldNames(conn, track);
struct slName *pastBin = fieldList;
if (sameString(pastBin->name, "bin"))
pastBin = pastBin->next;
struct slName *fieldName = slElementFromIx(pastBin, dataFieldIndex - 1);
if (fieldName == NULL)
errAbort("%s doesn't have enough fields", track);
char *field = fieldName->name;
assert(sqlFieldIndex(conn, track, field) >= 0);
/* Print reassuring status message */
verbose(1, "%s.%s has %d elements. Data field is %s\n", db, track, sqlTableSize(conn, track), field);
/* Get min/max dataValues in fields. Do it ourselves rather than using SQL min/max because sometimes
* the data field is a name column.... */
char query[512];
safef(query, sizeof(query), "select %s from %s", field, track);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
row = sqlNextRow(sr);
assert(row != NULL);
double val = sqlDouble(row[0]);
double minLimit = val, maxLimit = val;
while ((row = sqlNextRow(sr)) != 0)
{
double val = sqlDouble(row[0]);
if (val < minLimit) minLimit = val;
if (val > maxLimit) maxLimit = val;
}
sqlFreeResult(&sr);
verbose(1, " %g %g\n", minLimit, maxLimit);
/* Output original table plus new minLimit/maxLimit. */
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s %s\n", el->name, (char *)el->val);
fprintf(f, "minLimit %g\n", minLimit);
fprintf(f, "maxLimit %g\n", maxLimit);
fprintf(f, "\n");
sqlDisconnect(&conn);
slFreeList(&fieldList);
slPairFreeValsAndList(&list);
}
lineFileClose(&lf);
carefulClose(&f);
}
