struct wigSection *wigSectionRead(struct lineFile *lf)
/* Parse out next section of wig. */
{
static double *vals = NULL;
static int valAlloc = 0;
/* Get "fixedStep" line and parse it. */
char *line;
if (!lineFileNextReal(lf, &line))
return NULL;
char *pattern = "fixedStep ";
int patSize = 10;
if (!startsWith(pattern, line))
errAbort("Expecting fixedStep line %d of %s", lf->lineIx, lf->fileName);
line += patSize;
struct hash *varHash = hashVarLine(line, lf->lineIx);
int step = sqlUnsigned(requiredVal(lf, varHash, "step"));
int start = sqlUnsigned(requiredVal(lf, varHash, "start"));
char *chrom = cloneString(requiredVal(lf, varHash, "chrom"));
hashFree(&varHash);
/* Parse out numbers until next fixedStep. */
int valCount = 0;
int i;
for (;;)
{
if (!lineFileNextReal(lf, &line))
break;
if (startsWith(pattern, line))
{
lineFileReuse(lf);
break;
}
for (i=0; i<step; ++i)
{
if (valCount >= valAlloc)
{
int newAlloc = valAlloc + 1024;
ExpandArray(vals, valAlloc, newAlloc);
valAlloc = newAlloc;
}
vals[valCount] = lineFileNeedDouble(lf, &line, 0);
++valCount;
}
}
/* Create wigSection. */
struct wigSection *section;
AllocVar(section);
section->chrom = chrom;
section->chromStart = start;
section->chromEnd = start + valCount;
section->vals = CloneArray(vals, valCount);
return section;
}
void userSettingsUseNamed(struct userSettings *us, char *setName)
/* Use named collection of settings. */
{
struct cart *cart = us->cart;
char *varName = settingsVarName(us->savePrefix, setName);
char *settings = cartOptionalString(cart, varName);
if (settings != NULL)
{
struct hash *hash = hashVarLine(settings, 1);
struct hashEl *list = hashElListHash(hash);
struct hashEl *el;
for (el = list; el != NULL; el = el->next)
cartSetString(cart, el->name, el->val);
slFreeList(&list);
hashFree(&hash);
}
freez(&varName);
}
void wigToBedGraph(char *wigIn, char *bedOut)
/* wigToBedGraph - Convert wig files to bedGraph, merging adjacent items with identical values
* when possible.. */
{
struct lineFile *lf = lineFileOpen(wigIn, TRUE);
FILE *f = mustOpen(bedOut, "w");
struct bgOut *out = bgOutNew(f);
char *line;
while (lineFileNextReal(lf, &line))
{
char *firstWord = nextWord(&line);
struct hash *vars = hashVarLine(line, lf->lineIx);
if (sameString("fixedStep", firstWord))
convertFixedStepSection(lf, vars, out);
else if (sameString("variableStep", firstWord))
convertVariableStepSection(lf, vars, out);
else
errAbort("Expecting fixedStep or variableStep line %d of %s, got:\n\t%s", lf->lineIx,
lf->fileName, line);
freeHashAndVals(&vars);
}
bgOutFree(&out);
carefulClose(&f);
}
