static void parseSteppedSection(struct lineFile *lf, boolean clipDontDie,
struct hash *chromSizeHash, char *initialLine,
struct lm *lm, int itemsPerSlot, struct bwgSection **pSectionList)
/* Parse out a variableStep or fixedStep section and add it to list, breaking it up as need be. */
{
/* Parse out first word of initial line and make sure it is something we recognize. */
char *typeWord = nextWord(&initialLine);
enum bwgSectionType type = bwgTypeFixedStep;
if (sameString(typeWord, "variableStep"))
type = bwgTypeVariableStep;
else if (sameString(typeWord, "fixedStep"))
type = bwgTypeFixedStep;
else
errAbort("Unknown type %s\n", typeWord);
/* Set up defaults for values we hope to parse out of rest of line. */
int span = 0;
bits32 step = 0;
bits32 start = 0;
char *chrom = NULL;
/* Parse out var=val pairs. */
char *varEqVal;
while ((varEqVal = nextWord(&initialLine)) != NULL)
{
char *wordPairs[2];
int wc = chopByChar(varEqVal, '=', wordPairs, 2);
if (wc != 2)
errAbort("strange var=val pair line %d of %s", lf->lineIx, lf->fileName);
char *var = wordPairs[0];
char *val = wordPairs[1];
if (sameString(var, "chrom"))
chrom = cloneString(val);
else if (sameString(var, "span"))
span = parseUnsignedVal(lf, var, val);
else if (sameString(var, "step"))
step = parseUnsignedVal(lf, var, val);
else if (sameString(var, "start"))
{
start = parseUnsignedVal(lf, var, val);
}
else
errAbort("Unknown setting %s=%s line %d of %s", var, val, lf->lineIx, lf->fileName);
}
/* Check that we have all that are required and no more, and call type-specific routine to parse
* rest of section. */
if (chrom == NULL)
errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
bits32 chromSize = (chromSizeHash ? hashIntVal(chromSizeHash, chrom) : BIGNUM);
if (start > chromSize)
{
warn("line %d of %s: chromosome %s has %u bases, but item starts at %u",
lf->lineIx, lf->fileName, chrom, chromSize, start);
if (!clipDontDie)
noWarnAbort();
}
if (type == bwgTypeFixedStep)
{
if (start == 0)
errAbort("Missing start= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (step == 0)
errAbort("Missing step= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (span == 0)
span = step;
parseFixedStepSection(lf, clipDontDie, lm, itemsPerSlot,
chrom, chromSize, span, start-1, step, pSectionList);
}
else
{
if (start != 0)
errAbort("Extra start= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (step != 0)
errAbort("Extra step= setting line %d of %s\n", lf->lineIx, lf->fileName);
if (span == 0)
span = 1;
parseVariableStepSection(lf, clipDontDie, lm, itemsPerSlot,
chrom, chromSize, span, pSectionList);
}
}
static void parseSteppedSection(struct lineFile *lf, char *initialLine, struct pos *pos)
/* Parse out stepped section, adding info about it to pos. */
{
/* Parse out first word of initial line and make sure it is something we recognize. */
char *typeWord = nextWord(&initialLine);
enum bwgSectionType type = bwgTypeFixedStep;
if (sameString(typeWord, "variableStep"))
type = bwgTypeVariableStep;
else if (sameString(typeWord, "fixedStep"))
type = bwgTypeFixedStep;
else
errAbort("Unknown type %s\n", typeWord);
/* Set up defaults for values we hope to parse out of rest of line. */
bits32 start = 0;
char *chrom = NULL;
/* Parse out var=val pairs. */
char *varEqVal;
while ((varEqVal = nextWord(&initialLine)) != NULL)
{
char *wordPairs[2];
int wc = chopByChar(varEqVal, '=', wordPairs, 2);
if (wc != 2)
errAbort("strange var=val pair line %d of %s", lf->lineIx, lf->fileName);
char *var = wordPairs[0];
char *val = wordPairs[1];
if (sameString(var, "chrom"))
chrom = cloneString(val);
else if (sameString(var, "start"))
start = parseUnsignedVal(lf, var, val);
}
/* Check that we have all that are required and no more, and call type-specific routine to parse
* rest of section. */
if (chrom == NULL)
errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
pos->chrom = chrom;
if (type == bwgTypeFixedStep)
{
if (start == 0)
errAbort("Missing start= setting line %d of %s\n", lf->lineIx, lf->fileName);
for (;;)
{
char *line;
if (!lineFileNextReal(lf, &line))
break;
if (steppedSectionEnd(line, 1))
{
lineFileReuse(lf);
break;
}
}
}
else
{
for (;;)
{
char *line;
if (!lineFileNextReal(lf, &line))
break;
if (steppedSectionEnd(line, 2))
{
lineFileReuse(lf);
break;
}
bits32 s = atoi(line);
if (start == 0 || s < start)
start = s;
}
}
pos->start = start-1;
}