static struct pgSnp *vcfFileToPgSnp(struct vcfFile *vcff, struct trackDb *tdb)
/* Convert vcff's records to pgSnp; don't free vcff until you're done with pgSnp
* because it contains pointers into vcff's records' chrom. */
{
struct pgSnp *pgsList = NULL;
struct vcfRecord *rec;
int maxLen = 33;
int maxAlCount = 5;
for (rec = vcff->records; rec != NULL; rec = rec->next)
{
struct pgSnpVcfStartEnd *psvs = needMem(sizeof(*psvs));
psvs->vcfStart = vcfRecordTrimIndelLeftBase(rec);
psvs->vcfEnd = vcfRecordTrimAllelesRight(rec);
struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
memcpy(&(psvs->pgs), pgs, sizeof(*pgs));
pgs = (struct pgSnp *)psvs; // leak mem
// Insertion sequences can be quite long; abbreviate here for display.
int len = strlen(pgs->name);
if (len > maxLen)
{
int maxAlLen = (maxLen / min(rec->alleleCount, maxAlCount)) - 1;
pgs->name[0] = '\0';
int i;
for (i = 0; i < rec->alleleCount; i++)
{
if (i > 0)
safencat(pgs->name, len+1, "/", 1);
if (i >= maxAlCount)
{
safecat(pgs->name, len+1, "...");
pgs->alleleCount = maxAlCount;
break;
}
if (strlen(rec->alleles[i]) > maxAlLen-3)
strcpy(rec->alleles[i]+maxAlLen-3, "...");
safencat(pgs->name, len+1, rec->alleles[i], maxAlLen);
}
}
slAddHead(&pgsList, pgs);
}
slReverse(&pgsList);
return pgsList;
}
static char *readHtmlRecursive(char *fileName, char *database)
/* Slurp in an html file. Wherever it contains insertHtmlRegex, recursively slurp that in
* and replace insertHtmlRegex with the contents. */
{
char *html;
readInGulp(fileName, &html, NULL);
if (isEmpty(html))
return html;
regmatch_t substrs[4];
while (regexMatchSubstr(html, insertHtmlRegex, substrs, ArraySize(substrs)))
{
struct dyString *dy = dyStringNew(0);
// All text before the regex match:
dyStringAppendN(dy, html, substrs[0].rm_so);
// Is there an #if before the #insert ?
boolean doInsert = TRUE;
if (substrs[1].rm_so != -1 &&
(! sameStringN(database, html+substrs[2].rm_so, (substrs[2].rm_eo - substrs[2].rm_so))))
doInsert = FALSE;
if (doInsert)
{
// Recursively pull in inserted file contents from relative path, replacing regex match:
char dir[PATH_LEN];
splitPath(fileName, dir, NULL, NULL);
char insertFileName[PATH_LEN+FILENAME_LEN];
safecpy(insertFileName, sizeof(insertFileName), dir);
safencat(insertFileName, sizeof(insertFileName), html+substrs[3].rm_so,
(substrs[3].rm_eo - substrs[3].rm_so));
if (!fileExists(insertFileName))
errAbort("readHtmlRecursive: relative path '%s' (#insert'ed in %s) not found",
insertFileName, fileName);
char *insertedText = readHtmlRecursive(insertFileName, database);
dyStringAppend(dy, insertedText);
freez(&insertedText);
}
// All text after the regex match:
dyStringAppend(dy, html+substrs[0].rm_eo);
freez(&html);
html = dyStringCannibalize(&dy);
}
return html;
}
