static struct lineFile *astLFOpen(char *fileOrUrl)
/* Figure out if fileOrUrl is file or URL and open an lf accordingly. */
{
if (startsWith("http://", fileOrUrl) || startsWith("https://", fileOrUrl) ||
startsWith("ftp://", fileOrUrl))
return netLineFileOpen(fileOrUrl);
else
return lineFileOpen(fileOrUrl, TRUE);
}
struct hash *bbiChromSizesFromFile(char *fileName)
/* Read two column file into hash keyed by chrom. */
{
struct hash *hash = hashNew(0);
struct lineFile *lf = netLineFileOpen(fileName);
char *row[2];
while (lineFileRow(lf, row))
hashAddInt(hash, row[0], sqlUnsigned(row[1]));
lineFileClose(&lf);
return hash;
}
struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords)
/* Parse a VCF file into a vcfFile object. If maxErr not zero, then
* continue to parse until this number of error have been reached. A maxErr
* less than zero does not stop and reports all errors. */
{
struct lineFile *lf = NULL;
if (startsWith("http://", fileOrUrl) || startsWith("ftp://", fileOrUrl) ||
startsWith("https://", fileOrUrl))
lf = netLineFileOpen(fileOrUrl);
else
lf = lineFileMayOpen(fileOrUrl, TRUE);
struct vcfFile *vcff = vcfFileHeaderFromLineFile(lf, maxErr);
vcfParseData(vcff, maxRecords);
return vcff;
}
struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords, boolean parseAll)
/* Open fileOrUrl and parse VCF header; return NULL if unable.
* If parseAll, then read in all lines, parse and store in
* vcff->records; if maxErr >= zero, then continue to parse until
* there are maxErr+1 errors. A maxErr less than zero does not stop
* and reports all errors. Set maxErr to VCF_IGNORE_ERRS for silence */
{
struct lineFile *lf = NULL;
if (startsWith("http://", fileOrUrl) || startsWith("ftp://", fileOrUrl) ||
startsWith("https://", fileOrUrl))
lf = netLineFileOpen(fileOrUrl);
else
lf = lineFileMayOpen(fileOrUrl, TRUE);
struct vcfFile *vcff = vcfFileHeaderFromLineFile(lf, maxErr);
if (parseAll)
{
vcff->records = vcfParseData(vcff, maxRecords);
lineFileClose(&(vcff->lf)); // Not sure why it is closed. Angie?
}
return vcff;
}
char *customPpNext(struct customPp *cpp)
/* Return next line. */
{
/* Check first for line to reuse. */
struct slName *reused = cpp->reusedLines;
if (reused)
{
/* We need to keep line actually reusing in memory until next
* call to customPpNext, so we move it to inReuse rather than
* immediately freeing it. */
freeMem(cpp->inReuse);
cpp->reusedLines = reused->next;
cpp->inReuse = reused;
return reused->name;
}
/* Get next line from file on top of stack. If at EOF
* go to next file in stack. If get a http:// or https:// or ftp:// line
* open file this references and push it onto stack. Meanwhile
* squirrel away 'browser' lines. */
struct lineFile *lf;
while ((lf = cpp->fileStack) != NULL)
{
char *line;
if (lineFileNext(lf, &line, NULL))
{
// if user pastes just a URL, create a track line automatically
// also allow a filename from a local directory if it has been allowed via udc.localDir in hg.conf
bool isLocalFile = cfgOption("udc.localDir")!=NULL && startsWith(cfgOption("udc.localDir"), line);
if (startsWith("http://", line) || startsWith("https://", line) || startsWith("ftp://", line) ||
isLocalFile)
{
if (customTrackIsBigData(line))
line = bigUrlToTrackLine(line);
else
{
lf = netLineFileOpen(line);
slAddHead(&cpp->fileStack, lf);
#ifdef PROGRESS_METER
off_t remoteSize = 0;
remoteSize = remoteFileSize(line);
cpp->remoteFileSize = remoteSize;
#endif
continue;
}
}
else if (!cpp->ignoreBrowserLines && startsWith("browser", line))
{
char afterPattern = line[7];
if (isspace(afterPattern) || afterPattern == 0)
{
slNameAddTail(&cpp->browserLines, line);
continue;
}
}
return line;
}
else
{
cpp->fileStack = lf->next;
lineFileClose(&lf);
}
}
return NULL;
}
struct meta *metaLoadAll(char *fileName, char *keyTag, char *parentTag,
boolean ignoreOtherStanzas, boolean ignoreIndent)
/* Loads in all ra stanzas from file and turns them into a list of meta, some of which
* may have children. The keyTag parameter is optional. If non-null it should be set to
* the tag name that starts a stanza. If null, the first tag of the first stanza will be used.
* The parentTag if non-NULL will be a tag name used to define the parent of a stanza.
* The ignoreOtherStanzas flag if set will ignore stanzas that start with other tags.
* If not set the routine will abort on such stanzas. The ignoreIndent if set will
* use the parentTag (which must be set) to define the hierarchy. Otherwise the program
* will look at the indentation, and if there is a parentTag complain about any
* disagreements between indentation and parentTag. */
{
struct lineFile *lf = netLineFileOpen(fileName);
struct meta *meta, *forest = NULL, *lastMeta = NULL;
if (ignoreIndent)
{
errAbort("Currently metaLoadAll can't ignore indentation, sorry.");
}
while ((meta = metaNextStanza(lf)) != NULL)
{
struct meta **pList;
if (forest == NULL) /* First time. */
{
if (meta->indent != 0)
errAbort("Initial stanza of %s should not be indented", fileName);
if (keyTag == NULL)
keyTag = meta->tagList->tag;
pList = &forest;
}
else
{
if (!sameString(keyTag, meta->tagList->tag))
{
if (ignoreOtherStanzas)
{
metaFree(&meta);
continue;
}
else
errAbort("Stanza beginning with %s instead of %s line %d of %s",
meta->tagList->tag, keyTag, lf->lineIx, lf->fileName);
}
if (meta->indent > lastMeta->indent)
{
pList = &lastMeta->children;
meta->parent = lastMeta;
}
else if (meta->indent == lastMeta->indent)
{
if (meta->indent == 0)
pList = &forest;
else
{
pList = &lastMeta->parent->children;
meta->parent = lastMeta->parent;
}
}
else /* meta->indent < lastMeta->indent */
{
/* Find sibling at same level as us. */
struct meta *olderSibling;
for (olderSibling = lastMeta->parent;
olderSibling != NULL; olderSibling = olderSibling->parent)
{
if (meta->indent == olderSibling->indent)
break;
}
if (olderSibling == NULL)
{
warn("Indentation inconsistent in stanza ending line %d of %s.",
lf->lineIx, lf->fileName);
warn("If you are using tabs, check your tab stop is set to 8.");
warn("Otherwise check that when you are reducing indentation in a stanza");
warn("that it is the same as the previous stanza at the same level.");
noWarnAbort();
}
if (olderSibling->parent == NULL)
pList = &forest;
else
{
pList = &olderSibling->parent->children;
meta->parent = olderSibling->parent;
}
}
}
slAddHead(pList, meta);
lastMeta = meta;
}
lineFileClose(&lf);
forest = rReverseMetaList(forest);
return forest;
}
