static struct ccdsGeneMap *ccdsGetGenes(struct sqlConnection *conn, char *mapTable,
char *ccdsId)
/* Get ccdsGeneMap objects for a ccdsId. Returns only
* the best overlapping ones (ones with the same cdsSimilariy as
* the highest cdsSimilariy. */
{
struct ccdsGeneMap *ccdsGenes = NULL, *bestCcdsGenes = NULL, *ccdsGene;
/* filter by chrom due to PAR */
ccdsGenes = ccdsGeneMapSelectByCcds(conn, mapTable, ccdsId, seqName, 0.0);
if (ccdsGenes == NULL)
return NULL;
bestCcdsGenes = slPopHead(&ccdsGenes); /* seed with first */
while ((ccdsGene = slPopHead(&ccdsGenes)) != NULL)
{
if (ccdsGene->cdsSimilarity == bestCcdsGenes->cdsSimilarity)
{
/* same as best, keep */
slAddHead(&bestCcdsGenes, ccdsGene);
}
else if (ccdsGene->cdsSimilarity > bestCcdsGenes->cdsSimilarity)
{
/* new best, replace list */
ccdsGeneMapFreeList(&bestCcdsGenes);
bestCcdsGenes = ccdsGene;
}
else
{
/* worse, drop */
ccdsGeneMapFree(&ccdsGene);
}
}
/* only keep one of each gene */
slUniqify(&bestCcdsGenes, ccdsGeneMapGeneIdCmp, ccdsGeneMapFree);
return bestCcdsGenes;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && !optionExists("settings"))
usage();
struct trackHubCheckOptions *checkOptions = NULL;
AllocVar(checkOptions);
checkOptions->specHost = (optionExists("test") ? "genome-test.soe.ucsc.edu" : "genome.ucsc.edu");
checkOptions->specHost = optionVal("specHost", checkOptions->specHost);
checkOptions->printMeta = optionExists("printMeta");
checkOptions->checkFiles = !optionExists("noTracks");
checkOptions->checkSettings = optionExists("checkSettings");
struct trackHubSettingSpec *setting = NULL;
AllocVar(setting);
setting->level = optionVal("level", "all");
if (trackHubSettingLevel(setting) < 0)
{
fprintf(stderr, "ERROR: Unrecognized support level %s\n\n", setting->level);
usage();
}
checkOptions->level = setting->level;
char *version = NULL;
if (optionExists("version"))
version = optionVal("version", NULL);
checkOptions->version = version;
char *extraFile = optionVal("extra", NULL);
if (extraFile != NULL)
addExtras(extraFile, checkOptions);
cacheTime = optionInt("cacheTime", cacheTime);
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
knetUdcInstall(); // make the htslib library use udc
if (optionExists("settings"))
{
showSettings(checkOptions);
return 0;
}
struct dyString *errors = newDyString(1024);
if (trackHubCheck(argv[1], checkOptions, errors))
{
// uniquify and count errors
struct slName *errs = slNameListFromString(errors->string, '\n');
slUniqify(&errs, slNameCmp, slNameFree);
int errCount = slCount(errs);
printf("Found %d problem%s:\n", errCount, errCount == 1 ? "" : "s");
printf("%s\n", slNameListToString(errs, '\n'));
return 1;
}
return 0;
}
