int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clSeq = optionVal("seq", clSeq);
clStart = optionInt("start", clStart);
clEnd = optionInt("end", clEnd);
clSeqList = optionVal("seqList", clSeqList);
clBpt = optionVal("bpt", clBpt);
clBed = optionVal("bed", clBed);
clBedPos = optionExists("bedPos");
noMask = optionExists("noMask");
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (clBedPos && !clBed)
errAbort("the -bedPos option requires the -bed option");
if (clBed != NULL)
{
if (clSeqList != NULL)
errAbort("Can only have seqList or bed options, not both.");
if (clSeq != NULL)
errAbort("Can only have seq or bed options, not both.");
}
if ((clStart > clEnd) && (clSeq == NULL))
errAbort("must specify -seq with -start and -end");
if ((clSeq != NULL) && (clSeqList != NULL))
errAbort("can't specify both -seq and -seqList");
dnaUtilOpen();
twoBitToFa(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
twoBitDup(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (argc != 2)
usage();
bigWigInfo(argv[1]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clChrom = optionVal("chrom", clChrom);
clStart = optionInt("start", clStart);
clEnd = optionInt("end", clEnd);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
bigWigToWig(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
char *hubUrl = optionVal("addHub", NULL);
if (hubUrl != NULL)
return hubPublicAdd(argv[1],hubUrl);
else
return hubPublicCheck(argv[1]);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
clChrom = optionVal("chrom", clChrom);
clStart = optionInt("start", clStart);
clEnd = optionInt("end", clEnd);
maxItems = optionInt("maxItems", maxItems);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (argc != 3)
usage();
bigBedToBed(argv[1], argv[2]);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (trackHubCrawl(argv[1]))
{
return 1;
}
return 0;
}
bigWig_t * bigwig_load(const char * filename, const char * udc_dir) {
bigWig_t * bigwig = NULL;
struct errCatch * err;
/* set cache */
if (udc_dir != NULL)
udcSetDefaultDir((char*) udc_dir);
/* setup error management & try to open file */
err = errCatchNew();
if (errCatchStart(err))
bigwig = bigWigFileOpen((char*)filename);
errCatchEnd(err);
if (err->gotError) {
fprintf(stderr, "error: %s\n", err->message->string);
errCatchFree(&err);
return NULL;
}
errCatchFree(&err);
return bigwig;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
if (optionExists("fields"))
{
if (argc < 2)
usage();
bigBedFields(argv[1]);
}
else
{
summaryType = optionVal("type", summaryType);
if (argc != 6)
usage();
bigBedSummary(argv[1], argv[2], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]), sqlUnsigned(argv[5]));
}
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
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;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
blockSize = optionInt("blockSize", blockSize);
itemsPerSlot = optionInt("itemsPerSlot", itemsPerSlot);
asFile = optionVal("as", asFile);
doCompress = !optionExists("unc");
sizesIs2Bit = optionExists("sizesIs2Bit");
extraIndex = optionVal("extraIndex", NULL);
tabSep = optionExists("tab");
udcDir = optionVal("udcDir", udcDefaultDir());
if (argc != 4)
usage();
udcSetDefaultDir(udcDir);
if (optionExists("type"))
{
// parse type
char *btype = cloneString(optionVal("type", ""));
char *plus = strchr(btype, '+');
if (plus)
{
*plus++ = 0;
if (isdigit(*plus))
bedP = sqlUnsigned(plus);
}
if (!startsWith("bed", btype))
errAbort("type must begin with \"bed\"");
btype +=3;
bedN = sqlUnsigned(btype);
if (bedN < 3)
errAbort("Bed must be 3 or higher, found %d\n", bedN);
if (bedN > 15)
errAbort("Bed must be 15 or lower, found %d\n", bedN);
}
else
{
if (asText)
errAbort("If you specify the .as file, you must specify the -type as well so that\n"
"the number of standard BED columns is known.");
}
/* If the haven't set bedN and bedP from the type var in the command line, then we sniff it
* out from file. */
char *bedFileName = argv[1];
if (bedN == 0)
{
/* Just read in single line and count fields. */
struct lineFile *lf = lineFileOpen(bedFileName, TRUE);
char *line;
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
int fieldCount;
if (tabSep)
fieldCount = chopByChar(line, '\t', NULL, 0); // Do not use chopString, see GOTCHA
else
fieldCount = chopByWhite(line, NULL, 0);
if (fieldCount > 256)
errAbort("Too many columns in %s, you sure it's a bed file?", lf->fileName);
lineFileClose(&lf);
/* Set up so that it looks like we are straight up bed for that many fields,
* or if more than or maximum defined fields, then for bed15+ */
bedN = fieldCount;
if (bedN > bedKnownFields)
{
bedP = bedN - bedKnownFields;
bedN = bedKnownFields;
}
}
/* Make sure that fields are defined, from bed spec if nowhere else. */
if (asFile)
readInGulp(asFile, &asText, NULL);
else
asText = bedAsDef(bedN, bedN + bedP);
bedToBigBed(bedFileName, argv[2], argv[3]);
optionFree();
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
{
optionInit(&argc, argv, optionSpecs);
if (argc < 2 || argc > 3)
usage();
pushCarefulMemHandler(LIMIT_2or6GB);
char *db = argv[1];
char *test = NULL;
boolean doAllTests = (argc == 2);
if (!doAllTests)
{
if (sameString(argv[2], pgSnpDbToTabOut) ||
sameString(argv[2], pgSnpKgDbToTabOutShort) ||
sameString(argv[2], pgSnpKgDbToTabOutLong) ||
sameString(argv[2], pgSnpKgDbToGpFx) ||
sameString(argv[2], snpConsDbToTabOutShort) ||
sameString(argv[2], snpConsDbToTabOutLong) ||
sameString(argv[2], vcfEx1) ||
sameString(argv[2], vcfEx2) ||
sameString(argv[2], bigBedToTabOut) ||
sameString(argv[2], snpBigWigToTabOut) ||
sameString(argv[2], vepOut) ||
sameString(argv[2], gpFx))
test = cloneString(argv[2]);
else
{
warn("Unrecognized test name '%s'\n", argv[2]);
usage();
}
}
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
udcSetDefaultDir("./udcCache");
struct annoAssembly *assembly = getAnnoAssembly(db);
// First test: some rows of a pgSnp table
struct streamerInfo pgSnpInfo = { NULL, assembly, db, "pgNA12878", arWords, pgSnpAsObj() };
if (doAllTests || sameString(test, pgSnpDbToTabOut))
dbToTabOut(&pgSnpInfo, "stdout", "chr1", 705881, 752721, FALSE);
// Second test: some rows of a pgSnp table integrated with knownGene
struct streamerInfo kgInfo = { NULL, assembly, db, "knownGene", arWords,
asParseFile("../knownGene.as") };
pgSnpInfo.next = &kgInfo;
if (doAllTests || sameString(test, pgSnpKgDbToTabOutShort))
dbToTabOut(&pgSnpInfo, "stdout", "chr1", 705881, 752721, FALSE);
// Third test: all rows of a pgSnp table integrated with knownGene
if (doAllTests || sameString(test, pgSnpKgDbToTabOutLong))
dbToTabOut(&pgSnpInfo, "stdout", NULL, 0, 0, FALSE);
// Fourth test: some rows of snp135 integrated with phyloP scores
if (doAllTests || sameString(test, snpConsDbToTabOutShort) ||
sameString(test, snpConsDbToTabOutLong))
{
struct streamerInfo snp135Info = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
struct streamerInfo phyloPInfo = { NULL, assembly, db, "phyloP46wayPlacental", arWig, NULL };
snp135Info.next = &phyloPInfo;
if (sameString(test, snpConsDbToTabOutShort))
dbToTabOut(&snp135Info, "stdout", "chr1", 737224, 738475, FALSE);
else
dbToTabOut(&snp135Info, "stdout", NULL, 0, 0, FALSE);
}
// Fifth test: VCF with genotypes
if (doAllTests || sameString(test, vcfEx1))
{
#if (defined USE_TABIX && defined KNETFILE_HOOKS)
knetUdcInstall();
#endif//def USE_TABIX && KNETFILE_HOOKS
struct streamerInfo vcfEx1 = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz",
arWords, vcfAsObj() };
dbToTabOut(&vcfEx1, "stdout", NULL, 0, 0, FALSE);
}
if (doAllTests || sameString(test, vcfEx2))
{
struct streamerInfo vcfEx2 = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf",
arWords, vcfAsObj() };
dbToTabOut(&vcfEx2, "stdout", NULL, 0, 0, FALSE);
}
if (doAllTests || sameString(test, pgSnpKgDbToGpFx))
{
struct streamerInfo pg2SnpInfo = { NULL, assembly, NULL,
"input/annoGrator/pgForTestingGpFx.pgSnp.tab",
arWords, pgSnpAsObj() };
pg2SnpInfo.next = &kgInfo;
dbToTabOut(&pg2SnpInfo, "stdout", NULL, 0, 0, TRUE);
/*
FIXME
// 3base insertion CDS - chr3:124,646,699-124,646,718
dbToTabOut(&pg2SnpInfo, "stdout", "chr3",124646699,124646718, TRUE);
*/
}
if (doAllTests || sameString(test, bigBedToTabOut))
{
struct streamerInfo bigBedInfo = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb",
arWords, NULL };
dbToTabOut(&bigBedInfo, "stdout", "chr21", 34716800, 34733700, FALSE);
}
if (doAllTests || sameString(test, snpBigWigToTabOut))
{
struct streamerInfo snp135Info = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
struct streamerInfo bigWigInfo = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw",
arWig, NULL };
snp135Info.next = &bigWigInfo;
dbToTabOut(&snp135Info, "stdout", "chr21", 34716800, 34733700, FALSE);
}
if (doAllTests || sameString(test, vepOut))
{
struct streamerInfo vepSamplePgSnp = { NULL, assembly, NULL,
"input/annoGrator/vepSample.pgSnp.tab",
arWords, asParseFile("../pgSnp.as") };
struct streamerInfo kgInfo = { NULL, assembly, db, "ensGene", arWords,
asParseFile("../genePredExt.as") };
struct streamerInfo snpInfo = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
vepSamplePgSnp.next = &kgInfo;
kgInfo.next = &snpInfo;
// Instead of dbToTabOut, we need to make a VEP config data structure and
// use it to create an annoFormatVep.
struct streamerInfo *primaryInfo = &vepSamplePgSnp;
struct annoStreamer *primary = NULL;
struct annoGrator *gratorList = NULL;
sourcesFromInfoList(primaryInfo, TRUE, &primary, &gratorList);
struct annoStreamer *gpVarSource = (struct annoStreamer *)gratorList;
struct annoStreamer *snpSource = gpVarSource->next;
struct annoFormatter *vepOut = annoFormatVepNew("stdout", FALSE, primary, "vepSamplePgSnp",
gpVarSource, "UCSC Genes ...",
snpSource, "just dbSNP 135");
struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
annoGratorQuerySetRegion(query, "chr1", 876900, 886920);
annoGratorQueryExecute(query);
annoGratorQuerySetRegion(query, "chr5", 135530, 145535);
annoGratorQueryExecute(query);
annoGratorQueryFree(&query);
}
if (doAllTests || sameString(test, gpFx))
{
struct streamerInfo variants = { NULL, assembly, NULL,
"input/annoGrator/moreVariants.pgSnp.tab",
arWords, asParseFile("../pgSnp.as") };
struct streamerInfo kgInfo = { NULL, assembly, db, "knownGene", arWords,
asParseFile("../knownGene.as") };
struct streamerInfo snpInfo = { NULL, assembly, db, "snp137", arWords,
asParseFile("../snp132Ext.as") };
struct asObject *dbNsfpSeqChangeAs =
bigBedAsFromFileName("/gbdb/hg19/dbNsfp/dbNsfpSeqChange.bb");
struct streamerInfo dbNsfpSeqChange =
{ NULL, assembly, NULL, "/gbdb/hg19/dbNsfp/dbNsfpSeqChange.bb",
arWords, dbNsfpSeqChangeAs };
struct asObject *dbNsfpSiftAs = bigBedAsFromFileName("/gbdb/hg19/dbNsfp/dbNsfpSift.bb");
struct streamerInfo dbNsfpSift = { NULL, assembly, NULL, "/gbdb/hg19/dbNsfp/dbNsfpSift.bb",
arWords, dbNsfpSiftAs };
variants.next = &kgInfo;
kgInfo.next = &snpInfo;
snpInfo.next = &dbNsfpSeqChange;
dbNsfpSeqChange.next = &dbNsfpSift;
// Instead of dbToTabOut, we need to make a VEP config data structure and
// use it to create an annoFormatVep.
struct streamerInfo *primaryInfo = &variants;
struct annoStreamer *primary = NULL;
struct annoGrator *gratorList = NULL;
sourcesFromInfoList(primaryInfo, TRUE, &primary, &gratorList);
struct annoStreamer *gpVarSource = (struct annoStreamer *)gratorList;
struct annoStreamer *snpSource = gpVarSource->next;
struct annoStreamer *dbNsfpSource = snpSource->next->next;
struct annoFormatter *vepOut = annoFormatVepNew("stdout", FALSE, primary, "some more variants",
gpVarSource, "UCSC Genes of course",
snpSource, "now snp137.");
annoFormatVepAddExtraItem(vepOut, dbNsfpSource, "SIFT", "SIFT score from dbNSFP", "");
struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
annoGratorQuerySetRegion(query, "chr19", 45405960, 45419476);
annoGratorQueryExecute(query);
annoGratorQueryFree(&query);
}
return 0;
}
