int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(100000000);
if (argc != 2)
usage();
freen(argv[1]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(950000000);
optionInit(&argc, argv, options);
if (argc != 3)
usage();
mafCoverage(argv[1], argv[2], optionVal("restrict", NULL), optionInt("count",DEFCOUNT));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
pushCarefulMemHandler(100000000);
if (argc != 2)
usage();
test(atoi(argv[1]));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionHash(&argc, argv);
restrictFile = optionVal("restrict", NULL);
if (argc != 5)
usage();
pushCarefulMemHandler(1000*1000*1000);
ggcPic(argv[1], argv[2], argv[3], argv[4], optionVal("geneParts", NULL));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 4)
usage();
pushCarefulMemHandler(100000000);
initTrTable();
initLiteral();
jccTest(argv[1], argv[2], argv[3]);
printf("total mem used %ld\n", carefulTotalAllocated());
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(200000000);
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clDb = optionVal("db", clDb);
clOrg = optionVal("org", clOrg);
clSearch = optionVal("search", clSearch);
dataDir = optionVal("dataDir", dataDir);
clRepeat = optionInt("repeat", clRepeat);
/* Seed the random number generator. */
seed = optionInt("seed",time(NULL));
printf("seed=%d\n",seed);
srand(seed);
hgNearTest(argv[1], argv[2]);
carefulCheckHeap();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(500000000);
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clDb = optionVal("db", clDb);
clOrg = optionVal("org", clOrg);
clGroup = optionVal("group", clGroup);
clTrack = optionVal("track", clTrack);
clTable = optionVal("table", clTable);
clDbs = optionInt("dbs", clDbs);
clOrgs = optionInt("orgs", clOrgs);
clGroups = optionInt("groups", clGroups);
clTracks = optionInt("tracks", clTracks);
clTables = optionInt("tables", clTables);
appendLog = optionExists("appendLog");
if (clOrg != NULL)
clOrgs = BIGNUM;
hgTablesTest(argv[1], argv[2]);
carefulCheckHeap();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
pushCarefulMemHandler(100000000);
cgiSpoof(&argc, argv);
htmlSetStyle(htmlStyleUndecoratedLink);
htmlSetBgColor(HG_CL_OUTSIDE);
oldCart = hashNew(10);
cart = cartAndCookie(hUserCookie(), excludeVars, oldCart);
getDbAndGenome(cart, &database, &genome, oldCart);
//hSetDb(database);
conn = hAllocConn(database);
database = strdup("h1n1");
/* Get sortOn. Revert to default by subject Id. */
orderOn = cartUsualString(cart, orderVarName, "+subjId");
displayCountString = cartUsualString(cart, countVarName, "50");
if (sameString(displayCountString, "all"))
displayCount = BIGNUM;
else
displayCount = atoi(displayCountString);
colList = getColumns(conn);
if (cgiVarExists("submit_filter"))
{
struct dyString *head = dyStringNew(1024);
boolean redir = cgiVarExists(redirectName);
struct subjInfo *subjList = NULL;
struct column *ordList = colList;
struct column *ord = curOrder(ordList);
subjList = getOrderedList(ord, colList, conn, BIGNUM);
saveSubjList(subjList);
if ((!subjList || redir))
{
if (subjList && redir)
{
dyStringPrintf(head,
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"0;URL=/cgi-bin/%s\">"
"<META HTTP-EQUIV=\"Pragma\" CONTENT=\"no-cache\">"
"<META HTTP-EQUIV=\"Expires\" CONTENT=\"-1\">"
, cgiString(redirectName));
cartRemove(cart, redirectName);
}
htmStartWithHead(stdout, head->string, "GISAID Table View");
if (!subjList) /* if everything has been filtered out, we'll have to go back */
{
hPrintf("No subject(s) found with the filtering conditions specified.<br>");
hPrintf("Click <a href=\"gisaidTable?gisaidTable.do.advFilter=filter+%%28now+on%%29\">here</a> "
"to return to Select Subjects.<br>");
}
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
return 0;
}
}
htmStart(stdout, "GISAID Table View");
cartWarnCatcher(doMiddle, cart, htmlVaWarn);
cartCheckout(&cart);
htmlEnd();
hFreeConn(&conn);
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;
}