void bigWigInfo(char *fileName)
/* bigWigInfo - Print out information about bigWig file.. */
{
struct bbiFile *bwf = bigWigFileOpen(fileName);
if (optionExists("minMax"))
{
struct bbiSummaryElement sum = bbiTotalSummary(bwf);
printf("%f %f\n", sum.minVal, sum.maxVal);
return;
}
printf("version: %d\n", bwf->version);
printf("isCompressed: %s\n", (bwf->uncompressBufSize > 0 ? "yes" : "no"));
printf("isSwapped: %d\n", bwf->isSwapped);
printLabelAndLongNumber("primaryDataSize", bwf->unzoomedIndexOffset - bwf->unzoomedDataOffset);
if (bwf->levelList != NULL)
{
long long indexEnd = bwf->levelList->dataOffset;
printLabelAndLongNumber("primaryIndexSize", indexEnd - bwf->unzoomedIndexOffset);
}
printf("zoomLevels: %d\n", bwf->zoomLevels);
if (optionExists("zooms"))
{
struct bbiZoomLevel *zoom;
for (zoom = bwf->levelList; zoom != NULL; zoom = zoom->next)
printf("\t%d\t%d\n", zoom->reductionLevel, (int)(zoom->indexOffset - zoom->dataOffset));
}
struct bbiChromInfo *chrom, *chromList = bbiChromList(bwf);
printf("chromCount: %d\n", slCount(chromList));
if (optionExists("chroms"))
for (chrom=chromList; chrom != NULL; chrom = chrom->next)
printf("\t%s %d %d\n", chrom->name, chrom->id, chrom->size);
struct bbiSummaryElement sum = bbiTotalSummary(bwf);
printLabelAndLongNumber("basesCovered", sum.validCount);
printf("mean: %f\n", sum.sumData/sum.validCount);
printf("min: %f\n", sum.minVal);
printf("max: %f\n", sum.maxVal);
printf("std: %f\n", calcStdFromSums(sum.sumData, sum.sumSquares, sum.validCount));
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2)
usage();
fieldListIn = optionVal("fieldListIn", NULL);
fieldListOut = optionVal("fieldListOut", NULL);
identifier = optionVal("identifier", NULL);
database = optionVal("database", NULL);
checkFields = optionExists("fields");
foreignKeys = optionExists("keys");
dbCoverage = optionExists("dbCoverage");
tableCoverage = optionExists("tableCoverage");
checkTimes = optionExists("times");
if (optionExists("all"))
{
checkFields = foreignKeys = dbCoverage = tableCoverage = checkTimes = TRUE;
}
allDbHash = sqlHashOfDatabases();
if (database)
{
if (! hashLookup(allDbHash, database))
errAbort("specified database '%s' not available", database);
}
joinerCheck(argv[1]);
return 0;
}
CmdArgs::CmdArgs(int argc, char **argv) {
if(optionExists(argv, argv + argc, "--help"))
printHelpAndQuit(argc, argv);
if(argc < 4)
printErrorAndQuit(argc, argv);
// Parse positional arguments.
_input = argv[1];
_output = argv[2];
_numSamples = (int) strtol(argv[3], NULL, 10);
stop_if(_numSamples <= 0, "Number of samples must be > 0.");
// Init options with default values.
_width = 800;
_height = 600;
_aaLevel = 1; // No AA.
// Parse options.
if(optionExists(argv, argv + argc, "-w")) {
char *opt = getOption(argv, argv + argc, "-w");
if(!opt) printErrorAndQuit(argc, argv);
_width = (int) strtol(opt, NULL, 10);
}
if(optionExists(argv, argv + argc, "-h")) {
char *opt = getOption(argv, argv + argc, "-h");
if(!opt) printErrorAndQuit(argc, argv);
_height = (int) strtol(opt, NULL, 10);
}
if(optionExists(argv, argv + argc, "-aa")) {
char *opt = getOption(argv, argv + argc, "-aa");
if(!opt) printErrorAndQuit(argc, argv);
_aaLevel = (int) strtol(opt, NULL, 10);
stop_if(_aaLevel <= 0,
"Invalid anti aliasing level: must be > 0.");
}
}
int main(int argc, char *argv[])
/* Check parameters, set up, loop through each GenBank file. */
{
char *gbName;
int argi = 1;
struct hash *estAuthorHash = NULL;
char *pepFa;
optionInit(&argc, argv, optionSpecs);
if (argc < 4)
usage();
gByAccPrefixSize = optionInt("byAccPrefix", 0);
gbIdxName = optionVal("gbidx", NULL);
pepFa = optionVal("pepFa", NULL);
gbType = gbParseType(optionVal("type", "mrna,est"));
gbOrg = optionVal("org", NULL);
inclXMs = optionExists("inclXMs");
if (gByAccPrefixSize > 4) /* keep small to avoid tons of open files */
errAbort("max value of -byAccPrefix is 4");
gCurAccPrefix[0] = '\0';
faName = argv[argi++];
raName = argv[argi++];
estAuthorHash = newHash(23);
kvt = newKvt(5*1024);
gbfInit();
if (pepFa != NULL)
gPepFa = gbFaOpen(pepFa,"w");
char *blackList = optionVal("blackList", NULL);
if (blackList != NULL)
blackListRanges = genbankBlackListParse(blackList);
while (argi < argc)
{
gbName = argv[argi++];
printf("Processing %s into %s and %s\n", gbName, faName, raName);
procOneGbFile(gbName, estAuthorHash);
}
gbFaClose(&faFile);
gbFaClose(&gPepFa);
carefulClose(&raFile);
carefulClose(&gbIdxFile);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
workChr = optionVal("chr", NULL);
bedFileName = optionVal("bedFile", NULL);
insane = optionExists("insane");
minGap = optionInt("minGap", minGap);
gapToLift(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
boolean doGl = FALSE;
optionHash(&argc, argv);
if (argc != 4 && argc != 3)
usage();
noLoad = optionExists("noLoad");
if (noLoad)
verbose(2,"#\tnoLoad option, leaving SQL files, no table loading\n");
doGl = !(optionExists("noGl") || optionExists("nogl"));
if (argc == 3)
hgGoldGap(argv[1], argv[2]);
else
hgGoldGapGl(argv[1], argv[2], argv[3], doGl, optionVal("chrom", NULL));
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
clMaxErr = optionInt("maxErr", clMaxErr);
clSqlSymbols = optionExists("sqlSymbols");
if (!clSqlSymbols)
gReservedHash = sqlReservedHash();
tagStormCheck(argv[1], argv[2]);
return 0;
}
void alphaChain(char *readsFile, char *monomerOrderFile, char *outFile)
/* alphaChain - Create Markov chain of words and optionally output chain in two formats. */
{
struct wordStore *store = wordStoreForChainsInFile(readsFile, maxChainSize);
struct wordTree *wt = store->markovChains;
wordStoreLoadMonomerOrder(store, readsFile, monomerOrderFile);
wordStoreNormalize(store, outSize);
if (optionExists("chain"))
{
char *fileName = optionVal("chain", NULL);
wordTreeWrite(wt, store->maxChainSize, fileName);
}
wordTreeGenerateFile(store, store->maxChainSize, pickRandom(wt->children), outSize, outFile);
if (optionExists("afterChain"))
{
char *fileName = optionVal("afterChain", NULL);
wordTreeWrite(wt, store->maxChainSize, fileName);
}
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 6)
usage();
minSpace = optionInt("minSpace", minSpace);
minFill = optionInt("minFill", minSpace/2);
minScore = optionInt("minScore", minScore);
inclHap = optionExists("inclHap");
chainNet(argv[1], argv[2], argv[3], argv[4], argv[5]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 7)
usage();
geneName = optionVal("geneName", geneName);
geneList = optionVal("geneList", geneList);
onlyChrom = optionVal("chrom", onlyChrom);
inExons = optionExists("exons");
noTrans = optionExists("noTrans");
transUC = optionExists("transUC");
delay = optionInt("delay", delay);
if ((geneName != NULL) && (geneList != NULL))
errAbort("cannot specify both geneList and geneName");
mafToProtein(argv[1],argv[2],argv[3],argv[4],argv[5],argv[6]);
return 0;
}
void borfMatcher(char *bedIn, char *borfIn, char *bedOutFile, char *genePredOutFile)
/* Top level function to open files and call other functions. */
{
struct borf *borf = NULL, *borfList = NULL;
struct bed *bed = NULL, *bedList = NULL;
struct genePred *gp = NULL;
float threshold = optionFloat("minScore", 50);
FILE *bedOut = mustOpen(bedOutFile, "w");
FILE *genePredOut = mustOpen(genePredOutFile, "w");
boolean keepSmall = optionExists("keepSmall");
boolean keepNmd = optionExists("keepNmd");
borfList = borfLoadAll(borfIn);
bedList = bedLoadAll(bedIn);
dotForUserInit(slCount(bedList)/10);
for(bed = bedList, borf = borfList; bed != NULL && borf != NULL; bed = bed->next, borf = borf->next)
{
dotForUser();
if(!stringIn(bed->name, borf->name))
errAbort("Trying to match up %s bed with %s borf - bad idea!", bed->name, borf->name);
/* Have to adjust cds end. Borf puts stop codon outside of cds,
we put it inside. */
borf->cdsEnd = min(borf->cdsEnd+3, borf->size);
if((borf->score > threshold || (keepSmall && borf->cdsSize > 0)) && sameString(borf->strand, "+"))
{
setThickStartStop(bed, borf);
if(keepNmd || !nmdTarget(bed))
{
gp = bedToGenePred(bed);
bedTabOutN(bed, 12, bedOut);
genePredTabOut(gp, genePredOut);
genePredFree(&gp);
}
}
}
warn("Done.");
carefulClose(&bedOut);
carefulClose(&genePredOut);
}
void hgLoadSqlTab(char *database, char *table, char *createFile,
int inCount, char *inNames[])
/* hgLoadSqlTab - Load table into database from SQL and text files. */
{
struct sqlConnection *conn = sqlConnect(database);
int loadOptions = 0;
int i=0;
boolean oldTable = optionExists("oldTable") || optionExists("append");
if (optionExists("warn"))
loadOptions |= SQL_TAB_FILE_WARN_ON_ERROR;
if (! optionExists("notOnServer"))
loadOptions |= SQL_TAB_FILE_ON_SERVER;
if (! oldTable)
{
struct dyString *dy = readAndReplaceTableName(createFile, table);
sqlRemakeTable(conn, table, dy->string);
dyStringFree(&dy);
}
verbose(1, "Scanning through %d files\n", inCount);
for (i=0; i < inCount; i++)
{
verbose(2, "Loading file %s into table %s\n", inNames[i], table);
if (sameString("stdin", inNames[i]))
sqlLoadTabFile(conn, "/dev/stdin", table,
(loadOptions & ~SQL_TAB_FILE_ON_SERVER));
else
sqlLoadTabFile(conn, inNames[i], table, loadOptions);
}
if (oldTable)
hgHistoryComment(conn, "Add contents of %d text file(s) to table %s.",
inCount, table);
else
hgHistoryComment(conn, "Load table %s directly from .sql and %d text file(s).",
table, inCount);
sqlDisconnect(&conn);
}
int main(int argc, char *argv[])
/* Process command line. */
{
char *database, *accFile, *outFaFile;
optionInit(&argc, argv, optionSpecs);
if (argc != 4)
usage();
database = argv[1];
accFile = argv[2];
outFaFile = argv[3];
cdsUpper = optionExists("cdsUpper");
cdsUpperAll = optionExists("cdsUpperAll");
if (cdsUpperAll)
cdsUpper = TRUE;
inclVer = optionExists("inclVer");
peptides = optionExists("peptides");
if (peptides && (cdsUpper || cdsUpperAll))
errAbort("can't specify -peptides with -cdsUpper or -cdsUpperAll");
getRna(database, accFile, outFaFile);
return 0;
}
void doGenePreds(struct sqlConnection *conn, char *db, char *orthoDb, char *chrom,
char *netTable, char *geneFileName, char *geneTableName,
char *outBedName, char *selectedFileName, int *foundCount, int *notFoundCount)
/* Map over genePreds. */
{
FILE *bedOut = NULL;
FILE *selectedOut = NULL;
FILE *cdsErrorFp = NULL;
struct genePred *gene = NULL, *geneList = NULL;
struct bed *bed = NULL;
//init output files
if(optionExists("cdsErrorFile"))
{
cdsErrorFp = fopen( optionVal("cdsErrorFile", NULL), "w" );
fprintf( cdsErrorFp, "#name\tchrom\ttxStart\ttxEnd\tcdsStart\tcdsEnd\tstrand\texonCount\n" );
fclose(cdsErrorFp);
}
warn("Loading Gene Predictions.");
assert(outBedName);
if(geneFileName)
geneList=genePredLoadAll(geneFileName);
else
geneList=loadGeneFromTable(conn, geneTableName, chrom, 0, BIGNUM);
/* Convert genePreds. */
warn("Converting genes.");
bedOut = mustOpen(outBedName, "w");
if (selectedFileName != NULL)
selectedOut = mustOpen(selectedFileName, "w");
for(gene = geneList; gene != NULL; gene = gene->next)
{
struct genePred *synGene = NULL;
if(differentString(gene->chrom, chrom))
continue;
synGene = orthoBedFromGene(conn, db, orthoDb, netTable, gene);
occassionalDot();
if(synGene != NULL && synGene->exonCount > 0)
{
(*foundCount)++;
genePredTabOut(synGene, bedOut);
if (selectedOut != NULL)
genePredTabOut(gene, selectedOut);
}
else
(*notFoundCount)++;
genePredFree(&synGene);
}
carefulClose(&selectedOut);
carefulClose(&bedOut);
}
void weedLines(char *weedFile, char *file, char *output,
boolean invert, char *invertOutput)
/* weedLines - Selectively remove lines from file. */
{
struct hash *hash = hashWordsInFile(weedFile, 16);
struct hashEl *weedList = hashElListHash(hash);
verbose(2, "%d words in weed file %s\n", hash->elCount, weedFile);
struct lineFile *lf = lineFileOpen(file, TRUE);
char *line, *word;
FILE *f = mustOpen(output, "w");
FILE *fInvert = NULL;
boolean embedded = optionExists("embedded");
if (invertOutput != NULL)
fInvert = mustOpen(invertOutput, "w");
while (lineFileNext(lf, &line, NULL))
{
boolean doWeed = FALSE;
char *dupe = NULL;
if (embedded)
{
struct hashEl *hel;
for (hel = weedList; hel != NULL; hel = hel->next)
{
if (stringIn(hel->name, line))
doWeed = TRUE;
}
}
else
{
dupe = cloneString(line);
while ((word = nextWord(&line)) != NULL)
{
if (hashLookup(hash, word))
doWeed = TRUE;
}
line = dupe;
}
if (invert)
doWeed = !doWeed;
if (!doWeed)
fprintf(f, "%s\n", line);
else
{
if (fInvert != NULL)
fprintf(fInvert, "%s\n", line);
}
freez(&dupe);
}
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
maxGap = optionInt("maxGap", maxGap);
maxChain = optionInt("maxChain", maxChain);
minIdRatio = optionFloat("minId", 0.0)/100.0;
minScore = optionFloat("minScore", minScore);
bedOut = optionExists("bed");
if (argc != 5)
usage();
doIt(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
database = optionVal("database", database);
doAverage = optionExists("average");
transpose = optionExists("transpose");
minAbsVal = optionFloat("minAbsVal", minAbsVal);
minMaxVal = optionInt("minMaxVal", minMaxVal);
c = optionDouble("addConst", c);
clump = optionVal("clump", clump);
doLoad = !optionExists("noLoad");
if (optionExists("tab"))
{
tabDir = optionVal("tab", tabDir);
makeDir(tabDir);
}
limit = optionInt("limit", limit);
hgRatioMicroarray(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
struct hash *totals = NULL;
if (optionExists("total"))
totals = newHash(0);
char *hubUrl = NULL;
if (argc == 2)
hubUrl = argv[1];
else if (argc != 1)
usage();
return hubTrackSettings(hubUrl, totals);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 6)
usage();
raName = optionVal("raName", raName);
release = optionVal("release", release);
releaseBit = getReleaseBit(release);
adjustTrackDbName(argv[3]);
hgFindSpec(argv[1], argv[2], argv[3], argv[4], argv[5],
optionExists("strict"));
return 0;
}
int main(int argc, char *argv[])
{
optionInit(&argc, argv, optionSpecs);
if(argc < 2)
usage();
convolve_count = optionInt("count", 4);
logs = optionExists("logs");
html = optionExists("html");
if (verboseLevel() >= 2)
{
printf("options: -verbose, input file(s):\n");
printf("-count=%d\n", convolve_count);
printf("data input is in %s format\n", logs ? "log" : "probability");
if (html) printf ("output in html format\n");
}
convolve(argc, argv);
return(0);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc < 3)
usage();
if (optionExists("clampMax"))
{
gotClampMax = TRUE;
clampMax = optionDouble("clampMax", clampMax);
}
wigCorrelate(argc-1, argv+1, "stdout");
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
database = optionVal("database", database);
chip = optionVal("chip", chip);
doLoad = !optionExists("noLoad");
noRound = optionExists("noRound");
chopName = optionVal("chopName", chopName);
expUrl = optionVal("url", expUrl);
expRef = optionVal("ref", expRef);
expCredit = optionVal("credit", expCredit);
if (optionExists("tab"))
{
tabDir = optionVal("tab", tabDir);
makeDir(tabDir);
}
limit = optionInt("limit", limit);
if (argc != 4)
usage();
hgGnfMicroarray(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct tm *tm;
if (argc < 2)
usage();
optionInit(&argc, argv, options);
if (!optionExists("age"))
{
verbose(1,"ERROR: must specify an age argument, e.g.: -age=8\n");
usage();
}
if (time(&timeNow) < 1)
errAbort("can not obtain current time via time() function\n");
tm = localtime(&timeNow);
ageHours = optionFloat("age", 0.0);
time_t ageSeconds = (time_t)(ageHours * 3600); /* age in seconds */
dropTime = timeNow - ageSeconds;
if (ageHours > 0.0)
{
verbose(2,"# specified age = %f hours = %ld seconds\n", ageHours,
(unsigned long)ageSeconds);
verbose(2,"# current time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)timeNow);
tm = localtime(&dropTime);
verbose(2,"# drop time: %d-%02d-%02d %02d:%02d:%02d %ld\n",
1900+tm->tm_year, 1+tm->tm_mon, tm->tm_mday,
tm->tm_hour, tm->tm_min, tm->tm_sec, (unsigned long)dropTime);
}
else
{
verbose(1,"ERROR: specified age %.f must be greater than 0.0\n", ageHours);
usage();
}
drop = optionExists("drop");
historyToo = optionExists("historyToo");
db = optionVal("db",db);
extFileCheck = optionExists("extFile");
extDel = optionExists("extDel");
tableStatus = optionExists("tableStatus");
topDir = optionVal("topDir", topDir);
verbose(2,"# drop requested: %s\n", drop ? "TRUE" : "FALSE");
verbose(2,"# historyToo: %s\n", historyToo ? "TRUE" : "FALSE");
verbose(2,"# extFile: %s\n", extFileCheck ? "TRUE" : "FALSE");
verbose(2,"# extDel: %s\n", extDel ? "TRUE" : "FALSE");
verbose(2,"# tableStatus: %s\n", tableStatus ? "TRUE" : "FALSE");
verbose(2,"# topDir: %s\n", topDir);
verbose(2,"# database: %s\n", db);
dbTrash(db);
if (verboseLevel() > 1)
printVmPeak();
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
warn("Program obsolete - try using alphaAsm instead");
optionInit(&argc, argv, options);
if (argc != 4)
usage();
maxChainSize = optionInt("size", maxChainSize);
outSize = optionInt("outSize", outSize);
fullOnly = optionExists("fullOnly");
int seed = optionInt("seed", (int)time(0));
srand(seed);
alphaChain(argv[1], argv[2], argv[3]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
ref = optionVal("ref", ref);
number = optionExists("number");
segSplitPairwise(argv[1], argv[2]);
return(EXIT_SUCCESS);
}
int main(int argc, char* argv[])
{
optionInit(&argc, argv, options);
if (argc != 3)
usage();
char *cdsFile = optionVal("cds", NULL);
bool doPosName = optionExists("posName");
struct hash *cdsHash = NULL;
if (cdsFile != NULL)
cdsHash = getCdsHash(cdsFile);
pslToBed(argv[1], argv[2], cdsHash, doPosName);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
test = optionExists("test");
mergeGap = optionInt("mergeGap", mergeGap);
minSize = optionInt("minSize", minSize);
maxSize = optionInt("maxSize", maxSize);
minSeqSize = optionInt("minSeqSize", minSeqSize);
if (argc != 4)
usage();
database = argv[1];
hgLoadMafSummary(database, argv[2], argv[3]);
return 0;
}
void paraTestJob(char *countString)
/* paraTestJob - A good test job to run on Parasol. Can be configured to take a long time or crash. */
{
int i, count = atoi(countString);
char *outName = optionVal("output", NULL);
int heavy = optionInt("heavy", 0);
FILE *f = NULL;
if (optionExists("input"))
countLines(optionVal("input", NULL));
if (outName != NULL)
f = mustOpen(outName, "w");
for (i=0; i<count; ++i)
{
compute();
if (f != NULL)
{
int j;
fprintf(f, "Computation number %d of %d. Error so far is %f\n",
i+1, count, cumErr);
for (j=0; j<heavy; ++j)
{
fprintf(f, " I'm a lumberjack and I'm ok. I work all night and I sleep all day\n");
}
}
}
printf("Cumulative error %f\n", cumErr);
if (optionExists("sleep"))
sleep(optionInt("sleep", 1));
if (optionExists("err"))
errAbort("Aborting with error");
if (optionExists("crash"))
{
char *s = NULL;
s[0] = 0;
}
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && argc != 3)
usage();
restrictFile = optionVal("restrict", restrictFile);
threshold = optionDouble("threshold", threshold);
rootNames = optionExists("rootNames");
if (argc == 3)
bigWigCorrelatePair(argv[1], argv[2]);
else
bigWigCorrelateList(argv[1]);
return 0;
}
void testIntersect(char *db, char *track1, char *track2)
/* testIntersect - Test some ideas on intersections. */
{
struct slName *chromList = NULL, *chrom;
struct sqlConnection *conn;
hSetDb(db);
if (optionExists("chrom"))
chromList = slNameNew(optionVal("chrom", NULL));
else
chromList = hAllChromNames();
conn = hAllocConn();
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
intersectOnChrom(db, conn, chrom->name, track1, track2);
hFreeConn(&conn);
}
