void featureBits(char *database, int tableCount, char *tables[])
/* featureBits - Correlate tables via bitmap projections and booleans. */
{
struct sqlConnection *conn = NULL;
char *bedName = optionVal("bed", NULL), *faName = optionVal("fa", NULL);
char *binName = optionVal("bin", NULL);
char *bedRegionInName = optionVal("bedRegionIn", NULL);
char *bedRegionOutName = optionVal("bedRegionOut", NULL);
FILE *bedFile = NULL, *faFile = NULL, *binFile = NULL;
FILE *bedRegionOutFile = NULL;
struct bed *bedRegionList = NULL;
boolean faIndependent = FALSE;
struct chromInfo *cInfo;
if (bedName)
bedFile = mustOpen(bedName, "w");
if (binName)
binFile = mustOpen(binName, "w");
if ((bedRegionInName && !bedRegionOutName) || (!bedRegionInName && bedRegionOutName))
errAbort("bedRegionIn and bedRegionOut must both be specified");
if (faName)
{
boolean faMerge = optionExists("faMerge");
faFile = mustOpen(faName, "w");
if (tableCount > 1)
{
if (!faMerge)
errAbort("For fa output of multiple tables you must use the "
"faMerge option");
}
faIndependent = (!faMerge);
}
if (chromSizes != NULL)
chromInfoList = chromInfoLoadAll(chromSizes);
else
chromInfoList = fbCreateChromInfoList(clChrom, database);
if (!countGaps)
conn = hAllocConn(database);
checkInputExists(conn, database, chromInfoList, tableCount, tables);
if (!faIndependent)
{
double totalBases = 0, totalBits = 0;
int firstTableBits = 0, secondTableBits = 0;
int *pFirstTableBits = NULL, *pSecondTableBits = NULL;
double totalFirstBits = 0, totalSecondBits = 0;
static int dotClock = 1;
if (calcEnrichment)
{
pFirstTableBits = &firstTableBits;
pSecondTableBits = &secondTableBits;
}
if (bedRegionInName)
{
struct lineFile *lf = lineFileOpen(bedRegionInName, TRUE);
struct bed *bed;
char *row[3];
bedRegionOutFile = mustOpen(bedRegionOutName, "w");
while (lineFileRow(lf, row))
{
if (startsWith(row[0],"#")||startsWith(row[0],"chrom"))
continue;
bed = bedLoad3(row);
slAddHead(&bedRegionList, bed);
}
lineFileClose(&lf);
slReverse(&bedRegionList);
}
for (cInfo = chromInfoList; cInfo != NULL; cInfo = cInfo->next)
{
if (inclChrom(cInfo->chrom))
{
int chromBitSize;
int chromSize = cInfo->size;
verbose(3,"chromFeatureBits(%s)\n", cInfo->chrom);
chromFeatureBits(conn, database, cInfo->chrom, tableCount, tables,
bedFile, faFile, binFile, bedRegionList, bedRegionOutFile,
chromSize, &chromBitSize, pFirstTableBits, pSecondTableBits
);
totalBases += countBases(conn, cInfo->chrom, chromSize, database);
totalBits += chromBitSize;
totalFirstBits += firstTableBits;
totalSecondBits += secondTableBits;
if (dots > 0)
{
if (--dotClock <= 0)
{
fputc('.', stdout);
fflush(stdout);
dotClock = dots;
}
}
}
}
if (dots > 0)
{
fputc('\n', stdout);
fflush(stdout);
}
if (calcEnrichment)
fprintf(stderr,"%s %5.3f%%, %s %5.3f%%, both %5.3f%%, cover %4.2f%%, enrich %4.2fx\n",
tables[0],
100.0 * totalFirstBits/totalBases,
tables[1],
100.0 * totalSecondBits/totalBases,
100.0 * totalBits/totalBases,
100.0 * totalBits / totalFirstBits,
(totalBits/totalSecondBits) / (totalFirstBits/totalBases) );
else
fprintf(stderr,"%1.0f bases of %1.0f (%4.3f%%) in intersection\n",
totalBits, totalBases, 100.0*totalBits/totalBases);
}
else
{
int totalItems = 0;
double totalBases = 0;
int itemCount, baseCount;
for (cInfo = chromInfoList; cInfo != NULL; cInfo = cInfo->next)
{
if (inclChrom(cInfo->chrom))
{
chromFeatureSeq(conn, database, cInfo->chrom, tables[0],
bedFile, faFile, &itemCount, &baseCount);
totalBases += countBases(conn, cInfo->chrom, baseCount, database);
totalItems += itemCount;
}
}
}
hFreeConn(&conn);
}
void oneChrom(char *database, char *chrom, char *refAliTrack, char *bedTrack,
struct hash *otherHash, struct stats *stats)
/* Process one chromosome. */
{
struct bed *bedList = NULL, *bed;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
struct psl *pslList = NULL;
struct dnaSeq *chromSeq = NULL;
if (endsWith(bedTrack, ".bed"))
{
struct lineFile *lf = lineFileOpen(bedTrack, TRUE);
char *row[3];
while (lineFileRow(lf, row))
{
if (sameString(chrom, row[0]))
{
bed = bedLoad3(row);
slAddHead(&bedList, bed);
}
}
lineFileClose(&lf);
}
else
{
sr = hChromQuery(conn, bedTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoad3(row+rowOffset);
slAddHead(&bedList, bed);
}
sqlFreeResult(&sr);
}
slReverse(&bedList);
uglyf("Loaded beds\n");
sr = hChromQuery(conn, refAliTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row + rowOffset);
slAddHead(&pslList, psl);
binKeeperAdd(bk, psl->tStart, psl->tEnd, psl);
}
sqlFreeResult(&sr);
uglyf("Loaded psls\n");
chromSeq = hLoadChrom(database, chrom);
/* Fetch entire chromosome into memory. */
uglyf("Loaded human seq\n");
for (bed = bedList; bed != NULL; bed = bed->next)
{
struct binElement *el, *list = binKeeperFind(bk, bed->chromStart, bed->chromEnd);
for (el = list; el != NULL; el = el->next)
{
struct psl *fullPsl = el->val;
struct psl *psl = pslTrimToTargetRange(fullPsl,
bed->chromStart, bed->chromEnd);
if (psl != NULL)
{
foldPslIntoStats(psl, chromSeq, otherHash, stats);
pslFree(&psl);
}
}
slFreeList(&list);
stats->bedCount += 1;
stats->bedBaseCount += bed->chromEnd - bed->chromStart;
sqlFreeResult(&sr);
}
freeDnaSeq(&chromSeq);
pslFreeList(&pslList);
binKeeperFree(&bk);
hFreeConn(&conn);
}
