void whyConserved(char *database, char *chrom, char *homologyTrack)
/* whyConserved - Try and analyse why a particular thing is conserved. */
{
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
conn = hAllocConn(database);
chromSize = hChromSize(database, chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(database, h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "mus", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "mus", "mus", "mus");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(database, h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "sanger22:CDS", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "refGene:CDS", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "est", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "intronEst:exon", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "blatMouse:exon", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "xenoMrna:exon", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "xenoEst:exon", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "genscan:exon", NULL);
explainSome(database, h**o, once, bits, chrom, chromSize, conn, "exoFish", NULL);
hFreeConn(&conn);
}
void trackOverlap(char *database, char *chrom, char *homologyTrack, char *specFile)
/* trackOverlap - Correlate a track with a series of tracks specified in specFile. */
{
struct lineFile *lf = NULL;
char *line = NULL;
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
lf = lineFileOpen(specFile, TRUE);
conn = hAllocConn(database);
chromSize = hChromSize(database, chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(database, h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "cov", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "cov", "cov", "cov");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(database, h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
while(lineFileNextReal(lf, &line))
{
explainSome(database, h**o, once, bits, chrom, chromSize, conn, line, NULL);
}
lineFileClose(&lf);
hFreeConn(&conn);
}
