void doMiddle()
{
char *preIntron, *startIntron, *endIntron, *postIntron;
int count = 0;
int matchCount = 0;
int maxCount;
struct nameOff *matchList;
boolean invert = cgiVarExists("Invert");
preIntron = cgiString("preIntron");
startIntron = cgiString("startIntron");
endIntron = cgiString("endIntron");
postIntron = cgiString("postIntron");
/* Just for debugging cut search short if matches special magic */
maxCount = atoi(preIntron);
if (maxCount <= 0)
maxCount = 0x7ffffff;
eraseWhiteSpace(preIntron);
eraseWhiteSpace(startIntron);
eraseWhiteSpace(endIntron);
eraseWhiteSpace(postIntron);
tolowers(preIntron);
tolowers(startIntron);
tolowers(endIntron);
tolowers(postIntron);
matchList = scanIntronFile(preIntron, startIntron, endIntron, postIntron, invert);
if (matchList == NULL)
errAbort("Sorry, no matches to %s%s %s %s %s", (invert ? "inverted " : ""), preIntron, startIntron, endIntron, postIntron);
printf("<P>%d introns matching %s%s(%s %s)%s. ", slCount(matchList),
(invert ? "inverted " : ""), preIntron, startIntron, endIntron, postIntron);
printf("Shortcut to <A HREF=\"#1\">frequency counts.</A></P>");
htmlHorizontalLine();
showMatches(matchList);
htmlHorizontalLine();
printf("<TT><PRE>");
printf("<A NAME=\"1\"></A>");
printAllHistograms();
printf("</TT></PRE>");
}
int main(int argc, char *argv[])
{
FILE *xaFile;
struct xaAli *xa;
struct gapInfo *gapList = NULL, *gaps;
int count = 0;
long startTime = clock1000();
char *xaName, *newName;
char *first;
boolean cbFirst;
if (argc != 4)
usage();
first = argv[1];
xaName = argv[2];
newName = argv[3];
if (sameWord("elegans", first))
cbFirst = FALSE;
else if (sameWord("briggsae", first))
cbFirst = TRUE;
else
usage();
dnaUtilOpen();
intronHash = newHash(0);
out = mustOpen(newName, "w");
xaFile = mustOpen(xaName, "r");
while ((xa = xaReadNext(xaFile, FALSE)) != NULL)
{
char *s;
if (!cbFirst)
{
char *swaps;
int swapi;
char swapc;
uglyf("Swapping....\n");
swaps = xa->query;
xa->query = xa->target;
xa->target = swaps;
swapi = xa->qStart;
xa->qStart = xa->tStart;
xa->tStart = swapi;
swapi = xa->qEnd;
xa->qEnd = xa->tEnd;
xa->tEnd = swapi;
swapc = xa->qStrand;
xa->qStrand = xa->tStrand;
xa->tStrand = swapc;
swaps = xa->qSym;
xa->qSym = xa->tSym;
xa->tSym = swaps;
swapSym(xa->hSym, xa->symCount);
}
uglyf("%d query %s target %s\n", count, xa->query, xa->target);
s = chromFromPath(xa->target);
freeMem(xa->target);
xa->target = s;
if (++count % 500 == 0)
printf("Processing %d\n", count);
gaps = findLargeGaps(xa, gapList);
gapList = slCat(gaps, gapList);
xaAliFree(xa);
}
slReverse(&gapList);
report(out, "Processing took %f seconds\n", (clock1000()-startTime)*0.001);
reportGaps(gapList, out);
printAllHistograms(out);
calcCeHomoCount();
printHomologousEndStats(out);
printSameIntronStats(out);
return 0;
}
