void xaAliFreeList(struct xaAli **pXa)
/* Free up a list of xaAlis. */
{
struct xaAli *xa, *next;
for (xa = *pXa; xa != NULL; xa = next)
{
next = xa->next;
xaAliFree(xa);
}
*pXa = NULL;
}
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;
}
