int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, optionSpecs);
if (argc != 7)
{
usage();
}
tMasked = optionExists("tMasked");
chainToPsl(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6]);
return 0;
}
static struct chromBins* loadMapChains(char *chainFile)
/* read a chain file, convert to mapAln object and chromBins by query locations. */
{
struct chromBins* mapAlns = chromBinsNew((chromBinsFreeFunc*)pslFree);
struct chain *ch;
struct lineFile *chLf = lineFileOpen(chainFile, TRUE);
while ((ch = chainRead(chLf)) != NULL)
{
struct mapAln *mapAln = chainToPsl(ch);
chromBinsAdd(mapAlns, mapAln->psl->qName, mapAln->psl->qStart, mapAln->psl->qEnd, mapAln);
chainFree(&ch);
}
lineFileClose(&chLf);
return mapAlns;
}
