// If there has been significant progress, display it.
void printStatus(unsigned current_value)
{
if (current_value >= m_next_threshold)
{
m_next_threshold += m_percent_interval;
printPercent(current_value / static_cast<double>(m_max_value) * 100.);
}
if (current_value + 1 == m_max_value)
std::cout << " 100%" << std::endl;
}
void dupeFoo(char *pslName, char *faName, char *regionFile)
/* dupeFoo - Do some duplication analysis. */
{
struct lineFile *lf;
struct frag *fragList = NULL, *frag;
struct hash *fragHash = newHash(16);
struct psl *psl;
int fragCount=0,missCount=0,dupeCount=0,kSub=0,
k1=0, k10=0,k100=0,k1000=0,k10000=0,diffChrom=0,distance;
/* Read in fragment list and put it in hash. */
fragList = readFragList(faName);
for (frag = fragList; frag != NULL; frag = frag->next)
hashAdd(fragHash, frag->name, frag);
/* Read psl's and store under the fragment the belong to. */
lf = pslFileOpen(pslName);
while ((psl = pslNext(lf)) != NULL)
{
if ((frag = hashFindVal(fragHash, psl->qName)) == NULL)
errAbort("Couldn't find %s in %s line %d of %s",
psl->qName, faName, lf->lineIx, lf->fileName);
slAddHead(&frag->pslList, psl);
}
lineFileClose(&lf);
/* Look through fragments and report missing and dupes. */
for (frag = fragList; frag != NULL; frag = frag->next)
{
++fragCount;
if ((psl = frag->pslList) == NULL)
{
++missCount;
printf("missing %s\n", frag->name);
}
else
{
for (psl = frag->pslList; psl != NULL; psl = psl->next)
{
if (sameString(psl->tName, frag->chrom))
{
distance = frag->start - psl->tStart;
if (distance != 0)
{
if (distance < 0) distance = -distance;
if (distance >= 10000000) ++k10000;
else if (distance >= 1000000) ++k1000;
else if (distance >= 100000) ++k100;
else if (distance >= 10000) ++k10;
else if (distance >= 1000) ++k1;
else ++kSub;
}
}
else
{
++diffChrom;
}
}
}
}
printPercent("Total", fragCount, fragCount);
printPercent("Unaligned", missCount, fragCount);
printPercent("Other Chrom", diffChrom, fragCount);
printPercent("Same Chrom >10M", k10000, fragCount);
printPercent("Same Chrom >1M", k1000, fragCount);
printPercent("Same Chrom >10Ok", k100, fragCount);
printPercent("Same Chrom >1Ok", k10, fragCount);
printPercent("Same Chrom >1k", k1, fragCount);
printPercent("Self-overlap", kSub, fragCount);
writeRegions(fragList, regionFile);
}
