void HaploTree::SetupTraversal(IntArray & pointer, IntArray & state) const
{
pointer.Clear();
pointer.Push(0);
state.Dimension(depth);
state.Set(-1);
}
bool Pedigree::TwinCheck()
{
bool fail = false;
IntArray mzTwins;
for (int f = 0; f < familyCount; f++)
{
mzTwins.Clear();
for (int i = families[f]->first, j; i <= families[f]->last; i++)
// Is this person an identical twin?
if (persons[i]->isMzTwin( *persons[i] ))
{
// Have we got another identical sib yet?
for ( j = 0; j < mzTwins.Length(); j++)
if ( persons[i]->isMzTwin( *persons[mzTwins[j]] ) )
break;
// If not, add to list of twins
if (j == mzTwins.Length())
{
mzTwins.Push(i);
continue;
}
// Check that their genotypes are compatible and
// merge new twin's genotypes into original twin...
Person * original = persons[mzTwins[j]];
Person * twin = persons[i];
for (int m = 0; m < Person::markerCount; m++)
{
if (!original->markers[m].isKnown())
original->markers[m] = twin->markers[m];
else
if (twin->markers[m].isKnown() &&
twin->markers[m] != original->markers[m])
printf("MZ Twins %s and %s in family %s have "
"different %s genotypes\n",
(const char *) original->pid,
(const char *) twin->pid,
(const char *) original->famid,
(const char *) Person::markerNames[m]),
fail = true;
if (twin->sex != original->sex)
printf("MZ Twins %s and %s in family %s have "
"different sexes\n",
(const char *) original->pid,
(const char *) twin->pid,
(const char *) original->famid),
fail = true;
}
}
if (mzTwins.Length() == 0) continue;
// In the second pass we copy merged twin genotypes
// from original twin to other twins
for (int i = families[f]->first, j; i <= families[f]->last; i++)
if (persons[i]->isMzTwin( *persons[i] ))
{
for ( j = 0; j < mzTwins.Length(); j++)
if ( persons[i]->isMzTwin( *persons[mzTwins[j]] ) )
break;
if (mzTwins[j] == i) continue;
Person * original = persons[mzTwins[j]];
Person * twin = persons[i];
for (int m = 0; m < Person::markerCount; m++)
twin->markers[m] = original->markers[m];
}
}
return fail;
}
