// Simple sweep through the MultiAlignment columns, looking for columns to merge and removing null
// columns
//
// Loop over all columns. If we do not merge, advance to the next column, otherwise, stay here and
// merge to the now different next column (mergeCompatible removes the column that gets merged into
// the current column).
//
// Note that _firstColumn is never removed. The second column could be merged into the first,
// and the second one then removed.
void
abAbacus::mergeColumns(bool highQuality) {
assert(_firstColumn != NULL);
abColumn *column = _firstColumn;
bool somethingMerged = false;
assert(column->prev() == NULL);
#if 0
fprintf(stderr, "mergeColumns()--\n");
display(stderr);
#endif
// If we merge, update the base call, and stay here to try another merge of the now different
// next column. Otherwise, we didn't merge anything, so advance to the next column.
while (column->next()) {
if (column->mergeWithNext(this, highQuality) == true)
somethingMerged = true;
else
column = column->next();
}
// If any merges were performed, refresh. This updates the column list.
if (somethingMerged)
refreshColumns();
}
void
abAbacus::recallBases(bool highQuality) {
//fprintf(stderr, "abAbacus::recallBases()-- highQuality=%d\n", highQuality);
// Given that _firstColumn is a valid column, walk to the start of the column list.
// We could use _columns[] instead.
while (_firstColumn->_prevColumn != NULL)
_firstColumn = _firstColumn->_prevColumn;
// Number the columns, so we can make sure the _columns array has enough space. Probably not
// needed to be done first, but avoids having the resize call in the next loop.
for (abColumn *column = _firstColumn; column; column = column->next())
column->baseCall(highQuality);
// After calling bases, we need to refresh to copy the bases from each column into
// _cnsBases and _cnsQuals.
refreshColumns();
}
