{AH} set pileup multiple_iterators to False for CRAM and warn, revert to True for others
@@ -2613,10 +2613,15 @@ cdef class IteratorColumnRegion(IteratorColumn):
int start = 0,
int stop = MAX_POS,
int truncate = False,
- int multiple_iterators = False,
+ int multiple_iterators = True,
**kwargs ):
- # initialize iterator
+ # initialize iterator. Multiple iterators not available
+ # for CRAM.
+ if multiple_iterators and samfile.is_cram:
+ warnings.warn("multiple_iterators not implemented for CRAM")
+ multiple_iterators = False
+
self._setup_iterator(tid, start, stop, multiple_iterators)
self.start = start
self.stop = stop
