def merge(self, other):
# type: (AlignmentStorage) -> AlignmentStorage
left_items = [(al, -1) for al in self]
right_items = [(al, 1) for al in other]
new_items = sorted(left_items + right_items, key = lambda (al, side): (al.seg_to.contig.id, al.seg_from.contig.id, al.seg_from.left))
new_storge = AlignmentStorage()
for (c_to, c_from), it in itertools.groupby(new_items, lambda al: (al[0].seg_to.contig, al[0].seg_from.contig)):
al_sides = list(it)
als_left = [al for al, side in al_sides if side == -1] # type: List[AlignmentPiece]
als_left = sorted(als_left, key = lambda al: al.seg_from.right)
als_right = [al for al, side in al_sides if side == 1] # type: List[AlignmentPiece]
als_right = sorted(als_right, key = lambda al: al.seg_from.left)
merged = []
for al in als_left:
for j in range(len(als_right)): # type: int
if als_right[j] is None:
continue
if als_right[j].seg_from.left >= al.seg_from.right:
break
if als_right[j] is not None and al.canMergeTo(als_right[j]):
tmp = AlignmentPiece.MergeOverlappingAlignments([al, als_right[j]])
if tmp is not None:
al = tmp
als_right[j] = None
break
merged.append(al)
new_storge.addAll(merged)
new_storge.addAll([al for al in als_right if al is not None])
return new_storge
def addAndMergeLeft(self, al):
# type: (AlignmentPiece) -> None
if self.isCanonical():
for i, al1 in enumerate(self.items): # type: int, AlignmentPiece
if al.seg_from.inter(al1.seg_from) and al.seg_to.inter(al1.seg_to) and al1.seg_from.left >= al.seg_from.left:
tmp = AlignmentPiece.MergeOverlappingAlignments([al, al1])
if tmp is not None:
self.items[i] = tmp
return
self.add(al)
else:
self.rc.addAndMergeRight(al.rc)
