Cigar tools: improve semantics of "closest"

It is now based on op index.

micall/core/contig_stitcher.py

@@ -297,8 +297,10 @@ def covered(contig, gap):
     def gap_boundaries(gap):
         midpoint = gap.r_st + (gap.r_ei - gap.r_st) / 2
         left_slice, right_slice = contig.cut_reference(floor(midpoint) + 0.5)
-        left_closest_query = left_slice.alignment.coordinate_mapping.ref_to_closest_query(midpoint)
-        right_closest_query = right_slice.alignment.coordinate_mapping.ref_to_closest_query(midpoint)
+        left_midpoint_ref = left_slice.alignment.coordinate_mapping.find_closest_ref(midpoint)
+        left_closest_query = left_slice.alignment.coordinate_mapping.ref_to_closest_query(left_midpoint_ref)
+        right_midpoint_ref = right_slice.alignment.coordinate_mapping.find_closest_ref(midpoint)
+        right_closest_query = right_slice.alignment.coordinate_mapping.ref_to_closest_query(right_midpoint_ref)
         left_closest_ref = left_slice.alignment.coordinate_mapping.query_to_ref(left_closest_query)
         right_closest_ref = right_slice.alignment.coordinate_mapping.query_to_ref(right_closest_query)
         return (left_closest_ref, right_closest_ref)

micall/tests/test_cigar_tools.py

@@ -51,9 +51,9 @@
                {0: 0, 1: 1, 2: 2, 3: 3, 4: 3, 5: 3, 6: 4, 7: 4, 8: 5}),
 
     # Edge cases
-    ('', {}, ValueError()),
-    ('12I', {}, ValueError()),
-    ('12D', {}, ValueError()),
+    ('', {}, KeyError()),
+    ('12I', {}, KeyError()),
+    ('12D', {}, KeyError()),
 ]
 
 

micall/utils/cigar_tools.py

@@ -84,27 +84,40 @@ def query_to_ref(self, index) -> Optional[int]:
         return self.query_to_ref_d.get(index, None)
 
 
+    def ref_to_leftsup_query(self, index) -> Optional[int]:
+        left_neihbourhood = (k for (k, v) in self.query_to_ref_d.items() if v <= index)
+        return max(left_neihbourhood, default=None)
+
+
+    def ref_to_rightinf_query(self, index) -> Optional[int]:
+        right_neihbourhood = (k for (k, v) in self.query_to_ref_d.items() if index <= v)
+        return min(right_neihbourhood, default=None)
+
+
+    @staticmethod
+    def _find_closest(collection, value) -> int:
+        return min(collection, key=lambda x: abs(x - value))
+
+
     @staticmethod
     def _find_closest_key(mapping: dict, index: int) -> int:
         return min(mapping, key=lambda k: abs(mapping[k] - index))
 
 
-    def ref_to_closest_query(self, index) -> int:
-        return CoordinateMapping._find_closest_key(self.query_to_ref_d, index)
+    def find_closest_ref(self, index) -> int:
+        return CoordinateMapping._find_closest(self.all_reference_coordinates(), index)
 
 
-    def query_to_closest_ref(self, index) -> int:
-        return CoordinateMapping._find_closest_key(self.ref_to_query_d, index)
+    def find_closest_query(self, index) -> int:
+        return CoordinateMapping._find_closest(self.all_query_coordinates(), index)
 
 
-    def ref_to_leftsup_query(self, index) -> Optional[int]:
-        left_neihbourhood = (k for (k, v) in self.query_to_ref_d.items() if v <= index)
-        return max(left_neihbourhood, default=None)
+    def ref_to_closest_query(self, index) -> int:
+        return CoordinateMapping._find_closest_key(self.query_to_op_d, self.ref_to_op_d[index])
 
 
-    def ref_to_rightinf_query(self, index) -> Optional[int]:
-        right_neihbourhood = (k for (k, v) in self.query_to_ref_d.items() if index <= v)
-        return min(right_neihbourhood, default=None)
+    def query_to_closest_ref(self, index) -> int:
+        return CoordinateMapping._find_closest_key(self.ref_to_op_d, self.query_to_op_d[index])
 
 
     def ref_or_query_to_op(self, ref_index: int, query_index: int, conflict):