Cigar tools: rename "gaps()" to "deletions()"

Author: Donaim

micall/core/contig_stitcher.py

@@ -590,7 +590,7 @@ def significant(gap):
         return gap.ref_length > 5
 
     def try_split(contig):
-        for gap in contig.alignment.gaps():
+        for gap in contig.alignment.deletions():
             if not significant(gap):
                 # Really we do not want to split on every little deletion
                 # because that would mean that we would need to stitch

micall/tests/test_cigar_tools.py

@@ -451,7 +451,7 @@ def test_cigar_hit_ref_cut_add_associativity(hit, cut_point):
                                  if not isinstance(x[2], Exception)])
 def test_cigar_hit_gaps_no_m_or_i(hit):
     hit = parsed_hit(hit)
-    gaps = list(hit.gaps())
+    gaps = list(hit.deletions())
 
     if 'D' in str(hit.cigar):
         assert len(gaps) > 0
@@ -465,7 +465,7 @@ def test_cigar_hit_gaps_no_m_or_i(hit):
                                  if not isinstance(x[2], Exception)])
 def test_cigar_hit_gaps_lengths(hit):
     hit = parsed_hit(hit)
-    gaps = list(hit.gaps())
+    gaps = list(hit.deletions())
 
     for gap in gaps:
         assert gap.query_length == 0

micall/tests/test_contig_stitcher.py

@@ -502,12 +502,12 @@ def test_stitching_contig_with_big_covered_gap(exact_aligner, visualizer):
 
     contigs = list(align_all_to_reference(contigs))
     assert len(contigs) == 2
-    assert len(list(contigs[0].alignment.gaps())) == 1
-    assert len(list(contigs[1].alignment.gaps())) == 0
+    assert len(list(contigs[0].alignment.deletions())) == 1
+    assert len(list(contigs[1].alignment.deletions())) == 0
 
     results = list(split_contigs_with_gaps(contigs))
     assert len(results) == 3
-    assert all(list(contig.alignment.gaps()) == [] for contig in results)
+    assert all(list(contig.alignment.deletions()) == [] for contig in results)
 
     assert len(visualizer().elements) > len(contigs)
 
@@ -536,8 +536,8 @@ def test_stitching_contig_with_small_covered_gap(exact_aligner, visualizer):
 
     contigs = list(align_all_to_reference(contigs))
     assert len(contigs) == 2
-    assert len(list(contigs[0].alignment.gaps())) == 1
-    assert len(list(contigs[1].alignment.gaps())) == 0
+    assert len(list(contigs[0].alignment.deletions())) == 1
+    assert len(list(contigs[1].alignment.deletions())) == 0
     results = list(split_contigs_with_gaps(contigs))
     assert len(results) == 3
 

micall/utils/cigar_tools.py

@@ -520,7 +520,7 @@ def touches(self, other) -> bool:
            and self.q_ei + 1 == other.q_st
 
 
-    def gaps(self) -> Iterable['CigarHit']:
+    def deletions(self) -> Iterable['CigarHit']:
         # TODO(vitalik): memoize whatever possible.
 
         covered_coordinates = self.coordinate_mapping.ref_to_query.keys()