potential fix for #196

functional tests failed to hit chain collapse

truvari/bench.py

@@ -37,7 +37,7 @@ def parse_args(args):
                         help="Output directory")
     parser.add_argument("-f", "--reference", type=str, default=None,
                         help="Fasta used to call variants. Turns on reference context sequence comparison")
-    parser.add_argument("--short", action="store_true", 
+    parser.add_argument("--short", action="store_true",
                         help="Short circuit comparisions. Faster, but fewer annotations")
     parser.add_argument("--debug", action="store_true", default=False,
                         help="Verbose logging")

truvari/collapse.py

@@ -94,6 +94,15 @@ def gt_conflict(self, other, which_gt):
         self.genotype_mask |= o_mask
         return False
 
+    def consolidate(self, other):
+        """
+        Add other's calls/matches to self's matches
+        """
+        self.matches.append(other.entry)
+        self.matches.extend(other.matches)
+        self.gt_consolidate_count += other.gt_consolidate_count
+        if self.genotype_mask != "" and other.genotype_mask != "":
+            self.genotype_mask |= other.genotype_mask
 
 def chain_collapse(cur_collapse, all_collapse, matcher):
     """
@@ -144,7 +153,7 @@ def collapse_chunk(chunk, matcher):
             if mat.state:
                 m_collap.matches.append(mat)
             elif mat.sizesim is not None and mat.sizesim < matcher.params.pctsize:
-                # Can we do this? The sort tells us that we're going through most->least 
+                # Can we do this? The sort tells us that we're going through most->least
                 # similar size. So the next one will only be worse...
                 break