fixed counting

I wasn't chunking correctly. But now it's looking consistent
Also, I might have test coverage for cmd_exe keyboard interrupt

truvari/matching.py

@@ -314,17 +314,15 @@ def chunker(matcher, *files):
             call_counts['__filtered'] += 1
             continue
 
-        if entry.alleles_variant_types[1] == 'BND':
-            cur_chunk[f'{key}_BND'].append(entry)
-            continue
+        is_bnd = entry.alleles_variant_types[1] == 'BND'
 
-        if matcher.size_filter(entry, key=='base'):
+        if not is_bnd and matcher.size_filter(entry, key=='base'):
             cur_chunk['__filtered'].append(entry)
             call_counts['__filtered'] += 1
             continue
 
         # check symbolic, resolve if needed/possible
-        if matcher.params.pctseq != 0 and (entry.alleles_variant_types[-1] == 'BND' or entry.alts[0].startswith('<')):
+        if not is_bnd and matcher.params.pctseq != 0 and entry.alts[0].startswith('<'):
             was_resolved = resolve_sv(entry,
                                       matcher.reference,
                                       matcher.params.dup_to_ins)
@@ -348,7 +346,11 @@ def chunker(matcher, *files):
 
         cur_chrom = entry.chrom
         cur_end = max(entry.stop, cur_end)
-        cur_chunk[key].append(entry)
+
+        if is_bnd:
+            cur_chunk[f'{key}_BND'].append(entry)
+        else:
+            cur_chunk[key].append(entry)
         call_counts[key] += 1
 
     chunk_count += 1

truvari/utils.py

@@ -179,6 +179,8 @@ def cmd_exe(cmd, stdin=None, timeout=-1, cap_stderr=True, pipefail=False):
         >>> ret = truvari.cmd_exe("sleep 5", pipefail=True, timeout=2/60) # Error logged is caught
         >>> ret.ret_code
         214
+        >>> import truvari
+        >>> ret = truvari.cmd_exe("(sleep 1 && kill -SIGINT $$) &") # Keyboard Interruptable
     """
     cmd_result = namedtuple("cmd_result", "ret_code stdout stderr run_time")
     t_start = time.time()