speed shortcuts

collapse - use available information to find out if a call can stop
being compared to its chunk early
bench - calculating all comparisons for every pair is useful for
ensuring full annotations are available on every compared call and
debugging and developers. But its slow. The `--short` option will
now stop comparing early and saves ~50% of bench runtime. This might
become the `--fullanno` option later.
matching - Don't pull alt '*' alleles.

truvari/bench.py

@@ -37,6 +37,8 @@ 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", 
+                        help="Short circuit comparisions. Faster, but fewer annotations")
     parser.add_argument("--debug", action="store_true", default=False,
                         help="Verbose logging")
 
@@ -751,7 +753,7 @@ def bench_main(cmdargs):
     matcher = truvari.Matcher(args)
 
     m_bench = Bench(matcher, args.base, args.comp, args.output,
-                    args.includebed, args.extend, args.debug, True)
+                    args.includebed, args.extend, args.debug, True, args.short)
     output = m_bench.run()
 
     logging.info("Stats: %s", json.dumps(output.stats_box, indent=4))

truvari/collapse.py

@@ -143,6 +143,10 @@ def collapse_chunk(chunk, matcher):
                 mat.state = False
             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 
+                # similar size. So the next one will only be worse...
+                break
 
         # Does this collap need to go into a previous collap?
         if not matcher.chain or not chain_collapse(m_collap, ret, matcher):

truvari/matching.py

@@ -155,7 +155,7 @@ def filter_call(self, entry, base=False):
         Returns True if the call should be filtered
         Base has different filtering requirements, so let the method know
         """
-        if self.params.check_monref and entry.alts is None:  # ignore monomorphic reference
+        if self.params.check_monref and entry.alts in (None, '*'):  # ignore monomorphic reference
             return True
 
         if self.params.check_multi and len(entry.alts) > 1: