Cleaning dead code

Stray pieces formerly called by refactored code

truvari/bench.py

@@ -293,19 +293,6 @@ def calc_performance(self):
             self["gt_concordance"] = float(self["TP-comp_TP-gt"]) / (self["TP-comp_TP-gt"] +
                                                                      self["TP-comp_FP-gt"])
 
-    def clean_out(self):
-        """
-        When reusing a StatsBox (typically inside refine), gt numbers
-        are typically invalidated. This removes those numbers from self to make
-        a cleaner report
-        """
-        del self["TP-comp_TP-gt"]
-        del self["TP-comp_FP-gt"]
-        del self["TP-base_TP-gt"]
-        del self["TP-base_FP-gt"]
-        del self["gt_concordance"]
-        del self["gt_matrix"]
-
     def write_json(self, out_name):
         """
         Write stats as json to file

truvari/collapse.py

@@ -85,15 +85,6 @@ def gt_conflict(self, other, which_gt):
         self.genotype_mask |= o_mask
         return False
 
-    def combine(self, other):
-        """
-        Add other's calls/matches to self's matches
-        """
-        self.matches.extend(other.matches)
-        self.gt_consolidate_count += other.gt_consolidate_count
-        if self.genotype_mask is not None and other.genotype_mask is not None:
-            self.genotype_mask |= other.genotype_mask
-
 
 def find_new_matches(base, remaining_calls, dest_collapse, params):
     """
@@ -241,44 +232,6 @@ def collapse_into_entry(entry, others, hap_mode=False):
     return entry, n_consolidate
 
 
-def gt_conflict(cur_collapse, entry, which_gt):
-    """
-    Return true if entry's genotypes conflict with any of the current collapse
-    which_gt all prevents variants present in the same sample from being collapsed
-    which_gt het only prevents two het variants from being collapsed.
-    Might be deprecated, now?
-    """
-    if which_gt == 'off':
-        return False
-
-    def checker(base, comp):
-        """
-        Return true if a conflict
-        """
-        i = 0
-        samps = list(base.samples)
-        while i < len(samps):
-            sample = samps[i]
-            gtA = base.samples[sample].allele_indices
-            gtB = comp.samples[sample].allele_indices
-            if which_gt == 'all':
-                if 1 in gtA and 1 in gtB:
-                    return True
-            elif gtA.count(1) == 1 and gtB.count(1) == 1:
-                return True
-            i += 1
-        return False
-    # Need to check the kept entry
-    if checker(cur_collapse.entry, entry):
-        return True
-    # And all removed entries
-    for mat in cur_collapse.matches:
-        if checker(entry, mat.comp):
-            return True
-
-    return False
-
-
 def get_ac(gt):
     """
     Helper method to get allele count. assumes only 1s as ALT