Broad XX support, performance upgrades (#33)

* handle broad XX codes

* relshp file

* packaging

* performance

* performance code clinic

* gitignore and performance enhancements to pyard.py

* validate XX codes

* minor fix to XX validation

Author: mmaiers-nmdp

pyard/pyard.py

@@ -205,7 +205,7 @@ def __init__(self, dbversion: str='Latest',
             locusbroad="*".join([locus,broad])  
             for split in dictbroad[(locus,broad)]:
                 locussplit="*".join([locus,split])
-                if locusbroad in self.xxcodes.keys():
+                if locusbroad in self.xxcodes:
                     self.xxcodes[locusbroad].extend(self.xxcodes[locussplit])
                 else:
                     self.xxcodes[locusbroad] = self.xxcodes[locussplit]
@@ -444,7 +444,8 @@ def redux_gl(self, glstring: str, redux_type: str) -> str:
         loc_name, code = loc_allele[0], loc_allele[1]
 
         # handle XX codes
-        if(ismac(glstring) and glstring.split(":")[1] == "XX"):
+        # test that they are valid
+        if(ismac(glstring) and glstring.split(":")[1] == "XX") and loc_name in self.xxcodes:
             loc, n = loc_name.split("*")
             return self.redux_gl("/".join(sorted(self.xxcodes[loc_name], key=functools.cmp_to_key(smart_sort_comparator))), redux_type)