cut genome names after 10 characters, replace nan with 1.0 in distance matrices

src/nejo_idx.py

@@ -43,6 +43,9 @@ class NeighborJoining:
       for j in range(0,i):
         if i < self._num_of_taxa:
           dist = dm.distance(i,j)
+          #for andi:
+          if str(dist) in ["nan"]:
+            dist = 1.0
           assert dist >= 0
         else:
           dist = None

src/parser.py

@@ -31,6 +31,9 @@ def parse_command_line():
                        "NJ-tree (derived from the distances delivered by\n"
                        "the corresponding tool) will be compared to the\n"
                        "reference tree.\n"
+                       "The genome names will be cut to 10 characters. \n"
+                       "The reference tree must contain the \n"
+                       "exact genome names resulting\n"
                        "For datafiles without reference and if at least\n"
                        "two tools have been specified, the resulting\n"
                        "NJ-trees are compared against each other."