From 94160ddbb26904362b757376abd13f658d8fdaf1 Mon Sep 17 00:00:00 2001
From: Luca Venturini <lucventurini@gmail.com>
Date: Mon, 10 Jun 2019 10:50:25 +0100
Subject: [PATCH] Fix #181 and small bug fix for parsing Mikado annotations.

---
 Mikado/parsers/bed12.py        | 3 ++-
 Mikado/parsers/gfannotation.py | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/Mikado/parsers/bed12.py b/Mikado/parsers/bed12.py
index 4f0044ed5..2ef630437 100644
--- a/Mikado/parsers/bed12.py
+++ b/Mikado/parsers/bed12.py
@@ -500,7 +500,8 @@ def _adjust_start(self, sequence, orf_sequence):
                     self.phase = 0
             else:
                 if self.end - self.thick_end <= 2:
-                    self.phase = self.end - self.thick_end
+                    new_phase = max(self.end - self.thick_end, 0)
+                    self.phase = new_phase
                     self.thick_end = self.end
                 else:
                     self.phase = 0
diff --git a/Mikado/parsers/gfannotation.py b/Mikado/parsers/gfannotation.py
index 39b3b5387..61215c7ec 100644
--- a/Mikado/parsers/gfannotation.py
+++ b/Mikado/parsers/gfannotation.py
@@ -240,6 +240,8 @@ def is_gene(self):
             elif self.id is not None and self.id.startswith("gene:"):
                 # Hack for EnsEMBL
                 return True
+            elif self.feature in ("sublocus", "monosublocus", "monosublocusholder"):
+                return True
         return False
 
     @property