From 66c6bbfcbbd5fb23145ec09956f4809e5f701bec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 5 Jun 2019 13:01:36 -0500
Subject: Fixed issue that caused interval mapping to not work because the
 python implementation of the reaper Dataset object doesn't include the
 addinterval method (so for those situations I still use reaper)

Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
---
 wqflask/base/data_set.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b324ac74..1fd1792e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -384,7 +384,7 @@ class DatasetGroup(object):
         [result.extend(l) for l in lists if l]
         return result
 
-    def read_genotype_file(self):
+    def read_genotype_file(self, use_reaper=False):
         '''Read genotype from .geno file instead of database'''
         #genotype_1 is Dataset Object without parents and f1
         #genotype_2 is Dataset Object with parents and f1 (not for intercross)
@@ -396,9 +396,12 @@ class DatasetGroup(object):
             full_filename = str(locate(self.genofile, 'genotype'))
         else:
             full_filename = str(locate(self.name + '.geno', 'genotype'))
-        #genotype_1.read(full_filename)
 
-        genotype_1 = gen_geno_ob.genotype(full_filename)
+        if use_reaper:
+            genotype_1 = reaper.Dataset()
+            genotype_1.read(full_filename)
+        else:
+            genotype_1 = gen_geno_ob.genotype(full_filename)
 
         if genotype_1.type == "group" and self.parlist:
             genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1])       #, F1=_f1)
-- 
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