From 47706ce52831bfe599d654c28ca711bcee98a6d6 Mon Sep 17 00:00:00 2001
From: Danilo Horta <danilo.horta@gmail.com>
Date: Wed, 5 Jul 2017 16:49:28 +0100
Subject: [PATCH] Redundant covariates ok

---
 glimix_core/lmm/core.py          | 8 ++++++--
 glimix_core/lmm/test/test_lmm.py | 3 +++
 setup.py                         | 2 +-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/glimix_core/lmm/core.py b/glimix_core/lmm/core.py
index fba27ccd..850b82a1 100644
--- a/glimix_core/lmm/core.py
+++ b/glimix_core/lmm/core.py
@@ -2,7 +2,7 @@
 
 from numpy import dot, log, maximum, sqrt, zeros
 from numpy_sugar import epsilon
-from numpy_sugar.linalg import ddot, economic_svd, solve
+from numpy_sugar.linalg import ddot, economic_svd, rsolve, solve
 
 from .scan import FastScanner
 
@@ -23,6 +23,7 @@ def get_fast_scanner(self):
 
     @property
     def X(self):
+        # m = self.m
         return dot(self._svd[0], ddot(self._svd[1], self._svd[2], left=True))
 
     @X.setter
@@ -54,7 +55,10 @@ def _tbeta(self, value):
 
     @property
     def beta(self):
-        return solve(self._svd[2].T, self._tbeta / sqrt(self._svd[1]))
+        SVs = ddot(self._svd[0], sqrt(self._svd[1]), left=False)
+        z = rsolve(SVs, self.m)
+        VsD = ddot(sqrt(self._svd[1]), self._svd[2], left=True)
+        return rsolve(VsD, z)
 
     @beta.setter
     def beta(self, value):
diff --git a/glimix_core/lmm/test/test_lmm.py b/glimix_core/lmm/test/test_lmm.py
index 0b4b2d63..f1a569ba 100644
--- a/glimix_core/lmm/test/test_lmm.py
+++ b/glimix_core/lmm/test/test_lmm.py
@@ -113,6 +113,9 @@ def test_fastlmm_fast_scan_redundant():  # pylint: disable=R0914
         ],
         rtol=1e-5)
 
+    lmm.beta
+    pass
+
 
 def test_lmm_learn():
     random = RandomState(9458)
diff --git a/setup.py b/setup.py
index c7398625..4817b9cb 100644
--- a/setup.py
+++ b/setup.py
@@ -31,7 +31,7 @@ def setup_package():
 
     metadata = dict(
         name='glimix-core',
-        version='1.2.17',
+        version='1.2.18',
         maintainer="Limix Developers",
         maintainer_email="horta@ebi.ac.uk",
         license="MIT",