From 38594c7781b587a24be14b9631a73662ee3fdc2b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 20 Mar 2015 12:18:03 +0300
Subject: Fall back on calculate_kinship_new again

---
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py    | 2 +-
 wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index c040e3c2..a649029c 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -277,7 +277,7 @@ def run_other_old(pheno_vector,
     print("Running the original LMM engine in run_other (old)")
     print("REML=",restricted_max_likelihood," REFIT=",refit)
     with Bench("Calculate Kinship"):
-        kinship_matrix,genotype_matrix = calculate_kinship_old(genotype_matrix, tempdata)
+        kinship_matrix,genotype_matrix = calculate_kinship_new(genotype_matrix, tempdata)
     
     print("kinship_matrix: ", pf(kinship_matrix))
     print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 6a38da56..88e2a033 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -184,7 +184,7 @@ elif cmd == 'kinship':
     gnt = None
 
     if options.test_kinship:
-        K = kinship_full(np.copy(G))
+        K = kinship_full(np.copy(G),uses)
         print "Genotype",G.shape, "\n", G
         print "first Kinship method",K.shape,"\n",K
         k1 = round(K[0][0],4)
-- 
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