2 files changed, 27 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index 28f2042d..bb4f5ace 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -21,10 +21,12 @@
 import sys
 import os
 import numpy as np
+from scipy import linalg
 import multiprocessing as mp # Multiprocessing is part of the Python stdlib
 import Queue
 import time
 
+
 from optmatrix import matrix_initialize, matrixMultT
 
 def kinship_full(G):
@@ -153,5 +155,23 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
    #    np.savetxt(outFile+".kve",Kve)
    return K      
 
+def kvakve(K, verbose=True):
+   """
+   Obtain eigendecomposition for K and return Kva,Kve where Kva is cleaned
+   of small values < 1e-6 (notably smaller than zero)
+   """
+   if verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
+   
+   Kva,Kve = linalg.eigh(K)
+   if verbose:
+      print("self.Kva is: ", Kva.shape, Kva)
+      print("self.Kve is: ", Kve.shape, Kve)
+
+   if sum(Kva < 1e-6):
+      if verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(Kva < 1e-6)))
+      Kva[Kva < 1e-6] = 1e-6
+   return Kva,Kve
+
+
 
 
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 1fa7a895..17fe952a 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -49,7 +49,7 @@ has_gn2=True
 
 from utility.benchmark import Bench
 from utility import temp_data
-from kinship import kinship, kinship_full
+from kinship import kinship, kinship_full, kvakve
 import genotype
 
 try:
@@ -532,11 +532,12 @@ class LMM:
        print("this K is:", K.shape, pf(K))
        
        if len(Kva) == 0 or len(Kve) == 0:
-          if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
-          begin = time.time()
-          Kva,Kve = linalg.eigh(K)
-          end = time.time()
-          if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
+          # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
+          # begin = time.time()
+          # Kva,Kve = linalg.eigh(K)
+          # end = time.time()
+          # if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
+          Kva,Kve = kvakve(K)
 
        self.K = K
        self.Kva = Kva