Fix

bed2npy.py

@@ -72,7 +72,7 @@ def convertPlink_inner(G, D, S, N):
 for c in tqdm(range(args.chunks), desc="Reading chunks"):
 	G_chunk = G[idx_split[c], :].compute().T
 	D[:, idx_split[c]] = convertPlink(G_chunk, args.t)
-	del G, G_chunk
+del G, G_chunk
 
 # Saving 8-bit integer matrix
 np.save(args.o, D)

flashpcangsd.py

@@ -178,8 +178,7 @@ def computeSVD(D, E, f, e, chunks, chunk_N, method, power):
 	for thread in threads:
 		thread.join()
 
-	U = None
-	return W, s
+	return W
 
 # Update E directly from SVD
 @jit("void(i1[:, :], f4[:, :], f4[:], f4[:, :], f4[:], f4[:, :], i8, i8)", nopython=True, nogil=True, cache=True)
@@ -300,13 +299,13 @@ def flashPCAngsd(D, f, e, K, F=None, Pvec=None, M=100, M_tole=1e-5, method="arpa
 		return V, s, U
 	else:
 		# Estimate initial individual allele frequencies
-		W, s = computeSVD(D, E, f, e, chunks, chunk_N, method, svd_iter)
+		W = computeSVD(D, E, f, e, chunks, chunk_N, method, svd_iter)
 		prevW = np.copy(W)
 		print "Individual allele frequencies estimated (1)"
 
 		# Iterative estimation of individual allele frequencies
 		for iteration in xrange(2, M+1):
-			W, s = computeSVD(D, E, f, e, chunks, chunk_N, method, svd_iter)
+			W = computeSVD(D, E, f, e, chunks, chunk_N, method, svd_iter)
 
 			# Break iterative update if converged
 			diff = rmse(W, prevW, chunks, chunk_N)
@@ -315,7 +314,7 @@ def flashPCAngsd(D, f, e, K, F=None, Pvec=None, M=100, M_tole=1e-5, method="arpa
 				print "Estimation of individual allele frequencies has converged."
 				break
 			prevW = np.copy(W)
-		del W, s, U, prevW
+		del W, prevW
 
 		# Estimate eigenvectors
 		print "Inferring final set of eigenvector(s)."