diff --git a/src/0.deprecated/BayesCDom.jl b/src/0.deprecated/BayesCDom.jl index 30ebf07b..1af929d5 100644 --- a/src/0.deprecated/BayesCDom.jl +++ b/src/0.deprecated/BayesCDom.jl @@ -26,13 +26,13 @@ function sampleEffectsBayesCDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, markerM probDelta1::Float64 = 1.0/(1.0 + exp(logDelta0[1] - logDelta1)) if (rand() < probDelta1) a[j] = gHat + randn()*sqrt(invLhs) - BLAS.axpy!(olda-a[j],x,yCorr) - BLAS.axpy!(a[j],x,gj) + axpy!(olda-a[j],x,yCorr) + axpy!(a[j],x,gj) nAddEff = nAddEff + 1 δ[j,1] = 1 else if (δ[j,1]!=0) - BLAS.axpy!(olda,x,yCorr) + axpy!(olda,x,yCorr) end a[j] = 0 δ[j,1] = 0 @@ -52,13 +52,13 @@ function sampleEffectsBayesCDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, markerM probDelta1 = 1.0/(1.0 + exp(logDelta0[2] - logDelta1)) if (rand() < probDelta1) d[j] = gHat + randn()*sqrt(invLhs) - BLAS.axpy!(oldd-d[j],w,yCorr) - BLAS.axpy!(d[j],w,gj) + axpy!(oldd-d[j],w,yCorr) + axpy!(d[j],w,gj) nDomEff = nDomEff + 1 δ[j,2] = 1 else if (δ[j,2]!=0) - BLAS.axpy!(oldd,w,yCorr) + axpy!(oldd,w,yCorr) end d[j] = 0 δ[j,2] = 0 @@ -67,15 +67,15 @@ function sampleEffectsBayesCDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, markerM # estimate substitution effect by OLS if (a[j]!=0 && d[j]==0) α[j] = a[j] - BLAS.axpy!(1,gj,g) - BLAS.axpy!(1,gj,u) + axpy!(1,gj,g) + axpy!(1,gj,u) elseif (a[j]==0 && d[j]!=0) α[j] = 0 - BLAS.axpy!(1,gj,g) + axpy!(1,gj,g) elseif (a[j]!=0 && d[j]!=0) α[j] = dot(x,gj-mean(gj))/dot(x,x) - BLAS.axpy!(1,gj,g) - BLAS.axpy!(α[j],x,u) + axpy!(1,gj,g) + axpy!(α[j],x,u) else α[j] = 0 end @@ -235,4 +235,3 @@ function BayesCDom!(options,X,y,C,Rinv) return output end - diff --git a/src/0.deprecated/BayesCPiDom.jl b/src/0.deprecated/BayesCPiDom.jl index c4da3fba..351d8ef2 100644 --- a/src/0.deprecated/BayesCPiDom.jl +++ b/src/0.deprecated/BayesCPiDom.jl @@ -28,13 +28,13 @@ function sampleEffectsBayesCPiDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, marke probDelta1::Float64 = 1.0/(1.0 + exp(logDelta0[1] - logDelta1)) if (rand() < probDelta1) a[j] = gHat + randn()*sqrt(invLhs) - BLAS.axpy!(olda-a[j],x,yCorr) - BLAS.axpy!(a[j],x,gj) + axpy!(olda-a[j],x,yCorr) + axpy!(a[j],x,gj) nAddEff = nAddEff + 1 δ[j,1] = 1 else if (δ[j,1]!=0) - BLAS.axpy!(olda,x,yCorr) + axpy!(olda,x,yCorr) end a[j] = 0 δ[j,1] = 0 @@ -54,13 +54,13 @@ function sampleEffectsBayesCPiDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, marke probDelta1 = 1.0/(1.0 + exp(logDelta0[2] - logDelta1)) if (rand() < probDelta1) d[j] = gHat + randn()*sqrt(invLhs) - BLAS.axpy!(oldd-d[j],w,yCorr) - BLAS.axpy!(d[j],w,gj) + axpy!(oldd-d[j],w,yCorr) + axpy!(d[j],w,gj) nDomEff = nDomEff + 1 δ[j,2] = 1 else if (δ[j,2]!=0) - BLAS.axpy!(oldd,w,yCorr) + axpy!(oldd,w,yCorr) end d[j] = 0 δ[j,2] = 0 @@ -69,15 +69,15 @@ function sampleEffectsBayesCPiDom!(yCorr, nObs, nMarkers, xArray, XpRinvX, marke # estimate substitution effect by OLS if (a[j]!=0 && d[j]==0) α[j] = a[j] - BLAS.axpy!(1,gj,g) - BLAS.axpy!(1,gj,u) + axpy!(1,gj,g) + axpy!(1,gj,u) elseif (a[j]==0 && d[j]!=0) α[j] = 0 - BLAS.axpy!(1,gj,g) + axpy!(1,gj,g) elseif (a[j]!=0 && d[j]!=0) α[j] = dot(x,gj-mean(gj))/dot(x,x) - BLAS.axpy!(1,gj,g) - BLAS.axpy!(α[j],x,u) + axpy!(1,gj,g) + axpy!(α[j],x,u) else α[j] = 0 end @@ -224,4 +224,3 @@ function BayesCPiDom!(options,X,y,C,Rinv) return output end - diff --git a/src/0.deprecated/BayesN.jl b/src/0.deprecated/BayesN.jl index b73cee11..4490dc08 100644 --- a/src/0.deprecated/BayesN.jl +++ b/src/0.deprecated/BayesN.jl @@ -38,7 +38,7 @@ function sampleEffectsBayesN!(yCorr, nObs, nWindows, windows, windowSizes, xArra probDelta1 = 1.0/(1.0 + exp(logDelta0ToDelta1)) if (rand() < probDelta1) if (Δ[i]==0) - BLAS.axpy!(-1,windowEffect,yCorr) + axpy!(-1,windowEffect,yCorr) end Δ[i] = 1 π = (windowSizes[i] - k)/windowSizes[i] @@ -168,4 +168,3 @@ function BayesN!(options,X,y,C,Rinv) return output end - diff --git a/src/0.deprecated/MCMC_BayesCC.jl b/src/0.deprecated/MCMC_BayesCC.jl index 31e3fb47..8e9e5c5f 100644 --- a/src/0.deprecated/MCMC_BayesCC.jl +++ b/src/0.deprecated/MCMC_BayesCC.jl @@ -333,7 +333,7 @@ function sampleMarkerEffectsBayesCC!(xArray,xpx,wArray,alphaArray,meanAlphaArray # adjust for locus j for trait = 1:ntraits - BLAS.axpy!(oldu[trait]-newu[trait],x,wArray[trait]) + axpy!(oldu[trait]-newu[trait],x,wArray[trait]) meanAlphaArray[trait][j] += (α[trait] - meanAlphaArray[trait][j])/iIter meanDeltaArray[trait][j] += (δ[trait] - meanDeltaArray[trait][j])/iIter meanuArray[trait][j] += (newu[trait] - meanuArray[trait][j])/iIter diff --git a/src/0.deprecated/Tools.jl b/src/0.deprecated/Tools.jl index 05bca33c..919d504a 100644 --- a/src/0.deprecated/Tools.jl +++ b/src/0.deprecated/Tools.jl @@ -20,7 +20,7 @@ end function center!(X) nrow,ncol = size(X) colMeans = mean(X,1) - BLAS.axpy!(-1,ones(nrow)*colMeans,X) + axpy!(-1,ones(nrow)*colMeans,X) return colMeans end @@ -41,5 +41,3 @@ function get_dom_cov(x, n) # create dominance covariates from additive covariat end return w end - - diff --git a/src/1.JWAS/src/markers/BayesianAlphabet/BayesABC.jl b/src/1.JWAS/src/markers/BayesianAlphabet/BayesABC.jl index 002fa5bc..e0ccb1f9 100644 --- a/src/1.JWAS/src/markers/BayesianAlphabet/BayesABC.jl +++ b/src/1.JWAS/src/markers/BayesianAlphabet/BayesABC.jl @@ -40,10 +40,10 @@ function BayesABC!(xArray,xRinvArray,xpRinvx, δ[j] = 1 β[j] = gHat + randn()*sqrt(invLhs) α[j] = β[j] - BLAS.axpy!(oldAlpha-α[j],x,yCorr) + axpy!(oldAlpha-α[j],x,yCorr) else if (oldAlpha!=0) - BLAS.axpy!(oldAlpha,x,yCorr) + axpy!(oldAlpha,x,yCorr) end δ[j] = 0 β[j] = randn()*sqrt(varEffects[j]) diff --git a/src/1.JWAS/src/markers/BayesianAlphabet/BayesC0L.jl b/src/1.JWAS/src/markers/BayesianAlphabet/BayesC0L.jl index ad1f5770..949d2adb 100644 --- a/src/1.JWAS/src/markers/BayesianAlphabet/BayesC0L.jl +++ b/src/1.JWAS/src/markers/BayesianAlphabet/BayesC0L.jl @@ -42,6 +42,6 @@ function BayesL!(xArray,xRinvArray,xpRinvx, mean = invLhs*rhs oldAlpha = α[j] α[j] = mean + randn()*sqrt(invLhs*vRes) - BLAS.axpy!(oldAlpha-α[j],x,yCorr) + axpy!(oldAlpha-α[j],x,yCorr) end end diff --git a/src/1.JWAS/src/markers/BayesianAlphabet/MTBayesABC.jl b/src/1.JWAS/src/markers/BayesianAlphabet/MTBayesABC.jl index 1e4045a0..d9e86510 100644 --- a/src/1.JWAS/src/markers/BayesianAlphabet/MTBayesABC.jl +++ b/src/1.JWAS/src/markers/BayesianAlphabet/MTBayesABC.jl @@ -70,13 +70,13 @@ function MTBayesABC!(xArray,xRinvArray,xpRinvx, if(rand()