Attachment 206236 Details for Bug 239613 – patch

[patch] patch

bolt-lmm.patch (text/plain), 6.60 KB, created by Piotr Kubaj on 2019-08-03 12:47:49 UTC

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Creator: Piotr Kubaj

Created: 2019-08-03 12:47:49 UTC

Size: 6.60 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 507525)
>+++ Makefile	(working copy)
>@@ -25,6 +25,7 @@
> INSTALL_WRKSRC=	${WRKDIR}/${DISTNAME}/src
> CXXFLAGS_i386=	-DUSE_SSE -msse -msse2
> CXXFLAGS_amd64=	-DUSE_SSE
>+CXXFLAGS_powerpc64=	-DNO_WARN_X86_INTRINSICS -mvsx
> 
> PORTEXAMPLES=	*
> 
>Index: files/patch-src_Jackknife.cpp
>===================================================================
>--- files/patch-src_Jackknife.cpp	(nonexistent)
>+++ files/patch-src_Jackknife.cpp	(working copy)
>@@ -0,0 +1,13 @@
>+--- src/Jackknife.cpp.orig	2019-08-03 00:15:27 UTC
>++++ src/Jackknife.cpp
>+@@ -28,8 +28,8 @@ namespace Jackknife {
>+   using std::make_pair;
>+ 
>+   double stddev(const vector <double> &x, int n) {
>+-    for (int i = 0; i < n; i++) if (isnan(x[i])) return NAN;
>+-    for (int i = 0; i < n; i++) if (isinf(x[i])) return INFINITY;
>++    for (int i = 0; i < n; i++) if (std::isnan(x[i])) return NAN;
>++    for (int i = 0; i < n; i++) if (std::isinf(x[i])) return INFINITY;
>+     double s = 0.0, s2 = 0.0;
>+     for (int i = 0; i < n; i++) {
>+       s += x[i];
>
>Property changes on: files/patch-src_Jackknife.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-src_LDscoreCalibration.cpp
>===================================================================
>--- files/patch-src_LDscoreCalibration.cpp	(nonexistent)
>+++ files/patch-src_LDscoreCalibration.cpp	(working copy)
>@@ -0,0 +1,24 @@
>+--- src/LDscoreCalibration.cpp.orig	2019-08-03 00:18:05 UTC
>++++ src/LDscoreCalibration.cpp
>+@@ -201,8 +201,8 @@ namespace LDscoreCalibration {
>+ 	snps[m].MAF >= minMAF &&      // MAF threshold
>+ 	statsRef[m] > 0 &&            // ref stat available
>+ 	statsCur[m] > 0 &&            // cur stat available
>+-	!isnan(LDscores[m]) &&   // LD Score available
>+-	!isnan(LDscoresChip[m]); // LD Score weight available
>++	!std::isnan(LDscores[m]) &&   // LD Score available
>++	!std::isnan(LDscoresChip[m]); // LD Score weight available
>+     
>+     // perform outlier removal
>+     double outlierChisqThresh = std::max(MIN_OUTLIER_CHISQ_THRESH, N * outlierVarFracThresh);
>+@@ -256,8 +256,8 @@ namespace LDscoreCalibration {
>+       maskSnps[m] =
>+ 	snps[m].MAF >= minMAF &&      // MAF threshold
>+ 	stats[m] > 0 &&               // stat available
>+-	!isnan(LDscores[m]) &&   // LD Score available
>+-	!isnan(LDscoresChip[m]); // LD Score weight available
>++	!std::isnan(LDscores[m]) &&   // LD Score available
>++	!std::isnan(LDscoresChip[m]); // LD Score weight available
>+     
>+     // perform outlier removal
>+     double outlierChisqThresh = std::max(MIN_OUTLIER_CHISQ_THRESH, N * outlierVarFracThresh);
>
>Property changes on: files/patch-src_LDscoreCalibration.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-src_SnpData.cpp
>===================================================================
>--- files/patch-src_SnpData.cpp	(nonexistent)
>+++ files/patch-src_SnpData.cpp	(working copy)
>@@ -0,0 +1,20 @@
>+--- src/SnpData.cpp.orig	2019-08-03 00:23:17 UTC
>++++ src/SnpData.cpp
>+@@ -996,7 +996,7 @@ namespace LMM {
>+     for (int w = 0; w < W; w++)
>+       if (isProximal(m, mp, windows[w].first, windows[w].second)) {
>+ 	foundProximal = true;
>+-	if (!isnan(r2)) {
>++	if (!std::isnan(r2)) {
>+ 	  for (int a = 0; a < A; a++) {
>+ 	    double weight = pow((snps[mp].MAF * (1-snps[mp].MAF)), alphaMAFdeps[a]);
>+ 	    LDscores[w*A+a] += weight * r2;
>+@@ -1048,7 +1048,7 @@ namespace LMM {
>+       if (snps[mp].chrom != snps[m].chrom) {
>+ 	fillSnpRow(&mpRow[0], mp);
>+ 	double r2 = compute_r2(&mRow[0], &mpRow[0], Nstride);
>+-	if (!isnan(r2)) {
>++	if (!std::isnan(r2)) {
>+ 	  totOffChrom_r2s += r2;
>+ 	  numOffChrom_r2s++;
>+ 	}
>
>Property changes on: files/patch-src_SnpData.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-src_StatsUtils.cpp
>===================================================================
>--- files/patch-src_StatsUtils.cpp	(nonexistent)
>+++ files/patch-src_StatsUtils.cpp	(working copy)
>@@ -0,0 +1,13 @@
>+--- src/StatsUtils.cpp.orig	2019-08-03 00:24:37 UTC
>++++ src/StatsUtils.cpp
>+@@ -33,8 +33,8 @@ namespace StatsUtils {
>+     if (n <= 1) return NAN;
>+     double s = 0.0, s2 = 0.0;
>+     for (uint64 i = 0; i < n; i++) {
>+-      if (isnan(x[i])) return NAN;
>+-      if (isinf(x[i])) return INFINITY;
>++      if (std::isnan(x[i])) return NAN;
>++      if (std::isinf(x[i])) return INFINITY;
>+       s += x[i];
>+       s2 += x[i]*x[i];
>+     }
>
>Property changes on: files/patch-src_StatsUtils.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-src_Timer.cpp
>===================================================================
>--- files/patch-src_Timer.cpp	(nonexistent)
>+++ files/patch-src_Timer.cpp	(working copy)
>@@ -0,0 +1,22 @@
>+--- src/Timer.cpp.orig	2019-08-03 00:25:18 UTC
>++++ src/Timer.cpp
>+@@ -35,7 +35,19 @@ double Timer::update_time(void) {
>+ 
>+ unsigned long long Timer::rdtsc(void) {
>+   unsigned int hi, lo;
>++#ifdef __amd64__
>+   __asm__ __volatile__ ("rdtsc" : "=a"(lo), "=d"(hi));
>++#elif __powerpc__
>++  unsigned int tmp;
>++  __asm__ ("0:"
>++            "mftbu %[hi32]\n"
>++            "mftb %[lo32]\n"
>++            "mftbu %[tmp]\n"
>++            "cmpw %[tmp],%[hi32]\n"
>++            "bne 0b\n"
>++            : [hi32] "=r"(hi), [lo32] "=r"(lo),
>++            [tmp] "=r"(tmp));
>++#endif
>+   return ((unsigned long long) lo) | (((unsigned long long) hi)<<32);
>+ }
>+ 
>
>Property changes on: files/patch-src_Timer.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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pkubaj: maintainer-approval? (jwb)

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Attachments on bug 239613: 206236