biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream

1 files changed, 0 insertions, 20 deletions

diff --git a/biology/bolt-lmm/files/patch-src_SnpData.cpp b/biology/bolt-lmm/files/patch-src_SnpData.cpp
deleted file mode 100644
index 5763ee62879c..000000000000
--- a/biology/bolt-lmm/files/patch-src_SnpData.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- 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++;
- 	}