From cdd2c0e9b9f34e168dabfc1b3654658dcaa1cdee Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Tue, 13 Aug 2019 15:30:21 +0000 Subject: 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 --- .../files/patch-src_LDscoreCalibration.cpp | 24 ---------------------- 1 file changed, 24 deletions(-) delete mode 100644 biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp (limited to 'biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp') diff --git a/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp b/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp deleted file mode 100644 index 51a1ef896340..000000000000 --- a/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp +++ /dev/null @@ -1,24 +0,0 @@ ---- 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); -- cgit v1.2.3