From b42a02d02b3d9384b1da55bd091f0f89c808b626 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 20 Oct 2017 08:10:39 +0000
Subject: Travis-ci:

- Disabled gcc-6 since we develop with later tools anyway
- Turned the release test into a simple integration test
- Adding MacOSX on Travis-ci

Tests: Adding tests for Plink w. LOCO

Safety: Introduce strtok_safe to get rid of segfaults
---
 src/lmm.cpp | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

(limited to 'src/lmm.cpp')

diff --git a/src/lmm.cpp b/src/lmm.cpp
index e80cd76..ae8b747 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1197,16 +1197,16 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval,
   getline(infile, line);
 
   for (size_t t = 0; t < ng_total; t++) {
-    !safeGetline(infile, line).eof();
+    safeGetline(infile, line).eof();
     if (t % d_pace == 0 || t == ng_total - 1) {
       ProgressBar("Performing Analysis", t, ng_total - 1);
     }
-    ch_ptr = strtok((char *)line.c_str(), " , \t");
+    ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
     rs = ch_ptr;
 
     c_phen = 0;
     for (size_t i = 0; i < indicator_idv.size(); ++i) {
-      ch_ptr = strtok(NULL, " , \t");
+      ch_ptr = strtok_safe(NULL, " , \t");
       if (indicator_idv[i] == 0) {
         continue;
       }
@@ -1472,8 +1472,8 @@ void LMM::AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval,
     enforce_msg(ch_ptr, "Parsing BIMBAM genofile"); // ch_ptr should not be NULL
 
     auto snp = string(ch_ptr);
-    ch_ptr = strtok(NULL, " , \t"); // skip column
-    ch_ptr = strtok(NULL, " , \t"); // skip column
+    ch_ptr = strtok_safe(NULL, " , \t"); // skip column
+    ch_ptr = strtok_safe(NULL, " , \t"); // skip column
 
     gs.assign (ni_total,nan("")); // wipe values
 
@@ -1937,7 +1937,7 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval,
 
   // Start reading genotypes and analyze.
   for (size_t t = 0; t < indicator_snp.size(); ++t) {
-    !safeGetline(infile, line).eof();
+    safeGetline(infile, line).eof();
     if (t % d_pace == 0 || t == (ns_total - 1)) {
       ProgressBar("Reading SNPs", t, ns_total - 1);
     }
@@ -1945,16 +1945,16 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval,
       continue;
     }
 
-    ch_ptr = strtok((char *)line.c_str(), " , \t");
-    ch_ptr = strtok(NULL, " , \t");
-    ch_ptr = strtok(NULL, " , \t");
+    ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+    ch_ptr = strtok_safe(NULL, " , \t");
+    ch_ptr = strtok_safe(NULL, " , \t");
 
     x_mean = 0.0;
     c_phen = 0;
     n_miss = 0;
     gsl_vector_set_zero(x_miss);
     for (size_t i = 0; i < ni_total; ++i) {
-      ch_ptr = strtok(NULL, " , \t");
+      ch_ptr = strtok_safe(NULL, " , \t");
       if (indicator_idv[i] == 0) {
         continue;
       }
-- 
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