Debug: only output check on -debug

4 files changed, 18 insertions, 15 deletions

diff --git a/src/io.cpp b/src/io.cpp
index f5783cd..80adbe6 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -608,7 +608,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
                    const double &r2_level, map<string, string> &mapRS2chr,
                    map<string, long int> &mapRS2bp,
                    map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
-                   size_t &ns_test) {
+                   size_t &ns_test, bool debug) {
   indicator_snp.clear();
   snpInfo.clear();
 
@@ -679,10 +679,11 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
     }
 
     if (mapRS2bp.count(rs) == 0) {
-      std::string msg = "Can't figure out position for ";
-      msg += rs;
-      debug_msg(msg);
-
+      if (debug) {
+        std::string msg = "Can't figure out position for ";
+        msg += rs;
+        debug_msg(msg);
+      }
       chr = "-9";
       b_pos = -9;
       cM = -9;
@@ -1633,7 +1634,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
 // genotype and calculate K.
 bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
                    vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
-                   const bool calc_K) {
+                   const bool calc_K, bool debug) {
   igzstream infile(file_geno.c_str(), igzstream::in);
   if (!infile) {
     cout << "error reading genotype file:" << file_geno << endl;
@@ -1737,7 +1738,7 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
                    vector<int> &indicator_snp,
                    vector<vector<unsigned char>> &Xt, gsl_matrix *K,
                    const bool calc_K, const size_t ni_test,
-                   const size_t ns_test) {
+                   const size_t ns_test, bool debug) {
   igzstream infile(file_geno.c_str(), igzstream::in);
   if (!infile) {
     cout << "error reading genotype file:" << file_geno << endl;
diff --git a/src/io.h b/src/io.h
index 9edc5eb..d9253e3 100644
--- a/src/io.h
+++ b/src/io.h
@@ -64,7 +64,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
                    const double &r2_level, map<string, string> &mapRS2chr,
                    map<string, long int> &mapRS2bp,
                    map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
-                   size_t &ns_test);
+                   size_t &ns_test, bool debug);
 bool ReadFile_bed(const string &file_bed, const set<string> &setSnps,
                   const gsl_matrix *W, vector<int> &indicator_idv,
                   vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
@@ -94,7 +94,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
 
 bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
                    vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
-                   const bool calc_K);
+                   const bool calc_K, bool debug);
 bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
                   vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
                   const bool calc_K);
@@ -102,7 +102,7 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
                    vector<int> &indicator_snp,
                    vector<vector<unsigned char>> &Xt, gsl_matrix *K,
                    const bool calc_K, const size_t ni_test,
-                   const size_t ns_test);
+                   const size_t ns_test, bool debug);
 bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
                   vector<int> &indicator_snp, vector<vector<unsigned char>> &Xt,
                   gsl_matrix *K, const bool calc_K, const size_t ni_test,
diff --git a/src/param.cpp b/src/param.cpp
index c81eaf5..dce55e0 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -337,7 +337,7 @@ void PARAM::ReadFiles(void) {
     trim_individuals(indicator_cvt, ni_max, mode_debug);
     if (ReadFile_geno(file_geno, setSnps, W, indicator_idv, indicator_snp,
                       maf_level, miss_level, hwe_level, r2_level, mapRS2chr,
-                      mapRS2bp, mapRS2cM, snpInfo, ns_test) == false) {
+                      mapRS2bp, mapRS2cM, snpInfo, ns_test, mode_debug) == false) {
       error = true;
     }
     gsl_matrix_free(W);
@@ -445,7 +445,7 @@ void PARAM::ReadFiles(void) {
     while (!safeGetline(infile, file_name).eof()) {
       if (ReadFile_geno(file_name, setSnps, W, indicator_idv, indicator_snp,
                         maf_level, miss_level, hwe_level, r2_level, mapRS2chr,
-                        mapRS2bp, mapRS2cM, snpInfo, ns_test_tmp) == false) {
+                        mapRS2bp, mapRS2cM, snpInfo, ns_test_tmp, mode_debug) == false) {
         error = true;
       }
 
@@ -1338,7 +1338,7 @@ void PARAM::ReadGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_K) {
     }
   } else {
     if (ReadFile_geno(file_geno, indicator_idv, indicator_snp, UtX, K,
-                      calc_K) == false) {
+                      calc_K, mode_debug) == false) {
       error = true;
     }
   }
@@ -1358,7 +1358,7 @@ void PARAM::ReadGenotypes(vector<vector<unsigned char>> &Xt, gsl_matrix *K,
     }
   } else {
     if (ReadFile_geno(file_geno, indicator_idv, indicator_snp, Xt, K, calc_K,
-                      ni_test, ns_test) == false) {
+                      ni_test, ns_test, mode_debug) == false) {
       error = true;
     }
   }
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 67d9cba..9e49251 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -24,7 +24,8 @@ testBXDStandardRelatednessMatrixK() {
            -c ../example/BXD_covariates2.txt \
            -a ../example/BXD_snps.txt \
            -gk \
-           -debug -o $outn
+           -debug \
+           -o $outn
     assertEquals 0 $?
     outfn=output/$outn.cXX.txt
     assertEquals "198" `wc -l < $outfn`
@@ -38,6 +39,7 @@ testBXDMultivariateLinearMixedModel() {
            -a ../example/BXD_snps.txt \
            -k ./output/BXD.cXX.txt \
            -lmm 2 -maf 0.1 \
+           -debug \
            -o BXD_mvlmm
     assertEquals 0 $?