diff options
Diffstat (limited to 'src/gemma_io.cpp')
| -rw-r--r-- | src/gemma_io.cpp | 11 |
1 files changed, 8 insertions, 3 deletions
diff --git a/src/gemma_io.cpp b/src/gemma_io.cpp index 45d1eb4..962e0c0 100644 --- a/src/gemma_io.cpp +++ b/src/gemma_io.cpp @@ -150,7 +150,7 @@ std::istream &safeGetline(std::istream &is, std::string &t) { // Read SNP file. A single column of SNP names. bool ReadFile_snps(const string file_snps, set<string> &setSnps) { - debug_msg("entered"); + debug_msg("enter ReadFile_snps"); setSnps.clear(); igzstream infile(file_snps.c_str(), igzstream::in); @@ -329,6 +329,9 @@ bool ReadFile_anno(const string &file_anno, map<string, string> &mapRS2chr, mapRS2bp[rs] = b_pos; mapRS2cM[rs] = cM; } + // for (auto& [key, value] : mapRS2bp) { + // cerr << key << endl; + //} infile.close(); infile.clear(); @@ -693,6 +696,9 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, file_pos = 0; auto count_warnings = 0; auto infilen = file_geno.c_str(); + // for (auto& [key, value] : mapRS2bp) { + // cerr << key << endl; + // } while (!safe_get_line(infile, line).eof()) { ch_ptr = strtok_safe2((char *)line.c_str(), " ,\t",infilen); rs = ch_ptr; @@ -714,8 +720,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps, if (mapRS2bp.count(rs) == 0) { if (is_debug_mode() && count_warnings++ < 10) { - std::string msg = "Can't figure out position for "; - msg += rs; + std::string msg = "Can't figure out position for <" + rs + ">"; debug_msg(msg); if (count_warnings == 10) debug_msg("Skipping similar warnings"); |