Fixed popmap loading bugs. Small cleanup to logs format

src/main.cpp

@@ -34,7 +34,7 @@ inline Parameters parse_args(int& argc, char** argv) {
     distrib->add_option("-p,--popmap", parameters.popmap_file_path, "Path to a tabulated file specifying groups for all individuals (population map)")->required()->check(CLI::ExistingFile);
     distrib->add_option("-o,--output-file", parameters.output_file_path, "Path to the output file (distribution of markers between groups)")->required();
     distrib->add_option("-d,--min-depth", parameters.min_depth, "Minimum depth to consider a marker present in an individual", true)->check(CLI::Range(1, 9999));
-    distrib->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)");
+    distrib->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)")->delimiter(',');
     distrib->add_option("-S,--signif-threshold", parameters.signif_threshold, "P-value threshold to consider a marker significantly associated with a phenotypic group", true)->check(CLI::Range(0.0, 1.0));
     distrib->add_flag("-C,--disable-correction", parameters.disable_correction, "If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group");
     distrib->add_flag("-x,--output-matrix", parameters.output_matrix, "If set, the distribution will be output as a matrix instead of a table");
@@ -52,7 +52,7 @@ inline Parameters parse_args(int& argc, char** argv) {
     map->add_option("-p,--popmap", parameters.popmap_file_path, "Path to a tabulated file specifying groups for all individuals (population map)")->required()->check(CLI::ExistingFile);
     map->add_option("-g,--genome-file", parameters.genome_file_path, "Path to the genome file in fasta format")->required()->check(CLI::ExistingFile);
     map->add_option("-d,--min-depth", parameters.min_depth, "Minimum depth to consider a marker present in an individual", true)->check(CLI::Range(1, 9999));
-    map->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)");
+    map->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)")->delimiter(',');
     map->add_option("-q,--min-quality", parameters.map_min_quality, "Minimum mapping quality to retain a read", true)->check(CLI::Range(0, 60));
     map->add_option("-Q,--min-frequency", parameters.map_min_frequency, "Minimum frequency of individuals to retain a marker", true)->check(CLI::Range(0.0, 1.0));
     map->add_option("-S,--signif-threshold", parameters.signif_threshold, "P-value threshold to consider a marker significantly associated with a phenotypic group", true)->check(CLI::Range(0.0, 1.0));
@@ -71,7 +71,7 @@ inline Parameters parse_args(int& argc, char** argv) {
     signif->add_option("-p,--popmap", parameters.popmap_file_path, "Path to a tabulated file specifying groups for all individuals (population map)")->required()->check(CLI::ExistingFile);
     signif->add_option("-o,--output-file", parameters.output_file_path, "Path to the output file (marker depths table or fasta file for markers significantly associated with phenotypic group)")->required();
     signif->add_option("-d,--min-depth", parameters.min_depth, "Minimum depth to consider a marker present in an individual", true)->check(CLI::Range(1, 9999));
-    signif->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)");
+    signif->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)")->delimiter(',');
     signif->add_option("-S,--signif-threshold", parameters.signif_threshold, "P-value threshold to consider a marker significantly associated with a phenotypic group", true)->check(CLI::Range(0.0, 1.0));
     signif->add_flag("-C,--disable-correction", parameters.disable_correction, "If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group");
     signif->add_flag("-a,--output-fasta", parameters.output_fasta, "If set, markers will be output in fasta format instead of table format");
@@ -82,7 +82,7 @@ inline Parameters parse_args(int& argc, char** argv) {
     subset->add_option("-p,--popmap", parameters.popmap_file_path, "Path to a tabulated file specifying groups for all individuals (population map)")->required()->check(CLI::ExistingFile);
     subset->add_option("-o,--output-file", parameters.output_file_path, "Path to the output file (marker depths table or fasta file for extracted markers)")->required();
     subset->add_option("-d,--min-depth", parameters.min_depth, "Minimum depth to consider a marker present in an individual", true)->check(CLI::Range(1, 9999));
-    subset->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)");
+    subset->add_option("-G,--groups", groups, "Names of the groups to compare if there are more than two groups in the popmap (--groups group1,group2)")->delimiter(',');
     subset->add_option("-S,--signif-threshold", parameters.signif_threshold, "P-value threshold to consider a marker significantly associated with a phenotypic group", true)->check(CLI::Range(0.0, 1.0));
     subset->add_flag("-C,--disable-correction", parameters.disable_correction, "If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group");
     subset->add_flag("-a,--output-fasta", parameters.output_fasta, "If set, markers will be output in fasta format instead of table format");

src/popmap.cpp

@@ -39,12 +39,17 @@ Popmap load_popmap(Parameters& parameters) {
 
     if (popmap.counts.size() < 2) {
 
-        log("Found <" + std::to_string(popmap.counts.size()) + "> groups in the popmap file, but at least two are required", LOG_ERROR);
+        log("Found <" + std::to_string(popmap.counts.size()) + "> groups in the popmap file (" + print_groups(popmap) + ") but at least two are required", LOG_ERROR);
         exit(1);
 
     } else if (popmap.counts.size() > 2 and (parameters.group1 == "" or parameters.group2 == "")) {
 
-        log("Found <" + std::to_string(popmap.counts.size()) + "> groups in the popmap file, but groups to compare were not defined (use --groups group1,group2)", LOG_ERROR);
+        log("Found <" + std::to_string(popmap.counts.size()) + "> groups in the popmap file (" + print_groups(popmap) + ") but groups to compare were not defined (use --groups group1,group2)", LOG_ERROR);
+        exit(1);
+
+    } else if (popmap.counts.size() > 2 and (popmap.counts.find(parameters.group1) == popmap.counts.end() or popmap.counts.find(parameters.group2) == popmap.counts.end())) {
+
+        log("Groups specified with --groups (\"" + parameters.group1 + "\", \"" + parameters.group2 + "\") were not found in popmap groups (" + print_groups(popmap) + ")", LOG_ERROR);
         exit(1);
 
     } else {
@@ -54,17 +59,25 @@ Popmap load_popmap(Parameters& parameters) {
         parameters.group2 = (++i)->first;
     }
 
-    std::string popmap_success_message = "Loaded popmap (";
-    uint n = 1;
-    for (auto group: popmap.counts) {
-        popmap_success_message += group.first + ": " + std::to_string(group.second);
-        if (n < popmap.counts.size()) popmap_success_message += ", ";
-        ++n;
-    }
-    popmap_success_message += ")";
+    std::string popmap_success_message = "Loaded popmap (" + print_groups(popmap, true) + ")";
 
     log(popmap_success_message);
 
     return popmap;
 }
 
+
+
+std::string print_groups(Popmap& popmap, bool counts) {
+
+    std::string list = "";
+    uint n = 0;
+
+    for (auto group: popmap.counts) {
+        list += "\"" + group.first + "\"";
+        if (counts) list += ": " + std::to_string(group.second);
+        if (++n < popmap.counts.size()) list += ", ";
+    }
+
+    return list;
+}

src/popmap.h

@@ -14,3 +14,5 @@ struct Popmap {
 };
 
 Popmap load_popmap(Parameters& parameters);
+
+std::string print_groups(Popmap& popmap, bool counts = false);

src/utils.h

@@ -66,7 +66,9 @@ template<typename T>
 inline void log(T line, const std::string level = LOG_INFO, bool flushline = true) {
 
     char logtime[DTTMSZ];
-    std::cerr << "[" << print_time(logtime) << "]::" << level << "  " << std::boolalpha << line;
+    std::string indent((8 - level.size()), ' ');
+
+    std::cerr << "[" << print_time(logtime) << "]::" << level << indent << std::boolalpha << line;
     if (flushline) std::cerr << std::endl;
 }