Adding a check for valid counts file format for input files

Author: andrewdavidsmith

src/analysis/hmr-rep.cpp

@@ -415,6 +415,10 @@ main_hmr_rep(int argc, const char **argv) {
     const vector<string> cpgs_files(leftover_args);
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    for (auto &filename : cpgs_files)
+      if (!is_msite_file(filename))
+        throw runtime_error("malformed counts file: " + filename);
+
     vector<string> params_in_file;
     if (!params_in_files.empty()) {
       params_in_file = split_comma(params_in_files);

src/analysis/hmr.cpp

@@ -442,6 +442,9 @@ main_hmr(int argc, const char **argv) {
     const string cpgs_file = leftover_args.front();
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    if (!is_msite_file(cpgs_file))
+      throw runtime_error("malformed counts file: " + cpgs_file);
+
     // separate the regions by chrom and by desert
     vector<MSite> cpgs;
     vector<pair<double, double> > meth;

src/analysis/hypermr.cpp

@@ -278,6 +278,9 @@ main_hypermr(int argc, const char **argv) {
     const string cpgs_file = leftover_args.front();
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    if (!is_msite_file(cpgs_file))
+      throw runtime_error("malformed counts file: " + cpgs_file);
+
     if (VERBOSE) cerr << "[loading_data]" << endl;
     vector<MSite> cpgs;
     vector<pair<double, double>> meth;

src/analysis/levels.cpp

@@ -120,6 +120,9 @@ main_levels(int argc, const char **argv) {
     const string meth_file = leftover_args.front();
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    if (!is_msite_file(meth_file))
+      throw runtime_error("malformed counts file: " + meth_file);
+
     const counts_file_format guessed_format =
       guess_counts_file_format(meth_file);
     if (guessed_format != counts_file_format::ordinary) {

src/analysis/pmd.cpp

@@ -1173,7 +1173,10 @@ main_pmd(int argc, const char **argv) {
       assert(cpgs_file.size() == params_in_file.size());
     }
 
-    size_t n_replicates = cpgs_file.size();
+    const size_t n_replicates = cpgs_file.size();
+    for (auto &filename : cpgs_file)
+      if (!is_msite_file(filename))
+        throw runtime_error("malformed counts file: " + filename);
 
     bool insufficient_data = false; // ADS: this is used now to detect
                                     // when the counts files have

src/analysis/roimethstat.cpp

@@ -470,6 +470,9 @@ Columns (beyond the first 6) in the BED format output:
     const string cpgs_file = leftover_args.back();
     /****************** END COMMAND LINE OPTIONS *****************/
 
+    if (!is_msite_file(cpgs_file))
+      throw runtime_error("malformed counts file: " + cpgs_file);
+
     if (VERBOSE)
       cerr << "loading regions" << endl;