Making progress messages more uniform

Author: andrewdavidsmith

src/amrfinder/allelicmeth.cpp

@@ -265,7 +265,7 @@ process_chrom(const bool VERBOSE, const string &chrom_name,
     max_epiread_len = std::max(max_epiread_len, epireads[i].length());
   const size_t chrom_cpgs = get_n_cpgs(epireads);
   if (VERBOSE)
-    cerr << "PROCESSING: " << chrom_name << " "
+    cerr << "processing " << chrom_name << " "
          << "[reads: " << epireads.size() << "] "
          << "[cpgs: " << chrom_cpgs << "]" << endl;
 

src/amrfinder/amrfinder.cpp

@@ -305,7 +305,7 @@ process_chrom(const bool VERBOSE, const bool PROGRESS,
 
   const size_t chrom_cpgs = get_n_cpgs(epireads);
   if (VERBOSE)
-    cerr << "PROCESSING: " << chrom_name << " "
+    cerr << "processing " << chrom_name << " "
          << "[reads: " << epireads.size() << "] "
          << "[cpgs: " << chrom_cpgs << "]" << endl;
 

src/analysis/bsrate.cpp

@@ -330,7 +330,7 @@ main_bsrate(int argc, const char **argv) {
           throw runtime_error("chroms out of order in mapped reads file");
 
         if (VERBOSE)
-          cerr << "processing chromosome " << aln.rname << "\n";
+          cerr << "processing " << aln.rname << endl;
 
         chroms_seen.insert(aln.rname);
 

src/analysis/levels.cpp

@@ -112,7 +112,7 @@ main_levels(int argc, const char **argv) {
       if (site.chrom != prev_site.chrom) {
         ++chrom_count;
         if (VERBOSE)
-          cerr << "PROCESSING:\t" << site.chrom << "\n";
+          cerr << "processing " << site.chrom << endl;
       }
 
       cytosines.update(site);

src/analysis/methcounts.cpp

@@ -309,7 +309,7 @@ process_reads(const bool VERBOSE, SAMReader &in, T &out,
         throw runtime_error("chromosome not found: " + aln.rname);
 
       if (VERBOSE)
-        cerr << "PROCESSING:\t" << aln.rname << endl;
+        cerr << "processing " << aln.rname << endl;
 
       name = aln.rname;
       chrom_itr = begin(chroms) + chrom_idx->second;

src/analysis/methentropy.cpp

@@ -270,7 +270,7 @@ process_chrom(const bool VERBOSE, const size_t cpg_window,
 
   const size_t n_cpgs = cpg_lookup.size();
   if (VERBOSE)
-    cerr << "processing chrom: " << chrom
+    cerr << "processing " << chrom
          << " (cpgs = " << n_cpgs << ")" << endl;
 
   vector<double> site_probs;

src/radmeth/methdiff.cpp

@@ -157,7 +157,7 @@ process_sites(const bool VERBOSE, igzfstream &in_a, igzfstream &in_b,
       chrom_id_a = get_chrom_id(chrom_order, chroms_seen_a, a);
       prev_chrom_a = a.chrom;
       if (VERBOSE)
-        cerr << "[processing: " << a.chrom << "]" << endl;
+        cerr << "processing " << a.chrom << endl;
     }
     if (!site_precedes(prev_chrom_id_a, prev_pos_a, chrom_id_a, a.pos))
       throw runtime_error(bad_order(chrom_order, prev_chrom_a, prev_pos_a,