src/FalcoConfig.hcpp and src/falco.cpp: require a flag to report progress bar while running; this is to prevent CR chars unless the user wants it

Author: andrewdavidsmith

src/FalcoConfig.cpp

@@ -329,6 +329,7 @@ FalcoConfig::FalcoConfig(const int argc, char *argv[]) {
 
 
   quiet = false;
+  progress = false;
   tmpdir = ".";
 
   is_sam = false;

src/FalcoConfig.hpp

@@ -1,4 +1,4 @@
-/* Copyright (C) 2019-2022 Guilherme De Sena Brandine and
+/* Copyright (C) 2019-2026 Guilherme De Sena Brandine and
  *                         Andrew D. Smith
  * Authors: Guilherme De Sena Brandine, Andrew Smith
  *
@@ -42,7 +42,7 @@ struct FalcoConfig {
   bool extract;  // if set the zipped file will be uncompressed
   bool nogroup;  // disable grouping of bases for reads >50bp
   bool compressed;  // whether or not to inflate file
-  bool quiet;
+  bool quiet;   // suppress all progress output to terminal
   size_t read_step;  // only process reads that are multiple of read_step
   size_t threads;  // number of threads to read multiple files in parallel
   std::string call; // the function call
@@ -53,6 +53,9 @@ struct FalcoConfig {
   static const std::string html_template; // the html for the template
   std::string tmpdir;  // dir for temp files when generating report images
 
+  // Falco only
+  bool progress; // report the progress bar
+
   // config on how to handle reads
   bool do_duplication,
        do_kmer,

src/falco.cpp

@@ -64,12 +64,12 @@ read_stream_into_stats(T &in, FastqStats &stats, FalcoConfig &falco_config) {
   size_t tot_bytes_read = 0;
 
   // Read record by record
-  const bool quiet = falco_config.quiet;
+  const bool report_progress = falco_config.progress;
   ProgressBar progress(file_size, "running falco");
-  if (!quiet)
+  if (report_progress)
     progress.report(std::cerr, 0);
   while (in.read_entry(stats, tot_bytes_read)) {
-    if (!quiet && progress.time_to_report(tot_bytes_read))
+    if (report_progress && progress.time_to_report(tot_bytes_read))
       progress.report(std::cerr, tot_bytes_read);
   }
 
@@ -78,7 +78,7 @@ read_stream_into_stats(T &in, FastqStats &stats, FalcoConfig &falco_config) {
   if (in.tile_ignore)
     falco_config.do_tile = false;
 
-  if (!quiet && tot_bytes_read < file_size)
+  if (report_progress && tot_bytes_read < file_size)
     progress.report(std::cerr, file_size);
 }
 
@@ -538,6 +538,10 @@ main(int argc, char *argv[]) {
       "other parts of a workflow.",
       false, allow_empty_input);
 
+    opt_parse.add_opt("progress", '\0',
+                      "[Falco only] Report a progress bar while running.",
+                      false, falco_config.progress);
+
     std::vector<std::string> leftover_args;
     opt_parse.parse(argc, argv, leftover_args);
     if (argc == 1 || opt_parse.help_requested()) {