From 191fc2cede0fb3ec5cb8b7e626affce1f5029d9a Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Fri, 27 Feb 2026 14:05:10 -0800
Subject: [PATCH 1/2] 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

---
 src/FalcoConfig.cpp |  1 +
 src/FalcoConfig.hpp |  7 +++++--
 src/falco.cpp       | 12 ++++++++----
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/src/FalcoConfig.cpp b/src/FalcoConfig.cpp
index fed31e9..8f3164f 100644
--- a/src/FalcoConfig.cpp
+++ b/src/FalcoConfig.cpp
@@ -329,6 +329,7 @@ FalcoConfig::FalcoConfig(const int argc, char *argv[]) {
 
 
   quiet = false;
+  progress = false;
   tmpdir = ".";
 
   is_sam = false;
diff --git a/src/FalcoConfig.hpp b/src/FalcoConfig.hpp
index 4ec3a24..092b48d 100644
--- a/src/FalcoConfig.hpp
+++ b/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,
diff --git a/src/falco.cpp b/src/falco.cpp
index 0fd5955..53e789c 100644
--- a/src/falco.cpp
+++ b/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()) {

From 147d4ab5468020059bb9b04e74879be2d07c5a73 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Fri, 27 Feb 2026 14:20:05 -0800
Subject: [PATCH 2/2] documentation/docs/index.md: updating description of cli
 args

---
 documentation/docs/index.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/documentation/docs/index.md b/documentation/docs/index.md
index 900ef1e..572da17 100644
--- a/documentation/docs/index.md
+++ b/documentation/docs/index.md
@@ -283,6 +283,12 @@ Options:
                            (this may break the parse of fastqc_data.txt
                            in programs that are very strict about the
                            FastQC output format).
+      -allow-empty-input   [Falco only] allow empty input files and
+                           generate empty output files without en error
+                           state. WARNING: using this option can mask
+                           problems in other parts of a workflow.
+      -progress            [Falco only] Report a progress bar while
+                           running.
 
 Help options:
   -?, -help                print this help message
@@ -306,7 +312,7 @@ quality control of sequencing data. F1000Research 2021, 8:1874
 Copyright and License Information
 =================================
 
-Copyright (C) 2019-2024 Guilherme de Sena Brandine and
+Copyright (C) 2019-2026 Guilherme de Sena Brandine and
                         Andrew D. Smith
 
 Authors: Guilherme de Sena Brandine and Andrew D. Smith