Merge branch 'jdaw/disable-progress-bar-redirected' into 'master'

Disable progress bar for resume if stderr != tty

See merge request machine-learning/dorado!738

dorado/read_pipeline/ResumeLoaderNode.cpp

@@ -1,6 +1,7 @@
 #include "ResumeLoaderNode.h"
 
 #include "HtsReader.h"
+#include "utils/tty_utils.h"
 
 #include <htslib/sam.h>
 #include <indicators/indeterminate_progress_bar.hpp>
@@ -27,6 +28,11 @@ void ResumeLoaderNode::copy_completed_reads() {
                                              indicators::option::PostfixText{"Resuming from file"},
                                              indicators::option::Stream{std::cerr}};
 
+    // Only log using progress bar if stderr is tty. If stderr is being
+    // routed to a file, the IndeterminateProgressBar just spams the file
+    // with dots.
+    bool is_safe_to_log = utils::is_fd_tty(stderr);
+
     // Turn off logging for warnings.
     auto initial_hts_log_level = hts_get_log_level();
     hts_set_log_level(HTS_LOG_OFF);
@@ -39,7 +45,7 @@ void ResumeLoaderNode::copy_completed_reads() {
             std::string read_id = bam_get_qname(reader.record);
             m_processed_read_ids.insert(read_id);
             m_sink.push_message(BamPtr(bam_dup1(reader.record.get())));
-            if (m_processed_read_ids.size() % 100 == 0) {
+            if (is_safe_to_log && m_processed_read_ids.size() % 100 == 0) {
                 bar.tick();
             }
         }