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+_OPENSSL_LIBS_OTHER:INTERNAL= +_OPENSSL_LIBS_PATHS:INTERNAL= +_OPENSSL_MODULE_NAME:INTERNAL= +_OPENSSL_PREFIX:INTERNAL= +_OPENSSL_STATIC_CFLAGS:INTERNAL= +_OPENSSL_STATIC_CFLAGS_I:INTERNAL= +_OPENSSL_STATIC_CFLAGS_OTHER:INTERNAL= +_OPENSSL_STATIC_LIBDIR:INTERNAL= +_OPENSSL_STATIC_LIBS:INTERNAL= +_OPENSSL_STATIC_LIBS_L:INTERNAL= +_OPENSSL_STATIC_LIBS_OTHER:INTERNAL= +_OPENSSL_STATIC_LIBS_PATHS:INTERNAL= +_OPENSSL_VERSION:INTERNAL= +__pkg_config_checked__OPENSSL:INTERNAL=1 + diff --git a/dorado/3rdparty/cpp-httplib b/dorado/3rdparty/cpp-httplib index c7ed1796a..fee8e97b4 160000 --- a/dorado/3rdparty/cpp-httplib +++ b/dorado/3rdparty/cpp-httplib @@ -1 +1 @@ -Subproject commit c7ed1796a778592ae5a122287a16b1dd4770858a +Subproject commit fee8e97b4eeb34fe2e6e6294413d84e9e7a072a7 diff --git a/dorado/3rdparty/spdlog b/dorado/3rdparty/spdlog index 7e635fca6..936697e5b 160000 --- a/dorado/3rdparty/spdlog +++ b/dorado/3rdparty/spdlog @@ -1 +1 @@ -Subproject commit 7e635fca68d014934b4af8a1cf874f63989352b7 +Subproject commit 936697e5b1944bf1630cfbb9e82144f8bdc32815 diff --git a/dorado/cli/duplex.cpp b/dorado/cli/duplex.cpp index 652675588..b93d73cc2 100644 --- a/dorado/cli/duplex.cpp +++ b/dorado/cli/duplex.cpp @@ -68,6 +68,11 @@ int duplex(int argc, char* argv[]) { .default_value(default_parameters.overlap) .scan<'i', int>(); + parser.add_argument("-p", "--enable-progress-bar") + .default_value(false) + .implicit_value(true) + .help("Enable progress bar output to stderr"); + parser.add_argument("-r", "--recursive") .default_value(false) .implicit_value(true) @@ -117,6 +122,7 @@ int duplex(int argc, char* argv[]) { auto reads(parser.get("reads")); std::string pairs_file = parser.get("--pairs"); + auto enable_progress_bar = parser.get("--enable-progress-bar"); auto threads = static_cast(parser.get("--threads")); auto min_qscore(parser.get("--min-qscore")); auto ref = parser.get("--reference"); @@ -197,7 +203,7 @@ int duplex(int argc, char* argv[]) { torch::set_num_threads(1); std::vector stats_callables; - ProgressTracker tracker(num_reads, duplex); + ProgressTracker tracker(num_reads, duplex, enable_progress_bar); stats_callables.push_back( [&tracker](const stats::NamedStats& stats) { tracker.update_progress_bar(stats); }); stats::NamedStats final_stats; diff --git a/dorado/read_pipeline/ProgressTracker.h b/dorado/read_pipeline/ProgressTracker.h index 4f17d31a3..bffef95d3 100644 --- a/dorado/read_pipeline/ProgressTracker.h +++ b/dorado/read_pipeline/ProgressTracker.h @@ -24,8 +24,10 @@ namespace dorado { // overall performance. class ProgressTracker { public: - ProgressTracker(int total_reads, bool duplex) - : m_num_reads_expected(total_reads), m_duplex(duplex) { + ProgressTracker(int total_reads, bool duplex, bool enable_progress_bar = true) + : m_num_reads_expected(total_reads), + m_enable_progress_bar(enable_progress_bar), + m_duplex(duplex) { m_initialization_time = std::chrono::system_clock::now(); } @@ -96,7 +98,7 @@ class ProgressTracker { m_num_duplex_bases_filtered = fetch_stat("ReadFilterNode.duplex_bases_filtered"); // don't output progress bar if stderr is not a tty - if (!utils::is_fd_tty(stderr)) { + if (!utils::is_fd_tty(stderr) & !m_enable_progress_bar) { return; } @@ -112,9 +114,10 @@ class ProgressTracker { m_progress_bar.set_progress(progress); #ifndef WIN32 std::cerr << "\033[K"; +#else + std::cerr << "\r"; #endif // WIN32 m_last_progress_written = progress; - std::cerr << "\r"; } } else { std::cerr << "\r> Output records written: " << m_num_simplex_reads_written; @@ -141,6 +144,7 @@ class ProgressTracker { std::chrono::time_point m_end_time; bool m_duplex; + bool m_enable_progress_bar; #ifdef WIN32 indicators::ProgressBar m_progress_bar {