From 54af2748a7e28e435577dce96479bd4940bb3e1d Mon Sep 17 00:00:00 2001
From: Evelin <evelin.aasna@fu-berlin.de>
Date: Fri, 20 Sep 2024 13:29:09 +0200
Subject: [PATCH] Print warning for verbose output

---
 include/valik/search/producer_threads_parallel.hpp |  9 +++++++--
 include/valik/search/sync_out.hpp                  | 10 +++++++++-
 include/valik/shared.hpp                           |  1 +
 src/argument_parsing/search.cpp                    |  5 +++++
 4 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/include/valik/search/producer_threads_parallel.hpp b/include/valik/search/producer_threads_parallel.hpp
index 83590986..ccfea993 100644
--- a/include/valik/search/producer_threads_parallel.hpp
+++ b/include/valik/search/producer_threads_parallel.hpp
@@ -45,8 +45,13 @@ inline void prefilter_queries_parallel(seqan3::interleaved_bloom_filter<ibf_data
 
         auto prefilter_cb = [&queue,&arguments,&verbose_out,&ibf](query_t const& record, std::unordered_set<size_t> const& bin_hits)
         {
-            if (arguments.verbose && (bin_hits.size() > std::max((size_t) 4, (size_t) std::round(ibf.bin_count() / 2.0))))
-                verbose_out.write_record(record, bin_hits.size());
+            if (bin_hits.size() > std::max((size_t) 4, (size_t) std::round(ibf.bin_count() / 2.0)))
+            {
+                if (arguments.very_verbose)
+                    verbose_out.write_record(record, bin_hits.size());
+                else if (arguments.verbose)
+                    verbose_out.write_warning(record, bin_hits.size());
+            }
 
             for (size_t const bin : bin_hits)
             {
diff --git a/include/valik/search/sync_out.hpp b/include/valik/search/sync_out.hpp
index 2ea34bb0..42287cab 100644
--- a/include/valik/search/sync_out.hpp
+++ b/include/valik/search/sync_out.hpp
@@ -23,6 +23,14 @@ class sync_out
 
     sync_out(std::filesystem::path const & path) : file{path} {}
 
+    template <typename t>
+    void write_warning(t && query_record, size_t const & bin_count)
+    {
+        std::lock_guard<std::mutex> lock(write_mutex);
+        seqan3::debug_stream << "[Warning] Insufficient prefiltering. " << bin_count << " bins match query of length " << query_record.sequence.size() << '\n'; 
+    }
+    // outfile gets unlocked as soon as the current thread exits the write function
+
     template <typename t>
     void write_record(t && query_record, size_t const & bin_count)
     {
@@ -34,7 +42,7 @@ class sync_out
         fasta_string += '\n';
 
         std::lock_guard<std::mutex> lock(write_mutex);
-        seqan3::debug_stream << "[Warning] Insufficient prefiltering. " << bin_count << " bins match query:\n" << fasta_string << "\n"; 
+        seqan3::debug_stream << "[Warning] Insufficient prefiltering. " << bin_count << " bins match query:\n" << fasta_string << '\n';
     }
     // outfile gets unlocked as soon as the current thread exits the write function
 
diff --git a/include/valik/shared.hpp b/include/valik/shared.hpp
index e17cb9f5..8fd73483 100644
--- a/include/valik/shared.hpp
+++ b/include/valik/shared.hpp
@@ -181,6 +181,7 @@ struct search_arguments final : public minimiser_threshold_arguments, search_pro
     bool write_time{false};
     bool fast{false};
     bool verbose{false};
+    bool very_verbose{false};
 
     size_t cart_max_capacity{1000};
     size_t max_queued_carts{std::numeric_limits<size_t>::max()};
diff --git a/src/argument_parsing/search.cpp b/src/argument_parsing/search.cpp
index 131d0492..faf68f76 100644
--- a/src/argument_parsing/search.cpp
+++ b/src/argument_parsing/search.cpp
@@ -79,6 +79,11 @@ void init_search_parser(sharg::parser & parser, search_arguments & arguments)
                       .long_id = "without-parameter-tuning",
                       .description = "Preprocess database without setting default parameters.",
                       .advanced = true});
+    parser.add_flag(arguments.very_verbose,
+                    sharg::config{.short_id = '\0',
+                    .long_id = "very-verbose",
+                    .description = "Print very verbose output.",
+                    .advanced = true});
     parser.add_option(arguments.seg_count_in,
                       sharg::config{.short_id = 'n',
                       .long_id = "seg-count",