Code cleanup

eaasna · Mar 19, 2024 · 74e1693 · 74e1693
1 parent b211f66
commit 74e1693
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Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/include/valik/split/metadata.hpp b/include/valik/split/metadata.hpp
@@ -579,6 +579,7 @@ struct metadata
         {
             double fpr{1};
             double p = kmer_spurious_match_prob(params.k);
+            const double precision{1e-9};
             /*
             For parameters 
         
@@ -604,12 +605,14 @@ struct metadata
             size_t kmers_per_pattern = pattern_size - params.k + 1;
             for (uint8_t matching_kmer_count{0}; matching_kmer_count < params.t; matching_kmer_count++)
             {
+                if (fpr < precision) 
+                    break;
                 fpr -= combinations(matching_kmer_count, kmers_per_pattern) * 
                                     pow(p, matching_kmer_count) * 
                                     pow(1 - p, kmers_per_pattern - matching_kmer_count);
             }
 
-            return std::max(0.0, fpr);
+            return std::max(0.0, fpr - precision);
         }
 
         /**

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -8,11 +8,12 @@ add_library ("${PROJECT_NAME}_interface" INTERFACE)
 target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE seqan3::seqan3)
 target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE sharg::sharg)
 target_include_directories ("${PROJECT_NAME}_interface" INTERFACE ../include)
-target_include_directories ("${PROJECT_NAME}_interface" INTERFACE ../lib/raptor/include)
+# SYSTEM keyword turns off compiler warnings for subprojects
+target_include_directories ("${PROJECT_NAME}_interface" SYSTEM INTERFACE ../lib/raptor/include)
 target_include_directories ("${PROJECT_NAME}_interface" SYSTEM INTERFACE ../lib/stellar3/include)
-target_include_directories ("${PROJECT_NAME}_interface" INTERFACE ../lib/seqan/include)
-target_include_directories ("${PROJECT_NAME}_interface" INTERFACE ../lib/robin-hood-hashing/src/include)
-target_compile_options ("${PROJECT_NAME}_interface" INTERFACE "-pedantic" "-Wall" "-Wextra")
+target_include_directories ("${PROJECT_NAME}_interface" SYSTEM INTERFACE ../lib/seqan/include)
+target_include_directories ("${PROJECT_NAME}_interface" SYSTEM INTERFACE ../lib/robin-hood-hashing/src/include)
+target_compile_options ("${PROJECT_NAME}_interface" INTERFACE "-pedantic" "-Wall" "-Wextra" "-Wno-interference-size")
 
 # Parameter tuning
 add_library ("${PROJECT_NAME}_threshold_lib" STATIC threshold/find.cpp)

diff --git a/src/argument_parsing/search.cpp b/src/argument_parsing/search.cpp
@@ -46,10 +46,6 @@ void init_search_parser(sharg::parser & parser, search_arguments & arguments)
                       sharg::config{.short_id = '\0',
                       .long_id = "fast",
                       .description = "Execute the search in fast mode when few false negatives can be tolerated."});
-    parser.add_flag(arguments.compressed,
-                    sharg::config{.short_id = '\0',
-                    .long_id = "compressed",
-                    .description = "Build a compressed IBF."});
     parser.add_flag(arguments.write_time,
                     sharg::config{.short_id = '\0',
                     .long_id = "time",

diff --git a/src/threshold/find.cpp b/src/threshold/find.cpp
@@ -89,8 +89,8 @@ param_set get_best_params(search_pattern const & pattern,
  *        Consider different error rates up to max_err.
 */
 search_kmer_profile find_thresholds_for_kmer_size(metadata const & ref_meta,
-                                              kmer_loss const attr, 
-                                              uint8_t const max_errors)
+                                                  kmer_loss const attr, 
+                                                  uint8_t const max_errors)
 {
     param_space space;