Chopper layout

.clang-format

@@ -147,10 +147,14 @@ IncludeCategories:
     Priority:        7
     SortPriority:    0
     CaseSensitive:   false
-  - Regex:           '.*'
+  - Regex:           '<chopper/'
     Priority:        8
     SortPriority:    0
     CaseSensitive:   false
+  - Regex:           '.*'
+    Priority:        9
+    SortPriority:    0
+    CaseSensitive:   false
 IncludeIsMainRegex: '(Test)?$'
 IncludeIsMainSourceRegex: ''
 IndentAccessModifiers: false

include/ibf.hpp

@@ -32,7 +32,8 @@ std::vector<uint16_t> ibf(std::vector<std::filesystem::path> const & sequence_fi
                           std::vector<double> & fpr,
                           std::vector<uint8_t> & cutoffs,
                           std::filesystem::path const & expression_by_genome_file = "",
-                          size_t num_hash = 1);
+                          size_t num_hash = 1,
+                          bool const fast_layout = false);
 
 /*! \brief Creates IBFs based on the minimiser files
  * \param minimiser_files A vector of minimiser file paths.
@@ -48,4 +49,5 @@ std::vector<uint16_t> ibf(std::vector<std::filesystem::path> const & minimiser_f
                           estimate_ibf_arguments & ibf_args,
                           std::vector<double> & fpr,
                           std::filesystem::path const & expression_by_genome_file = "",
-                          size_t num_hash = 1);
+                          size_t num_hash = 1,
+                          bool const fast_layout = false);

include/misc/stream.hpp

@@ -6,6 +6,7 @@
 
 #include <cstdint>
 #include <filesystem>
+#include <functional>
 #include <iostream>
 
 #include <hibf/contrib/robin_hood.hpp>
@@ -42,3 +43,8 @@ void read_binary_start(minimiser_arguments & args,
                        std::filesystem::path const & filename,
                        uint64_t & num_of_minimisers,
                        uint8_t & cutoff);
+
+/*!\brief Iterate through a minimiser binary file and call callback(hash, count) for each entry.
+ */
+void iterate_minimiser_file(std::filesystem::path const & filename,
+                            std::function<void(uint64_t /*hash*/, uint16_t /*count*/)> callback);

src/CMakeLists.txt

@@ -26,6 +26,7 @@ add_library ("${PROJECT_NAME}_lib" STATIC ${NEEDLE_SOURCE_FILES})
 target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan3::seqan3)
 target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC sharg::sharg)
 target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC seqan::hibf)
+target_link_libraries ("${PROJECT_NAME}_lib" PUBLIC chopper::chopper)
 target_include_directories ("${PROJECT_NAME}_lib" PUBLIC ../include)
 
 add_subdirectory (layout)