edgo_io: not finish

src/cx1/cx1.h

@@ -41,7 +41,8 @@
  * @tparam NBuckets      number of buckets
  */
 template <typename TGlobal, unsigned NBuckets>
-struct CX1 {
+class CX1 {
+ private:
   typedef TGlobal global_data_t;
   // other settings, don't change
   static const int kLv1BytePerItem = 4;  // 32-bit differatial offset
@@ -78,9 +79,10 @@ struct CX1 {
   std::vector<int64_t> lv1_items_special_;
 
   // === functions to specify a CX1 instance ===
-  int64_t (*encode_lv1_diff_base_func_)(int64_t, global_data_t &);
-  void (*prepare_func_)(global_data_t &);  // num_items_, num_cpu_threads_ and num_output_threads_ must be set here
-  void *(*lv0_calc_bucket_size_func_)(void *);
+ public:
+  virtual int64_t encode_lv1_diff_base_func_(int64_t, global_data_t &) = 0;
+  virtual void prepare_func_(global_data_t &) = 0;  // num_items_, num_cpu_threads_ and num_output_threads_ must be set here
+  virtual void *(*lv0_calc_bucket_size_func_)(void *);
   void (*init_global_and_set_cx1_func_)(global_data_t &);  // xxx set here
   void *(*lv1_fill_offset_func_)(void *);
   void (*lv1_sort_and_proc)(global_data_t &);

src/cx1/cx1_kmer_count.cpp

@@ -274,11 +274,11 @@ void init_global_and_set_cx1(count_global_t &globals) {
   }
 
   // --- initialize writer ---
-  globals.edge_writer.set_file_prefix(globals.output_prefix);
-  globals.edge_writer.set_num_threads(globals.num_output_threads);
-  globals.edge_writer.set_kmer_size(globals.kmer_k);
-  globals.edge_writer.set_num_buckets(kNumBuckets);
-  globals.edge_writer.init_files();
+  globals.edge_writer.SetFilePrefix(globals.output_prefix);
+  globals.edge_writer.SetNumThreads(globals.num_output_threads);
+  globals.edge_writer.SetKmerSize(globals.kmer_k);
+  globals.edge_writer.SetNumBuckets(kNumBuckets);
+  globals.edge_writer.InitFiles();
 }
 
 void *lv1_fill_offset(void *_data) {
@@ -523,7 +523,7 @@ void lv2_output_(int64_t start_index, int64_t end_index, int thread_id, count_gl
 
     if (count >= globals.kmer_freq_threshold) {
       PackEdge(packed_edge, first_item, count, globals);
-      globals.edge_writer.write(packed_edge, packed_edge[0] >> (32 - 2 * kBucketPrefixLength), thread_id, &snapshot);
+      globals.edge_writer.Write(packed_edge, packed_edge[0] >> (32 - 2 * kBucketPrefixLength), thread_id, &snapshot);
     }
   }
 
@@ -623,7 +623,7 @@ void post_proc(count_global_t &globals) {
   fclose(counting_file);
 
   // --- cleaning ---
-  globals.edge_writer.destroy();
+  globals.edge_writer.Finalize();
 }
 
 }  // namespace cx1_kmer_count

src/cx1/cx1_seq2sdbg.cpp

@@ -344,16 +344,16 @@ void read_seq_and_prepare(seq2sdbg_global_t &globals) {
 
     if (globals.input_prefix != "") {
       MegahitEdgeReader edge_reader;
-      edge_reader.set_file_prefix(globals.input_prefix);
-      edge_reader.read_info();
+      edge_reader.SetFilePrefix(globals.input_prefix);
+      edge_reader.ReadInfo();
       int64_t num_edges = edge_reader.num_edges();
       xinfo("Number edges: %lld\n", (long long)num_edges);
 
       if (globals.need_mercy) {
         num_edges *= 1.25;  // it is rare that # mercy > 25%
       }
 
-      bases_to_reserve += num_edges * (edge_reader.kmer_size() + 1);
+      bases_to_reserve += num_edges * (edge_reader.k() + 1);
       num_multiplicities_to_reserve += num_edges;
     }
 

src/iterate/kmer_collector.h

@@ -26,11 +26,11 @@ class KmerCollector {
     words_per_kmer_ = DivCeiling(k_ * 2 + kBitsPerMul, 32);
     buffer_.resize(words_per_kmer_);
 
-    writer_.set_num_threads(1);
-    writer_.set_file_prefix(out_prefix);
-    writer_.set_unsorted();
-    writer_.set_kmer_size(k_ - 1);
-    writer_.init_files();
+    writer_.SetNumThreads(1);
+    writer_.SetFilePrefix(out_prefix);
+    writer_.SetUnsorted();
+    writer_.SetKmerSize(k_ - 1);
+    writer_.InitFiles();
   }
 
   void Insert(const KmerType &kmer, mul_t mul) { collection_.insert({kmer, mul}); }
@@ -62,7 +62,7 @@ class KmerCollector {
     *ptr = (w << last_shift_);
     assert((buffer_.back() & kMaxMul) == 0);
     buffer_.back() |= mul;
-    writer_.write_unsorted(buffer_.data(), 0);
+    writer_.WriteUnsorted(buffer_.data(), 0);
   }
 
  private: