Use another way to handle string in khash. Fix a small issue of initialization in mmcache (c1f625c9) · Commits · github_fork / Chromap

Makefile

+3 −2

Original line number	Diff line number	Diff line
		@@ -9,9 +9,10 @@ objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

		exec=chromap

		#asan=1
		ifneq ($(asan),)
		CXXFLAGS+=-fsanitize=address
		LDFLAGS+=-fsanitize=address -ldl
		CXXFLAGS+=-fsanitize=address -g
		LDFLAGS+=-fsanitize=address -ldl -g
		endif

		all: dir $(exec)

+1 −0

Original line number	Diff line number	Diff line
		@@ -88,6 +88,7 @@ class mm_cache {
		cache[i].finger_print_cnt_sum = 0;
		cache[i].activated = 0;
		}
		memset(head_mm, 0, sizeof(uint64_t) * HEAD_MM_ARRAY_SIZE);
		update_limit = 10;
		saturate_count = 100;
		}

+9 −3

Original line number	Diff line number	Diff line
		@@ -21,7 +21,7 @@

		namespace chromap {

		KHASH_INIT(k64_str, uint64_t, std::string, 1, kh_int64_hash_func, kh_int64_hash_equal);
		KHASH_INIT(k64_str, uint64_t, char *, 1, kh_int64_hash_func, kh_int64_hash_equal);

		enum MappingOutputFormat {
		MAPPINGFORMAT_UNKNOWN,
		@@ -73,7 +73,7 @@ private:

		int khash_return_code;
		khiter_t barcode_translate_table_iter = kh_put(k64_str, barcode_translate_table, from_seed, &khash_return_code);
		kh_value(barcode_translate_table, barcode_translate_table_iter) = to;
		kh_value(barcode_translate_table, barcode_translate_table_iter) = strdup(to.c_str());
		}

		public:
		@@ -84,6 +84,12 @@ public:

		~BarcodeTranslator() {
		if (barcode_translate_table != NULL) {
		khiter_t k ;
		for (k = kh_begin(barcode_translate_table) ; k != kh_end(barcode_translate_table); ++k)
		{
		if (kh_exist(barcode_translate_table, k))
		free(kh_value(barcode_translate_table, k)) ;
		}
		kh_destroy(k64_str, barcode_translate_table);
		}
		}
		@@ -118,7 +124,7 @@ public:
		std::cerr << "Barcode does not exist in the translation table.\n" << std::endl;
		exit(-1);
		}
		const std::string &bc_to = kh_value(barcode_translate_table, barcode_translate_table_iter);
		std::string bc_to(kh_value(barcode_translate_table, barcode_translate_table_iter));
		if (i == 0) {
		ret = bc_to;
		} else {