Merge pull request #3 from mahmudhera/main

Add md5sum code

.gitignore

@@ -1 +1,2 @@
-*.o
+*.o
+.vscode/settings.json

Makefile

@@ -71,6 +71,25 @@ CFLAGS	= -Wall -O3 -fsigned-char $(CPU_FLAGS) $(STATIC_CFLAGS) -std=c++14
 CLINK	= -lm $(STATIC_LFLAGS) -O3 -std=c++14
 PY_KMC_API_CFLAGS = $(PY_FLAGS) -Wall -shared -std=c++14 -O3
 
+
+# Find OpenSSL path using "which"
+OPENSSL_PATH := $(shell which openssl)
+
+# if open ssl is not found, then exit
+ifeq ($(OPENSSL_PATH),)
+$(error "OpenSSL not found. Please install OpenSSL")
+endif
+
+# Extract directory path from the full path
+OPENSSL_DIR := $(dir $(OPENSSL_PATH))
+
+# Set flags using the directory path
+CFLAGS += -I$(OPENSSL_DIR)/../include -lssl -lcrypto
+LDFLAGS += -L$(OPENSSL_DIR)/../lib -lssl -lcrypto
+
+# export LD_LIBRARY_PATH appropriately
+export LD_LIBRARY_PATH := $(OPENSSL_DIR)/../lib:$(LD_LIBRARY_PATH)
+
 KMC_CLI_OBJS = \
 $(KMC_CLI_DIR)/kmc.o
 
@@ -173,7 +192,7 @@ frackmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB)
 
 frackmcdump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
 	-mkdir -p $(OUT_BIN_DIR)
-	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
+	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ -lssl -lcrypto
 
 # frac_kmc: g++ -Wall -O3 wrappers/sketch/frac_kmc_sketch.cpp -o fracKmcSketch
 fracKmcSketch: wrappers/sketch/frac_kmc_sketch.cpp

kmc_dump/kmc_dump.cpp

@@ -22,6 +22,9 @@
 #include "../kmc_api/kmc_file.h"
 #include "nc_utils.h"
 #include <map>
+#include <openssl/md5.h>
+#include <sstream>
+#include <iomanip>
 
 using namespace std;
 
@@ -357,7 +360,30 @@ int main(int argc, char* argv[])
 
 		}
 
-		output_string = "], \"molecule\":\"dna\", \"md5sum\":\"abcd\"}], \"version\":0.1}]\n";
+
+        // compute md5sum
+        MD5_CTX md5_ctx;
+        MD5_Init(&md5_ctx);
+        // add ksize to md5sum
+        string ksize_str = to_string(ksize);
+        MD5_Update(&md5_ctx, ksize_str.c_str(), ksize_str.length());
+        // add the hashes to md5sum
+        for (int i=0; i<hashes.size(); i++)
+        {
+            string hash_str = to_string(hashes[i]);
+            MD5_Update(&md5_ctx, hash_str.c_str(), hash_str.length());
+        }
+        unsigned char md5sum[MD5_DIGEST_LENGTH];
+        MD5_Final(md5sum, &md5_ctx);
+        string md5sum_str = "";
+        std::ostringstream oss;
+        for(int i = 0; i < MD5_DIGEST_LENGTH; i++)
+        {
+            oss << std::hex << std::setw(2) << std::setfill('0') << (int)md5sum[i];
+        }
+        md5sum_str = oss.str();
+
+		output_string = "], \"molecule\":\"dna\", \"md5sum\":\"" + md5sum_str + "\"}], \"version\":0.1}]\n";
 		strcpy(str, output_string.c_str());
 		fwrite(str, 1, output_string.length(), out_file);