--- external/setcover/Main.cpp.dist	2020-06-23 10:07:23.207832931 -0700
+++ external/setcover/Main.cpp	2020-06-23 10:12:01.950624554 -0700
@@ -63,11 +63,11 @@
     unsigned short ** weights = ret_struct.weights;
     
     ret_struct.max_weight = 0;
     ret_struct.all_element_count=0;
     for(int i = 0; i<m; i++){
-        int element_counter=0;
+        unsigned int element_counter=0;
         for(int j = 0; j < 10; j++)        {
             int curr_element=rand()%(elment_count-2 + 1) + 1;
             if(curr_element == 0)
                 continue;
             element_buffer[element_counter++]=curr_element;
@@ -77,11 +77,11 @@
         if(ret_struct.max_weight < element_counter){
             ret_struct.max_weight = element_counter;
         }
         
         unsigned int * elements = new unsigned int[element_counter];
-        memcpy(elements,element_buffer,sizeof(int)*element_counter);
+        memcpy(elements,element_buffer,sizeof(unsigned int)*element_counter);
         unsigned short * weight = new unsigned short[element_counter];
         std::fill_n(weight, element_counter, 1);
         
         weights[i] = weight;
         sets[i] = elements;
@@ -148,11 +148,11 @@
     ret_struct.all_element_count=0;
 
     for(int i = 0; i<m; i++){
         std::getline(buffer, line);
         std::string token;
-        int element_counter=0;
+        unsigned int element_counter=0;
         line_stream.clear();
         line_stream.str(line);
         while (std::getline(line_stream, token, ' '))
         {
             int curr_element=atoi(token.c_str());
@@ -165,11 +165,11 @@
         if(ret_struct.max_weight < element_counter){
             ret_struct.max_weight = element_counter;
         }
 
         unsigned int * elements = new unsigned int[element_counter];
-        memcpy(elements,element_buffer,sizeof(int)*element_counter);
+        memcpy(elements,element_buffer,sizeof(unsigned int)*element_counter);
         unsigned short * weight = new unsigned short[element_counter];
         std::fill_n(weight, element_counter, 1);
 
         weights[i] = weight;
         sets[i] = elements;
@@ -200,11 +200,11 @@
                        set_data.max_weight,
                        set_data.all_element_count,
                        set_data.element_size_lookup
                        );
 
-    for(int i = 0; i < set_data.set_count; i++){
+    for(unsigned int i = 0; i < set_data.set_count; i++){
         setcover.add_set(i+1, set_data.set_sizes[i]
                          ,(const unsigned int*)set_data.sets[i],
                           (const unsigned short*)set_data.weights[i],
                           set_data.set_sizes[i]);
         free(set_data.sets[i]);
--- external/seqlib/htslib/sam.c.dist	2020-06-23 10:13:46.784811537 -0700
+++ external/seqlib/htslib/sam.c	2020-06-23 10:15:28.591855497 -0700
@@ -228,11 +228,11 @@
 int bam_hdr_write(BGZF *fp, const bam_hdr_t *h)
 {
     char buf[4];
     int32_t i, name_len, x;
     // write "BAM1"
-    strncpy(buf, "BAM\1", 4);
+    memcpy(buf, "BAM\1", 4);  // not strncpy, there is no space for a terminator
     if (bgzf_write(fp, buf, 4) < 0) return -1;
     // write plain text and the number of reference sequences
     if (fp->is_be) {
         x = ed_swap_4(h->l_text);
         if (bgzf_write(fp, &x, 4) < 0) return -1;
--- include/BooPHF.hpp.dist	2020-06-23 10:42:23.474905156 -0700
+++ include/BooPHF.hpp	2020-06-23 10:48:09.804083361 -0700
@@ -674,24 +674,24 @@
 		}
 
 		//for debug purposes
 		void print() const
 		{
-			printf("bit array of size %llu: \n",_size);
+			printf("bit array of size %" PRIu64 ": \n",_size);
 			for(uint64_t ii = 0; ii< _size; ii++)
 			{
 				if(ii%10==0)
-					printf(" (%llu) ",ii);
+					printf(" (%" PRIu64 ") ",ii);
 				int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1;
 				printf("%i",val);
 			}
 			printf("\n");
 
 			printf("rank array : size %lu \n",_ranks.size());
 			for (uint64_t ii = 0; ii< _ranks.size(); ii++)
 			{
-				printf("%llu :  %llu,  ",ii,_ranks[ii]);
+				printf("%" PRIu64 " :  %" PRIu64 ",  ",ii,_ranks[ii]);
 			}
 			printf("\n");
 		}
 
 		//return value at pos