ctx_server.c: fix uninitialised memory access, resolves #28

ctx_server.c:
- initialise output string memory to zero [resolves issue #28]
- add command prompt "> "

mccortex-server.py:
- strip prompt text from mccortex responses
- add example line to usage help

Update libraries

scripts/mccortex-server.py

@@ -32,6 +32,8 @@ def query_mccortex(proc,kmer):
     proc.stdin.flush()
     check_mccortex_alive(proc)
     line = proc.stdout.readline()
+    # Trim off prompt text
+    if line[0:2] == "> ": line = line[2:len(line)]
     check_mccortex_alive(proc)
     return line
 
@@ -113,6 +115,7 @@ def do_GET(self):
 def main():
     if len(sys.argv) < 3 or not sys.argv[1].isdigit():
         print("usage: %s <port> [mccortex args]" % (sys.argv[0]))
+        print("  e.g  %s 1888 -m 2G graph.ctx" % (sys.argv[0]))
         sys.exit(-1)
 
     port = int(sys.argv[1])

src/commands/ctx_server.c

@@ -63,11 +63,11 @@ static inline void kmer_response(StrBuf *resp, dBNode node, const char *keystr,
 
   // Edges
   Edges edges = db_node_get_edges_union(db_graph, node.key);
-  char edgesstr[9], left[5], right[5], *l, *r;
+  char edgesstr[9], left[5] = {0}, right[5] = {0}, *l = left, *r = right;
   db_node_get_edges_str(edges, edgesstr);
-  for(l = left, i = 0; i < 4; i++)
+  for(i = 0; i < 4; i++)
     if(edgesstr[i] != '.') { *l = toupper(edgesstr[i]); *(++l) = '\0'; }
-  for(r = right, i = 4; i < 8; i++)
+  for(i = 4; i < 8; i++)
     if(edgesstr[i] != '.') { *r = edgesstr[i]; *(++r) = '\0'; }
 
   strbuf_append_str(resp, "\"left\": \"");
@@ -371,8 +371,11 @@ int ctx_server(int argc, char **argv)
   bool success;
 
   // Read from input
-  while(futil_fcheck(strbuf_reset_readline(&line, stdin), stdin, "STDIN") > 0)
+  while(1)
   {
+    fprintf(stdout, "> "); fflush(stdout);
+    if(futil_fcheck(strbuf_reset_readline(&line, stdin), stdin, "STDIN") == 0)
+      break;
     strbuf_chomp(&line);
     if(strcmp(line.b,"q") == 0) { break; }
     else if(strcmp(line.b,"info") == 0) {