Merge bbb127b into 20df516

ezorita · Jun 13, 2018 · cb64262 · cb64262
2 parents 20df516 + bbb127b
commit cb64262
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Showing 3 changed files with 15 additions and 8 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,15 +1,14 @@
 language: c
 
 compiler:
-  - clang
   - gcc
 
 branches:
   only:
     - master
 
 before_install:
-  - sudo pip install cpp-coveralls
+  - sudo pip install -U cpp-coveralls
 
 script: make && make lib && python setup.py build && cd test && make test && python python_lib_test.py
 

diff --git a/src/libseeq.c b/src/libseeq.c
@@ -288,19 +288,27 @@ seeqStringMatch
          size_t j = 0;
          uint32_t rnode = DFA_ROOT_STATE;
          int d = sq->tau + 1;
+	 int last_d, ignores = 0;
          // Find match start with RDFA.
          do {
             int c = (int)translate[(int)data[i-++j]];
+	    last_d = d;
             if (c < NBASES) {
+	       ignores = 0;
                vertex_t * vertex = (vertex_t *) (((dfa_t *)sq->rdfa)->states + rnode * state_size);
                uint32_t next = vertex->next[c];
                if (next == DFA_COMPUTE)
                   if (dfa_step(rnode, c, sq->wlen, sq->tau, (dfa_t **) &(sq->rdfa), sq->rkeys, &next)) return -1;
                rnode = next;
                vertex = (vertex_t *) (((dfa_t *)sq->rdfa)->states + rnode * state_size);
                d = get_match(vertex->match);
-            } else continue;
-         } while (d > streak_dist && j < i);
+            } else {
+	       ignores++;
+	       continue;
+	    }
+	    //         } while (d > streak_dist && j < i);
+	 } while (d <= last_d && j < i);
+	 j = (last_d < d ? j-1 : j) - ignores;
          size_t match_start = i-j;
          size_t match_end   = i;
          int match_dist  = streak_dist;

diff --git a/test/python_lib_test.py b/test/python_lib_test.py
@@ -16,8 +16,8 @@ def test_matchPrefix(self):
       nomatch = "ATGCTGATGCTGGGGG"
       match = "GGGGCGCTAATAATGGAATGGGG"
 
-      self.assertEqual(matcher.matchPrefix(nomatch, True), "")
-      self.assertEqual(matcher.matchPrefix(nomatch, False), "")
+      self.assertEqual(matcher.matchPrefix(nomatch, True), None)
+      self.assertEqual(matcher.matchPrefix(nomatch, False), None)
       self.assertEqual(matcher.matchPrefix(match, True),
             "GGGGCGCTAATAATGGAAT")
       self.assertEqual(matcher.matchPrefix(match, False), "GGGG")
@@ -28,8 +28,8 @@ def test_matchSuffix(self):
       nomatch = "ATGCTGATGCTGGGGG"
       match = "GGGGCGCTAATAATGGAATGGGG"
 
-      self.assertEqual(matcher.matchSuffix(nomatch, True), "")
-      self.assertEqual(matcher.matchSuffix(nomatch, False), "")
+      self.assertEqual(matcher.matchSuffix(nomatch, True), None)
+      self.assertEqual(matcher.matchSuffix(nomatch, False), None)
       self.assertEqual(matcher.matchSuffix(match, True),
             "CGCTAATAATGGAATGGGG")
       self.assertEqual(matcher.matchSuffix(match, False), "GGGG")