Fixed off by one error.

OndrejSladky · Jul 6, 2024 · d425dc7 · d425dc7
1 parent 7f1df37
commit d425dc7
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Showing 3 changed files with 63 additions and 1 deletion.
diff --git a/src/fms_index.h b/src/fms_index.h
@@ -60,7 +60,8 @@ size_t rank(const fms_index& index, size_t i, byte c) {
     } else { // A/C
         auto c_position = index.ac_rank(i - gt_position);
         if (c == 0) { // A
-            return i - gt_position - c_position - (i >= index.dollar_position);
+            // Ranks are offset by 1 compared to the indices.
+            return i - gt_position - c_position - (i >= index.dollar_position + 1);
         } else { // C
             return c_position;
         }
@@ -151,6 +152,7 @@ fms_index construct(std::string ms) {
         bwt[isa[i+1]] = char_to_int(ms[i]);
         sa_transformed_mask[isa[i]] = is_upper(ms[i]);
     }
+
     index.dollar_position = isa[0];
     delete[] isa;
     index.sa_transformed_mask = sdsl::rrr_vector<>(sa_transformed_mask);

diff --git a/src/main.cpp b/src/main.cpp
@@ -284,6 +284,9 @@ int ms_query(int argc, char *argv[]) {
   } else if (fn.empty()) {
     std::cerr << "Path to the fasta file is a required argument." << std::endl;
     return usage_query();
+  } else if (k == 0) {
+    std::cerr << "k is a required argument." << std::endl;
+    return usage_query();
   }
 
   fms_index index = load_index(fn);

diff --git a/tests/fms_index_test.h b/tests/fms_index_test.h
@@ -22,6 +22,23 @@ namespace {
         ret.gt_rank.set_vector(&ret.gt);
         return ret;
     }
+    fms_index get_dummy_index2() {
+        fms_index ret = { //GGTAAGA$, 11001000$
+                sdsl::bit_vector({0, 1, 1, 0, 0, 0, 1, 1, 1}),
+                sdsl::rank_support_v5<1>(),
+                sdsl::bit_vector({0, 0, 0, 0}),
+                sdsl::rank_support_v5<1>(),
+                sdsl::bit_vector({0,1,0,1,0}),
+                sdsl::rank_support_v5<1>(),
+                sdsl::rrr_vector<>({0,0,1,0,0,1,1,0,0}),
+                std::vector<size_t>({1, 4, 4, 7}),
+                5
+        };
+        ret.ac_gt_rank.set_vector(&ret.ac_gt);
+        ret.ac_rank.set_vector(&ret.ac);
+        ret.gt_rank.set_vector(&ret.gt);
+        return ret;
+    }
 
     TEST(FMS_INDEX, RANK) {
         auto index = get_dummy_index();
@@ -48,6 +65,26 @@ namespace {
         }
     }
 
+    TEST(FMS_INDEX, RANK2) {
+        auto index = get_dummy_index2();
+        struct test_case {
+            size_t i;
+            byte c;
+            size_t want_result;
+        };
+        std::vector<test_case> tests = {
+                {4, 0, 2},
+                {5, 0, 3},
+                {6, 0, 3}
+        };
+
+        for (auto t: tests) {
+            auto got_result = rank(index, t.i, t.c);
+
+            EXPECT_EQ(got_result, t.want_result);
+        }
+    }
+
     TEST(FMS_INDEX, UPDATE_RANGE) {
         auto index = get_dummy_index();
         struct test_case {
@@ -100,6 +137,26 @@ namespace {
         }
     }
 
+    TEST(FMS_INDEX, QUERY2) {
+        auto index = get_dummy_index2();
+        struct test_case {
+            std::string query;
+            bool want_result;
+        };
+        std::vector<test_case> tests = {
+                {"AAGA", true},
+                {"AAGAA", false},
+                {"GGTTAAGA", true},
+                {"GTTAAGA", true},
+        };
+
+        for (auto t: tests) {
+            auto got_result = query(index, t.query, nullptr);
+
+            EXPECT_EQ(got_result, t.want_result);
+        }
+    }
+
     TEST (FMS_INDEX, CONSTRUCT) {
         std::string masked_superstring = "CaGGTag";
         fms_index index = construct(masked_superstring);