Improved code style in runs bugfix.

OndrejSladky · Feb 12, 2024 · 5f4647c · 5f4647c
1 parent 9e8919a
commit 5f4647c
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Showing 2 changed files with 7 additions and 33 deletions.
diff --git a/src/parser.h b/src/parser.h
@@ -186,11 +186,7 @@ std::pair<size_t, size_t> ReadIntervals(kh_O64_t *intervals, kh_S64_t *kMers, st
             currentKMer |= data;
             --beforeKMerEnd;
             if (beforeKMerEnd == 0) {
-                bool represented = kh_get_S64(kMers, currentKMer) != kh_end(kMers);
-                if (!represented && complements) {
-                    auto rc = ReverseComplement(currentKMer, k);
-                    represented = kh_get_S64(kMers, rc) != kh_end(kMers);
-                }
+                bool represented = containsKMer(kMers, currentKMer, k, complements);
                 bool set = false;
                 if (represented) {
                     interval_used = true;

diff --git a/tests/masks_unittest.h b/tests/masks_unittest.h
@@ -67,13 +67,13 @@ namespace {
 
     TEST(Mask, OptimizeRuns) {
         std::string path = std::filesystem::current_path();
-        path += "/tests/testdata/runstest.fa";
 
         struct TestCase {
             std::vector<kmer_t> kMers;
             int k;
             bool complements;
             bool approximate;
+            std::string relativePath;
             std::string wantResult;
         };
         std::vector<TestCase> tests = {
@@ -86,6 +86,7 @@ namespace {
                             KMerToNumber({"AT"})
                         },
                         2, false, false,
+                        "/tests/testdata/runstest.fa",
                         "> superstring\nacgcgttACGtATt\n"
                 },
                 {
@@ -97,52 +98,29 @@ namespace {
                                 KMerToNumber({"AT"})
                         },
                         2, false, true,
+                        "/tests/testdata/runstest.fa",
                         "> superstring\nACgCGTtACGtATt\n"
                 },
-        };
-
-        for (auto &t : tests) {
-            std::stringstream of;
-            auto kMersDict = kh_init_S64();
-            int ret;
-            for (auto &kMer : t.kMers) kh_put_S64(kMersDict, kMer, &ret);
-
-            OptimizeRuns(path, kMersDict, of, t.k, t.complements, t.approximate);
-
-            EXPECT_EQ(t.wantResult, of.str());
-        }
-    }
-
-    TEST(Mask, OptimizeRuns2) {
-        std::string path = std::filesystem::current_path();
-        path += "/tests/testdata/runstest2.fa"; // ACtaGta
-
-        struct TestCase {
-            std::vector<kmer_t> kMers;
-            int k;
-            bool complements;
-            bool approximate;
-            std::string wantResult;
-        };
-        std::vector<TestCase> tests = {
                 {
                         {
                                 KMerToNumber({"ACT"}),
                                 KMerToNumber({"CTA"}),
                                 KMerToNumber({"GTA"})
                         },
                         3, true, false,
+                        "/tests/testdata/runstest2.fa",
                         "> superstring\nACTAGta\n"
                 },
         };
 
         for (auto &t : tests) {
             std::stringstream of;
+            auto totalPath = path + t.relativePath;
             auto kMersDict = kh_init_S64();
             int ret;
             for (auto &kMer : t.kMers) kh_put_S64(kMersDict, kMer, &ret);
 
-            OptimizeRuns(path, kMersDict, of, t.k, t.complements, t.approximate);
+            OptimizeRuns(totalPath, kMersDict, of, t.k, t.complements, t.approximate);
 
             EXPECT_EQ(t.wantResult, of.str());
         }