suggested fix to handle RCs in opt.runs + minor change in the test

OndrejSladky · Feb 12, 2024 · 9e8919a · 9e8919a
1 parent 88b9e8f
commit 9e8919a
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 2 deletions.
diff --git a/src/parser.h b/src/parser.h
@@ -187,6 +187,10 @@ std::pair<size_t, size_t> ReadIntervals(kh_O64_t *intervals, kh_S64_t *kMers, st
             --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 set = false;
                 if (represented) {
                     interval_used = true;

diff --git a/tests/masks_unittest.h b/tests/masks_unittest.h
@@ -115,7 +115,7 @@ namespace {
 
     TEST(Mask, OptimizeRuns2) {
         std::string path = std::filesystem::current_path();
-        path += "/tests/testdata/runstest2.fa"; // ACTaGta
+        path += "/tests/testdata/runstest2.fa"; // ACtaGta
 
         struct TestCase {
             std::vector<kmer_t> kMers;

diff --git a/tests/testdata/runstest2.fa b/tests/testdata/runstest2.fa
@@ -1,2 +1,2 @@
 > superstring
-ACTaGta
+ACtaGta