Merge branch 'smalton/DOR-938-trimmed-modtags' into 'master'

[DOR-938] Invalid modtag Closes DOR-938 See merge request machine-learning/dorado!1283
nanoporetech · Nov 26, 2024 · afdb068 · afdb068
2 parents c397f72 + 4d37ddd
commit afdb068
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diff --git a/dorado/torch_utils/trim.cpp b/dorado/torch_utils/trim.cpp
@@ -174,9 +174,6 @@ std::tuple<std::string, std::vector<uint8_t>> trim_modbase_info(
                 }
                 mod.remove_prefix(std::min(comma_pos + 1, mod.length()));  // No comma at the end.
             }
-            if (counts.str().empty()) {
-                counts << ",";
-            }
             trimmed_modbase_str << std::string(prefix) << counts.str() << ";";
         }
     }

diff --git a/tests/TrimTest.cpp b/tests/TrimTest.cpp
@@ -162,14 +162,14 @@ TEST_CASE("Test trim mod base info", TEST_GROUP) {
         // the second mod is eliminated
         // in the third mod, first base position changes and the last is dropped
         auto [str, probs] = utils::trim_modbase_info(seq, modbase_str, modbase_probs, {3, 18});
-        CHECK(str == "A+a?,0,0;C+m?,;T+x?,1;");
+        CHECK(str == "A+a?,0,0;C+m?;T+x?,1;");
         const std::vector<uint8_t> expected = {2, 3, 20};
         CHECK_THAT(probs, Equals(expected));
     }
 
     SECTION("Trim whole sequence") {
         auto [str, probs] = utils::trim_modbase_info(seq, modbase_str, modbase_probs, {8, 8});
-        CHECK(str == "A+a?,;C+m?,;T+x?,;");
+        CHECK(str == "A+a?;C+m?;T+x?;");
         CHECK(probs.size() == 0);
     }
 }