Test for fail to load remaining cov values if HWE fails

raremetal/tests/tests.cpp

@@ -348,6 +348,52 @@ TEST_CASE("File I/O") {
     remove("test.group_var_missing_in_cov.meta.singlevar.results");
     remove("test.group_var_missing_in_cov.raremetal.log");
   }
+
+  SECTION("Regression test for HWE filtered variant stopping additional cov values from loading") {
+    /**
+     * Regression test for the following issue:
+     *   - Running meta-analysis with at least 2 studies
+     *   - Have a variant that fails HWE in one study, but not the other
+     *   - The variant failing HWE is present in a group
+     *
+     * A similar error will occur as in the "Regression test for group variant not present in covariance matrix file"
+     * test. The HWE filter causes the variant to be added to an exclusion list. When loading covariance for the study
+     * where the variant fails HWE, the program will stop loading covariance values for the remaining group variants
+     * while parsing that line of the covariance file.
+     */
+    Meta meta;
+    meta.prefix = "test.hwe_stops_cov_load";
+    meta.setLogFile();
+    meta.noPDF = true;
+    meta.Burden = true;
+    meta.HWE = 1e-05;
+    meta.MAF_cutoff = 1;
+
+    meta.scorefile.Add("tests/datasets/simulated/hwe_stops_cov_load/test.study1.MetaScore.assoc.gz");
+    meta.scorefile.Add("tests/datasets/simulated/hwe_stops_cov_load/test.study2.MetaScore.assoc.gz");
+    meta.covfile.Add("tests/datasets/simulated/hwe_stops_cov_load/test.study1.MetaCov.assoc.gz");
+    meta.covfile.Add("tests/datasets/simulated/hwe_stops_cov_load/test.study2.MetaCov.assoc.gz");
+
+    GroupFromAnnotation group;
+    group.groupFile = "tests/datasets/simulated/hwe_stops_cov_load/test.mask.tab";
+
+    meta.Prepare();
+    group.Run("", meta.log);
+    meta.PoolSummaryStat(group);
+    meta.WriteSingleVariantResults(group);
+    meta.Run(group);
+
+    auto results = RMGroupTestReader("test.hwe_stops_cov_load.meta.burden.results");
+    auto burden_p = results.get_record("FAIL1");
+
+    // If the bug is present, the p-value will be ~ 0.47, because it fails to load the cov value of 0.95 for study 1
+    REQUIRE(burden_p->pvalue == Approx(0.936002));
+
+    // Cleanup
+    remove("test.hwe_stops_cov_load.meta.burden.results");
+    remove("test.hwe_stops_cov_load.meta.singlevar.results");
+    remove("test.hwe_stops_cov_load.raremetal.log");
+  }
 }
 
 TEST_CASE("Heterogeneity statistics") {

tests/datasets/simulated/hwe_stops_cov_load/test.mask.tab

@@ -0,0 +1 @@
+FAIL1	1:14896:A:T	1:14897:T:C	1:14898:T:A