fix: fix genotype-ignoring recall computation

snakemake-workflows · Jul 20, 2022 · a83f00d · a83f00d
1 parent c490007
commit a83f00d
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/notebooks/plot-precision-recall.py.ipynb b/workflow/notebooks/plot-precision-recall.py.ipynb
@@ -119,7 +119,7 @@
     "    report[\"coverage\"] = report[\"coverage\"].apply(lambda cov: snakemake.params.cov_labels[cov])\n",
     "\n",
     "    report[\"tp_no_gt\"] = report[\"QUERY.TOTAL\"] - report[\"QUERY.FP\"] + report[\"FP.gt\"]\n",
-    "    report[\"t\"] = report[\"tp_no_gt\"] + report[\"TRUTH.FN\"]\n",
+    "    report[\"t\"] = report[\"tp_no_gt\"] + report[\"TRUTH.FN\"] - report[\"FP.gt\"] # TRUTH.FN alone also counts mismatched genotypes.\n",
     "    report[\"precision\"] = report[\"tp_no_gt\"] / report[\"QUERY.TOTAL\"]\n",
     "    report[\"recall\"] = report[\"tp_no_gt\"] / (report[\"t\"])\n",
     "    report[\"correct genotype\"] = \"no\"\n",