please please please

src/talos/RunHailFiltering.py

@@ -107,6 +107,23 @@ def annotate_exomiser(mt: hl.MatrixTable, exomiser: str | None = None) -> hl.Mat
     Returns:
         The same MatrixTable but with additional annotations
     """
+    if not exomiser or (
+        'exomiser'
+        in config_retrieve(
+            ['ValidateMOI', 'ignore_categories'],
+            [],
+        )
+    ):
+        get_logger().info('No exomiser table found, skipping annotation')
+        return mt.annotate_rows(info=mt.info.annotate(categorydetailsexomiser=MISSING_STRING))
+
+    get_logger().info(f'loading exomiser variants from {exomiser}')
+    exomiser_ht = hl.read_table(exomiser)
+    return mt.annotate_rows(
+        info=mt.info.annotate(
+            categorydetailsexomiser=hl.or_else(exomiser_ht[mt.row_key].proband_details, MISSING_STRING),
+        ),
+    )
 
     get_logger().info('No exomiser table found, skipping annotation')
     return mt.annotate_rows(info=mt.info.annotate(categorydetailsexomiser=MISSING_STRING))
@@ -235,16 +252,46 @@ def annotate_splicevardb(mt: hl.MatrixTable, svdb_path: str | None):
     Returns:
         Same MT with an extra category label
     """
+    if svdb_path is None or (
+        'svdb'
+        in config_retrieve(
+            ['ValidateMOI', 'ignore_categories'],
+            [],
+        )
+    ):
+        get_logger().info('Skipping SVDB annotation')
+        return mt.annotate_rows(
+            info=mt.info.annotate(
+                categorybooleansvdb=MISSING_INT,
+                svdb_location=MISSING_STRING,
+                svdb_method=MISSING_STRING,
+                svdb_doi=MISSING_STRING,
+            )
+        )
+
+        # read in the codon table
+    get_logger().info(f'Reading SpliceVarDB data from {svdb_path}')
+    svdb_ht = hl.read_table(svdb_path)
 
-    get_logger().info('SVDB table not found, skipping annotation')
+    # annotate relevant variants with the SVDB results
+    mt = mt.annotate_rows(
+        info=mt.info.annotate(
+            svdb_classification=hl.or_else(svdb_ht[mt.row_key].classification, MISSING_STRING),
+            svdb_location=hl.or_else(svdb_ht[mt.row_key].location, MISSING_STRING),
+            svdb_method=hl.or_else(svdb_ht[mt.row_key].method, MISSING_STRING),
+            svdb_doi=hl.or_else(svdb_ht[mt.row_key].doi, MISSING_STRING),
+        ),
+    )
+
+    # annotate category if Splice-altering according to SVDB
     return mt.annotate_rows(
         info=mt.info.annotate(
-            categorydetailssvdb=MISSING_STRING,
-            svdb_classification=MISSING_STRING,
-            svdb_location=MISSING_STRING,
-            svdb_method=MISSING_STRING,
-            svdb_doi=MISSING_STRING,
-        )
+            categorybooleansvdb=hl.if_else(
+                mt.info.svdb_classification.lower().contains(SPLICE_ALTERING),
+                ONE_INT,
+                MISSING_INT,
+            ),
+        ),
     )