Revert "update rmc browser globals"

This reverts commit 19d3b5e.

Author: ch-kr

rmc/utils/constraint.py

@@ -2089,45 +2089,50 @@ def _missing_aa_check(ht: hl.Table) -> Union[hl.Table, None]:
 
 
 def add_globals_rmc_browser(
-    ht: hl.Table,
-    filter_to_canonical: bool = True,
+    ht: hl.Table, filter_to_canonical: bool, keep_outliers: bool = True
 ) -> hl.Table:
     """
     Annotate HT globals with RMC transcript information.
 
     Function is used when reformatting RMC results for browser release.
-
-    Annotates two structs:
-        - `transcript_counts`: Counts of total transcripts and transcripts with/without evidence of RMC (QC pass only).
-        - `transcript_counts_all`: Counts of all transcripts, transcripts with/without evidence of RMC, and outlier transcripts.
-
+    Annotates:
+        - transcripts not searched for RMC
+        - transcripts without evidence of RMC
+        - outlier transcripts
     :param HT: Input Table. Should be RMC regions HT annotated with amino acid
         information for region starts and stops.
-    :param filter_to_canonical: Whether to filter to canonical transcripts only. Default is True.
+    :param filter_to_canonical: Whether to filter to canonical transcripts only.
+    :param keep_outliers: Whether to keep outlier transcripts.
+        Default is True.
     :return: RMC regions HT with updated globals annotations.
     """
-    # Get all transcripts with evidence of RMC
+    # Get transcripts with evidence of RMC
     rmc_transcripts = hl.literal(ht.aggregate(hl.agg.collect_as_set(ht.transcript)))
 
-    # Get all transcripts from constraint HT
-    all_transcripts = get_constraint_transcripts(
-        all_transcripts=True, filter_to_canonical=filter_to_canonical
+    # Get all QC pass transcripts
+    qc_pass_transcripts = get_constraint_transcripts(
+        filter_to_canonical=filter_to_canonical, outlier=False
     )
     outlier_transcripts = get_constraint_transcripts(
         filter_to_canonical=filter_to_canonical, outlier=True
     )
 
+    # Get all transcripts from constraint HT
+    all_transcripts = get_constraint_transcripts(
+        all_transcripts=True, filter_to_canonical=filter_to_canonical
+    )
+    if keep_outliers:
+        transcripts_no_rmc = all_transcripts.difference(rmc_transcripts)
+        transcripts_not_searched = hl.empty_array(hl.tstr)
+    else:
+        transcripts_no_rmc = qc_pass_transcripts.difference(rmc_transcripts)
+        transcripts_not_searched = all_transcripts.difference(qc_pass_transcripts)
+
     ht = ht.select_globals()
     return ht.annotate_globals(
-        transcript_counts=hl.struct(
-            all_transcripts=all_transcripts.difference(outlier_transcripts),
-            rmc_transcripts=rmc_transcripts.difference(outlier_transcripts),
-        ),
-        transcript_counts_all=hl.struct(
-            all_transcripts=all_transcripts,
-            rmc_transcripts=rmc_transcripts,
-            outlier_transcripts=outlier_transcripts,
-        ),
+        transcripts_not_searched=transcripts_not_searched,
+        transcripts_no_rmc=transcripts_no_rmc,
+        outlier_transcripts=outlier_transcripts,
     )