{"action":"created","comment":{"url":"https://api.github.com/repos/macarthur-lab/gnomad_hail/pulls/comments/171750020","pull_request_review_id":100659451,"id":171750020,"diff_hunk":"@@ -670,147 +493,134 @@ def read_list_data(input_file):\n \n \n def rename_samples(vds, input_file, filter_to_samples_in_file=False):\n+    \"\"\"\n     names = {old: new for old, new in [x.split(\"\\t\") for x in read_list_data(input_file)]}\n     logger.info(\"Found %d samples for renaming in input file %s.\" % (len(names.keys()), input_file))\n     logger.info(\"Renaming %d samples found in VDS\" % len(set(names.keys()).intersection(set(vds.sample_ids)) ))\n \n     if filter_to_samples_in_file:\n         vds = vds.filter_samples_list(names.keys())\n     return vds.rename_samples(names)\n+    \"\"\"\n+    raise NotImplementedError\n \n \n-def filter_low_conf_regions(vds, filter_lcr=True, filter_decoy=True, high_conf_regions=None):\n+def filter_low_conf_regions(vds, filter_lcr=True, filter_decoy=True, filter_segdup=True, high_conf_regions=None):\n     \"\"\"\n     Filters low-confidence regions\n \n-    :param VariantDataset vds: VDS to filter\n+    :param MatrixTable vds: VDS to filter\n     :param bool filter_lcr: Whether to filter LCR regions\n-    :param bool filter_decoy: Wheter to filter Segdup regions\n+    :param bool filter_decoy: Whether to filter decoy regions\n+    :param bool filter_segdup: Whether to filter Segdup regions\n     :param list of str high_conf_regions: Paths to set of high confidence regions to restrict to (union of regions)\n-    :return:\n+    :return: VDS with low confidence regions removed\n+    :rtype: MatrixTable\n     \"\"\"\n+    from gnomad_hail.resources import lcr_intervals_path, decoy_intervals_path, segdup_intervals_path\n \n     if filter_lcr:\n-        vds = vds.filter_variants_table(KeyTable.import_interval_list(lcr_intervals_path), keep=False)\n+        lcr = hl.import_interval_list(lcr_intervals_path)\n+        vds = vds.filter_rows(lcr[vds.locus], keep=False)\n \n     if filter_decoy:\n-        vds = vds.filter_variants_table(KeyTable.import_interval_list(decoy_intervals_path), keep=False)\n+        decoy = hl.import_interval_list(decoy_intervals_path)\n+        vds = vds.filter_rows(decoy[vds.locus], keep=False)\n+\n+    if filter_segdup:\n+        segdup = hl.import_interval_list(segdup_intervals_path)\n+        vds = vds.filter_rows(segdup[vds.locus], keep=False)\n \n     if high_conf_regions is not None:\n         for region in high_conf_regions:\n-            vds = vds.filter_variants_table(KeyTable.import_interval_list(region), keep=True)\n+            region = hl.import_interval_list(region)\n+            vds = vds.filter_rows(region[vds.locus], keep=True)\n \n     return vds\n \n \n-def process_consequences(vds, vep_root='va.vep', genes_to_string=True):\n+def process_consequences(vds, vep_root='vep'):\n     \"\"\"\n     Adds most_severe_consequence (worst consequence for a transcript) into [vep_root].transcript_consequences,\n-    and worst_csq and worst_csq_suffix (worst consequence across transcripts) into [vep_root]\n+    and worst_csq_by_gene, canonical_csq_by_gene, any_lof into [vep_root]\n \n-    :param VariantDataset vds: Input VDS\n-    :param str vep_root: Root for vep annotation (probably va.vep)\n+    :param MatrixTable vds: Input VDS\n+    :param str vep_root: Root for vep annotation (probably vep)\n     :return: VDS with better formatted consequences\n-    :rtype: VariantDataset\n+    :rtype: MatrixTable\n     \"\"\"\n-    if vep_root + '.worst_csq' in flatten_struct(vds.variant_schema, root='va'):\n-        vds = (vds.annotate_variants_expr('%(vep)s.transcript_consequences = '\n-                                          ' %(vep)s.transcript_consequences.map('\n-                                          '     csq => drop(csq, most_severe_consequence)'\n-                                          ')' % {'vep': vep_root}))\n-    vds = (vds.annotate_global('global.csqs', CSQ_ORDER, TArray(TString()))\n-           .annotate_variants_expr(\n-        '%(vep)s.transcript_consequences = '\n-        '   %(vep)s.transcript_consequences.map(csq => '\n-        '   let worst_csq = global.csqs.find(c => csq.consequence_terms.toSet().contains(c)) in'\n-        # '   let worst_csq_suffix = if (csq.filter(x => x.lof == \"HC\").length > 0)'\n-        # '       worst_csq + \"-HC\" '\n-        # '   else '\n-        # '       if (csq.filter(x => x.lof == \"LC\").length > 0)'\n-        # '           worst_csq + \"-LC\" '\n-        # '       else '\n-        # '           if (csq.filter(x => x.polyphen_prediction == \"probably_damaging\").length > 0)'\n-        # '               worst_csq + \"-probably_damaging\"'\n-        # '           else'\n-        # '               if (csq.filter(x => x.polyphen_prediction == \"possibly_damaging\").length > 0)'\n-        # '                   worst_csq + \"-possibly_damaging\"'\n-        # '               else'\n-        # '                   worst_csq in'\n-        '   merge(csq, {most_severe_consequence: worst_csq'\n-        # ', most_severe_consequence_suffix: worst_csq_suffix'\n-        '})'\n-        ')' % {'vep': vep_root}\n-    ).annotate_variants_expr(\n-        '%(vep)s.worst_csq = global.csqs.find(c => %(vep)s.transcript_consequences.map(x => x.most_severe_consequence).toSet().contains(c)),'\n-        '%(vep)s.worst_csq_suffix = '\n-        'let csq = global.csqs.find(c => %(vep)s.transcript_consequences.map(x => x.most_severe_consequence).toSet().contains(c)) in '\n-        'if (%(vep)s.transcript_consequences.filter(x => x.lof == \"HC\" && x.lof_flags == \"\").length > 0)'\n-        '   csq + \"-HC\" '\n-        'else '\n-        '   if (%(vep)s.transcript_consequences.filter(x => x.lof == \"HC\").length > 0)'\n-        '       csq + \"-HC-flag\" '\n-        '   else '\n-        '       if (%(vep)s.transcript_consequences.filter(x => x.lof == \"LC\").length > 0)'\n-        '           csq + \"-LC\" '\n-        '       else '\n-        '           if (%(vep)s.transcript_consequences.filter(x => x.polyphen_prediction == \"probably_damaging\").length > 0)'\n-        '               csq + \"-probably_damaging\"'\n-        '           else'\n-        '               if (%(vep)s.transcript_consequences.filter(x => x.polyphen_prediction == \"possibly_damaging\").length > 0)'\n-        '                   csq + \"-possibly_damaging\"'\n-        '               else'\n-        '                   if (%(vep)s.transcript_consequences.filter(x => x.polyphen_prediction == \"benign\").length > 0)'\n-        '                       csq + \"-benign\"'\n-        '                   else'\n-        '                       csq' % {'vep': vep_root}\n-    ).annotate_variants_expr(\n-        '{vep}.lof = \"-HC\" ~ {vep}.worst_csq_suffix, '\n-        '{vep}.worst_csq_genes = {vep}.transcript_consequences'\n-        '.filter(x => x.most_severe_consequence == {vep}.worst_csq).map(x => x.gene_symbol).toSet(){genes_to_string}'.format(\n-            vep=vep_root, genes_to_string='.mkString(\"|\")' if genes_to_string else '')\n-    ))\n-    return vds\n-\n-\n-def filter_vep_to_canonical_transcripts(vds, vep_root='va.vep'):\n-    return vds.annotate_variants_expr(\n-        '{vep}.transcript_consequences = '\n-        '   {vep}.transcript_consequences.filter(csq => csq.canonical == 1)'.format(vep=vep_root))\n-\n+    csqs = hl.capture(CSQ_ORDER)\n+    csq_dict = hl.capture(dict(zip(CSQ_ORDER, range(len(CSQ_ORDER)))))\n \n+    def add_most_severe_consequence(tc):\n+        \"\"\"\n+        Add most_severe_consequence annotation to transcript consequences\n+        This is for a given transcript, as there are often multiple annotations for a single transcript:\n+        e.g. splice_region_variant&intron_variant -> splice_region_variant\n \n+        :param StructExpression tc: Transcript consequences expression\n+        :return: Transcript consequences expression with most_severe_consequence\n+        :rtype StructExpression\n+        \"\"\"\n+        return hl.merge(tc, 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