Fix field references (#827)

* Fix field references

* Fix test

* Fix test

* Update tests

* Fix annotation

Author: bpblanken

v03_pipeline/lib/methods/relatedness.py

@@ -30,7 +30,7 @@ def call_relatedness(
     # - brew install lz4
     # - CXXFLAGS='-I/opt/homebrew/include/' HAIL_COMPILE_NATIVES=1 make -C hail install
     # Hail issue here: https://discuss.hail.is/t/noclassdeffounderror-could-not-initialize-class-is-hail-methods-ibsffi/2453
-    kin_ht = hl.identity_by_descent(mt, maf=mt.info.AF[0], min=0.10, max=1.0)
+    kin_ht = hl.identity_by_descent(mt, maf=mt['info.AF'][0], min=0.10, max=1.0)
     kin_ht = kin_ht.key_by('i', 'j')
     return kin_ht.select(
         ibd0=kin_ht.ibd.Z0,

v03_pipeline/lib/misc/vets.py

@@ -7,7 +7,7 @@
 
 
 def annotate_vets(mt: hl.MatrixTable) -> hl.MatrixTable:
-    if not hasattr(mt, 'info') or not hasattr(mt.info, 'CALIBRATION_SENSITIVITY'):
+    if not hasattr(mt, 'info.CALIBRATION_SENSITIVITY'):
         return mt
     return mt.annotate_rows(
         filters=hl.bind(
@@ -34,6 +34,6 @@ def annotate_vets(mt: hl.MatrixTable) -> hl.MatrixTable:
                 )
             ),
             hl.is_snp(mt.alleles[0], mt.alleles[1]),
-            hl.parse_float(mt.info.CALIBRATION_SENSITIVITY[mt.a_index - 1]),
+            hl.parse_float(mt['info.CALIBRATION_SENSITIVITY'][mt.a_index - 1]),
         ),
     )

v03_pipeline/lib/misc/vets_test.py

@@ -77,13 +77,13 @@ def test_annotate_vets(self) -> None:
                     hl.empty_set(hl.tstr),
                     hl.set(['NO_HQ_GENOTYPES']),
                 ],
-                'info': [
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.999']),
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.995']),
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.999']),
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.98']),
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.99']),
-                    hl.Struct(CALIBRATION_SENSITIVITY=['0.991']),
+                'info.CALIBRATION_SENSITIVITY': [
+                    ['0.999'],
+                    ['0.995'],
+                    ['0.999'],
+                    ['0.98'],
+                    ['0.99'],
+                    ['0.991'],
                 ],
             },
             cols={'s': ['sample_1']},

v03_pipeline/lib/tasks/write_relatedness_check_table_test.py

@@ -58,6 +58,7 @@ def setUp(self) -> None:
         # Force imported callset to be complete
         ht = import_vcf(TEST_VCF, ReferenceGenome.GRCh38)
         ht = ht.annotate_globals(sample_type=SampleType.WGS.value)
+        ht = ht.annotate_rows(**{'info.AF': ht.info.AF})
         ht.write(
             imported_callset_path(
                 ReferenceGenome.GRCh38,

v03_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.README.txt.crc

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.128-eead8100a1c1
-  Created at 2024/03/13 11:46:28
+  Written with version 0.2.130-bea04d9c79b5
+  Created at 2024/07/01 14:46:50

v03_pipeline/var/test/callsets/sex_and_relatedness_1.mt/.metadata.json.gz.crc

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.128-eead8100a1c1
-  Created at 2024/03/13 11:46:28
+  Written with version 0.2.130-bea04d9c79b5
+  Created at 2024/07/01 14:46:50

v03_pipeline/var/test/callsets/sex_and_relatedness_1.mt/README.txt

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.128-eead8100a1c1
-  Created at 2024/03/13 11:46:28
+  Written with version 0.2.130-bea04d9c79b5
+  Created at 2024/07/01 14:46:50

v03_pipeline/var/test/callsets/sex_and_relatedness_1.mt/cols/.README.txt.crc

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.128-eead8100a1c1
-  Created at 2024/03/13 11:46:28
+  Written with version 0.2.130-bea04d9c79b5
+  Created at 2024/07/01 14:46:50

v03_pipeline/var/test/callsets/sex_and_relatedness_1.mt/cols/.metadata.json.gz.crc

@@ -1,3 +1,3 @@
 This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-  Written with version 0.2.128-eead8100a1c1
-  Created at 2024/03/13 11:46:28
+  Written with version 0.2.130-bea04d9c79b5
+  Created at 2024/07/01 14:46:50