[query] Teach hail to export a VDS to an SVCR-VCF (hail-is#14743)

Usage and notes in the documentation for the new methods. Part of hail-is#14655. ## Security Assessment - This change has no security impact ### Impact Description Does not increase attack surface. New methods only call into old ones. --------- Co-authored-by: Patrick Schultz <[email protected]>
chrisvittal · Oct 30, 2024 · 056d9f2 · 056d9f2
1 parent 8cd0c70
commit 056d9f2
Show file tree

Hide file tree

Showing 3 changed files with 421 additions and 14 deletions.
diff --git a/hail/python/hail/vds/__init__.py b/hail/python/hail/vds/__init__.py
@@ -1,6 +1,7 @@
 from . import combiner
 from .combiner import load_combiner, new_combiner
 from .functions import lgt_to_gt, local_to_global
+from .impex import export_vcf, import_vcf
 from .methods import (
     filter_chromosomes,
     filter_intervals,
@@ -22,26 +23,28 @@
 
 __all__ = [
     'VariantDataset',
-    'read_vds',
+    'combiner',
+    'export_vcf',
+    'filter_chromosomes',
     'filter_intervals',
     'filter_samples',
     'filter_variants',
-    'filter_chromosomes',
-    'sample_qc',
-    'split_multi',
-    'to_dense_mt',
-    'to_merged_sparse_mt',
-    'combiner',
-    'load_combiner',
-    'new_combiner',
-    'write_variant_datasets',
-    'segment_reference_blocks',
-    'interval_coverage',
+    'import_vcf',
     'impute_sex_chr_ploidy_from_interval_coverage',
     'impute_sex_chromosome_ploidy',
-    'truncate_reference_blocks',
-    'merge_reference_blocks',
+    'interval_coverage',
     'lgt_to_gt',
+    'load_combiner',
     'local_to_global',
+    'merge_reference_blocks',
+    'new_combiner',
+    'read_vds',
+    'sample_qc',
+    'segment_reference_blocks',
+    'split_multi',
     'store_ref_block_max_length',
+    'to_dense_mt',
+    'to_merged_sparse_mt',
+    'truncate_reference_blocks',
+    'write_variant_datasets',
 ]