From 6aaee4feb35229e75455ce0ace01ae859b8119f2 Mon Sep 17 00:00:00 2001
From: willtyler <will.tyler11@gmail.com>
Date: Sat, 27 Jul 2024 16:21:33 +0000
Subject: [PATCH] Change local alleles default to false

---
 bio2zarr/cli.py                   | 2 +-
 bio2zarr/vcf2zarr/icf.py          | 2 +-
 bio2zarr/vcf2zarr/verification.py | 4 ----
 tests/test_cli.py                 | 6 +++---
 tests/test_vcf_examples.py        | 2 +-
 5 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/bio2zarr/cli.py b/bio2zarr/cli.py
index 98f39ee..0722521 100644
--- a/bio2zarr/cli.py
+++ b/bio2zarr/cli.py
@@ -152,7 +152,7 @@ def list_commands(self, ctx):
 local_alleles = click.option(
     "--local-alleles/--no-local-alleles",
     show_default=True,
-    default=True,
+    default=False,
     help="Use local allele fields to reduce the storage requirements of the output.",
 )
 
diff --git a/bio2zarr/vcf2zarr/icf.py b/bio2zarr/vcf2zarr/icf.py
index f5554c5..7646826 100644
--- a/bio2zarr/vcf2zarr/icf.py
+++ b/bio2zarr/vcf2zarr/icf.py
@@ -1155,7 +1155,7 @@ def init(
         if compressor is None:
             compressor = ICF_DEFAULT_COMPRESSOR
         if local_alleles is None:
-            local_alleles = True
+            local_alleles = False
         vcfs = [pathlib.Path(vcf) for vcf in vcfs]
         target_num_partitions = max(target_num_partitions, len(vcfs))
 
diff --git a/bio2zarr/vcf2zarr/verification.py b/bio2zarr/vcf2zarr/verification.py
index 1b414f9..27e86fe 100644
--- a/bio2zarr/vcf2zarr/verification.py
+++ b/bio2zarr/vcf2zarr/verification.py
@@ -170,10 +170,6 @@ def verify(vcf_path, zarr_path, show_progress=False):
     for colname in root.keys():
         if colname.startswith("call") and not colname.startswith("call_genotype"):
             vcf_name = colname.split("_", 1)[1]
-            if vcf_name == "LAA" and vcf_name not in format_headers:
-                continue  # LAA could have been computed during the explode step.
-            if vcf_name == "LPL" and vcf_name not in format_headers:
-                continue  # LPL could have been computed during the explode step.
             vcf_type = format_headers[vcf_name]["Type"]
             vcf_number = format_headers[vcf_name]["Number"]
             format_fields[vcf_name] = vcf_type, vcf_number, iter(root[colname])
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 5bcb0ba..4508637 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -14,7 +14,7 @@
     compressor=None,
     worker_processes=1,
     show_progress=True,
-    local_alleles=True,
+    local_alleles=False,
 )
 
 DEFAULT_DEXPLODE_PARTITION_ARGS = dict()
@@ -24,7 +24,7 @@
     column_chunk_size=64,
     compressor=None,
     show_progress=True,
-    local_alleles=True,
+    local_alleles=False,
 )
 
 DEFAULT_ENCODE_ARGS = dict(
@@ -54,7 +54,7 @@
     samples_chunk_size=None,
     show_progress=True,
     worker_processes=1,
-    local_alleles=True,
+    local_alleles=False,
 )
 
 DEFAULT_PLINK_CONVERT_ARGS = dict(
diff --git a/tests/test_vcf_examples.py b/tests/test_vcf_examples.py
index e4f48b5..5e2dfb8 100644
--- a/tests/test_vcf_examples.py
+++ b/tests/test_vcf_examples.py
@@ -537,7 +537,7 @@ class Test1000G2020Example:
     @pytest.fixture(scope="class")
     def ds(self, tmp_path_factory):
         out = tmp_path_factory.mktemp("data") / "example.vcf.zarr"
-        vcf2zarr.convert([self.data_path], out, worker_processes=0)
+        vcf2zarr.convert([self.data_path], out, worker_processes=0, local_alleles=True)
         return sg.load_dataset(out)
 
     def test_position(self, ds):