From 188b16db9c7127abba46c9fc3897e9e14cb0fd12 Mon Sep 17 00:00:00 2001
From: d-laub <dlaub@ucsd.edu>
Date: Sun, 2 Nov 2025 20:09:26 -0800
Subject: [PATCH 1/2] fix: use ak.str.length instead of ak.num to get ref and
 alt lengths. docs: shape docstring

---
 python/genvarloader/_dataset/_impl.py         |  2 +-
 python/genvarloader/_dataset/_rag_variants.py | 23 +++++++++++++++++--
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/python/genvarloader/_dataset/_impl.py b/python/genvarloader/_dataset/_impl.py
index 8136edb..8de4ceb 100644
--- a/python/genvarloader/_dataset/_impl.py
+++ b/python/genvarloader/_dataset/_impl.py
@@ -734,7 +734,7 @@ def ploidy(self) -> int | None:
 
     @property
     def shape(self) -> tuple[int, int]:
-        """Return the shape of the dataset. :code:`(n_samples, n_regions)`"""
+        """Return the shape of the dataset. :code:`(n_regions, n_samples)`"""
         return self.n_regions, self.n_samples
 
     @property
diff --git a/python/genvarloader/_dataset/_rag_variants.py b/python/genvarloader/_dataset/_rag_variants.py
index 15a2cfe..ee85ffe 100644
--- a/python/genvarloader/_dataset/_rag_variants.py
+++ b/python/genvarloader/_dataset/_rag_variants.py
@@ -31,7 +31,7 @@ class RaggedVariant(ak.Record):
 
 class RaggedVariants(ak.Array):
     """An awkward record array, typically with shape (batch, ploidy, ~variants).
-    Guaranteed to at least have the field "alts" and "v_starts" and one of "refs" or "ilens"."""
+    Guaranteed to at least have the field "alt" and "start" and one of "ref" or "ilen"."""
 
     def __init__(
         self,
@@ -59,6 +59,25 @@ def __init__(
 
         super().__init__(arr)
 
+    @classmethod
+    def from_ak(cls, arr: ak.Array) -> RaggedVariants:
+        """Create a RaggedVariants object from an awkward array.
+
+        Parameters
+        ----------
+        arr
+            The awkward array to create a RaggedVariants object from.
+        """
+        fields = set(arr.fields)
+
+        if missing := {"alt", "start"} - fields:
+            raise ValueError(f"Missing required fields: {missing}")
+
+        if {"ref", "ilen"}.isdisjoint(fields):
+            raise ValueError("Must have one of ref or ilen.")
+
+        return ak.with_parameter(arr, "__record__", RaggedVariants.__name__)
+
     @property
     def alt(self) -> ak.Array:
         """Alternative alleles."""
@@ -73,7 +92,7 @@ def start(self) -> Ragged[POS_TYPE]:
     def ilen(self) -> Ragged[np.int32]:
         """Indel lengths. Infallible."""
         if "ilen" not in self.fields:
-            ilen = ak.num(self.alt, -1) - ak.num(self.ref, -1)
+            ilen = ak.str.length(self.alt) - ak.str.length(self.ref)  # type: ignore
             ilen = Ragged(ilen)
             return ilen
 

From 46d0b4fdbda3eadf381d23464b50e404ae220837 Mon Sep 17 00:00:00 2001
From: d-laub <dlaub@ucsd.edu>
Date: Sun, 2 Nov 2025 20:14:13 -0800
Subject: [PATCH 2/2] fix: correctly parse and load variant fields (skip
 duplicates)

---
 python/genvarloader/_dataset/_impl.py        | 2 +-
 python/genvarloader/_dataset/_reconstruct.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/genvarloader/_dataset/_impl.py b/python/genvarloader/_dataset/_impl.py
index 8de4ceb..da53fcc 100644
--- a/python/genvarloader/_dataset/_impl.py
+++ b/python/genvarloader/_dataset/_impl.py
@@ -739,7 +739,7 @@ def shape(self) -> tuple[int, int]:
 
     @property
     def full_shape(self) -> tuple[int, int]:
-        """Return the full shape of the dataset, ignoring any subsetting. :code:`(n_samples, n_regions)`"""
+        """Return the full shape of the dataset, ignoring any subsetting. :code:`(n_regions, n_samples)`"""
         return self._idxer.full_shape
 
     @property
diff --git a/python/genvarloader/_dataset/_reconstruct.py b/python/genvarloader/_dataset/_reconstruct.py
index 33f70ba..1a328c4 100644
--- a/python/genvarloader/_dataset/_reconstruct.py
+++ b/python/genvarloader/_dataset/_reconstruct.py
@@ -80,7 +80,7 @@ def from_table(cls, path: str | Path, one_based: bool = True):
         info = {
             k: variants[k].to_numpy()
             for k, v in variants.schema.items()
-            if v.is_numeric()
+            if v.is_numeric() and k not in {"POS", "ILEN"}
         }
 
         ref = (