Initial pass at computing LAA values

Author: jeromekelleher

bio2zarr/vcf2zarr/vcz.py

@@ -197,6 +197,8 @@ def convert_local_allele_field_types(fields):
     gt = fields_by_name["call_genotype"]
     if gt.shape[-1] != 2:
         raise ValueError("Local alleles only supported on diploid data")
+    # TODO check if LAA is already in here
+
     shape = gt.shape[:-1]
     chunks = gt.chunks[:-1]
 
@@ -214,6 +216,7 @@ def convert_local_allele_field_types(fields):
     )
     pl = fields_by_name.get("call_PL", None)
     if pl is not None:
+        # TODO check if call_LPL is in the list already
         pl.name = "call_LPL"
         pl.vcf_field = None
         pl.shape = (*shape, 3)
@@ -511,6 +514,46 @@ def fromdict(d):
         return ret
 
 
+def compute_laa_field(genotypes, alleles) -> np.ndarray:
+    """
+    Computes the value of the LAA field for each sample given the genotypes
+    for a variant.
+
+    The LAA field is a list of one-based indices into the ALT alleles
+    that indicates which alternate alleles are observed in the sample.
+    """
+    alt_allele_count = len(alleles) - 1
+    allele_counts = np.zeros((genotypes.shape[0], len(alleles)), dtype=int)
+
+    genotypes = genotypes.clip(0, None)
+    genotype_allele_counts = np.apply_along_axis(
+        np.bincount, axis=1, arr=genotypes, minlength=len(alleles)
+    )
+    allele_counts += genotype_allele_counts
+
+    allele_counts[:, 0] = 0  # We don't count the reference allele
+    max_row_length = 1
+
+    def nonzero_pad(arr: np.ndarray, *, length: int):
+        nonlocal max_row_length
+        alleles = arr.nonzero()[0]
+        max_row_length = max(max_row_length, len(alleles))
+        pad_length = length - len(alleles)
+        return np.pad(
+            alleles,
+            (0, pad_length),
+            mode="constant",
+            constant_values=constants.INT_FILL,
+        )
+
+    alleles = np.apply_along_axis(
+        nonzero_pad, axis=1, arr=allele_counts, length=max(1, alt_allele_count)
+    )
+    alleles = alleles[:, :max_row_length]
+
+    return alleles
+
+
 @dataclasses.dataclass
 class VcfZarrWriteSummary(core.JsonDataclass):
     num_partitions: int
@@ -543,6 +586,12 @@ def has_genotypes(self):
                 return True
         return False
 
+    def has_local_alleles(self):
+        for field in self.schema.fields:
+            if field.name == "call_LAA" and field.vcf_field is None:
+                return True
+        return False
+
     #######################
     # init
     #######################
@@ -729,6 +778,8 @@ def encode_partition(self, partition_index):
                 self.encode_array_partition(array_spec, partition_index)
         if self.has_genotypes():
             self.encode_genotypes_partition(partition_index)
+        if self.has_local_alleles():
+            self.encode_local_alleles_partition(partition_index)
 
         final_path = self.partition_path(partition_index)
         logger.info(f"Finalising {partition_index} at {final_path}")
@@ -800,6 +851,30 @@ def encode_genotypes_partition(self, partition_index):
         self.finalise_partition_array(partition_index, "call_genotype_mask")
         self.finalise_partition_array(partition_index, "call_genotype_phased")
 
+    def encode_local_alleles_partition(self, partition_index):
+        call_LAA_array = self.init_partition_array(partition_index, "call_LAA")
+        partition = self.metadata.partitions[partition_index]
+        call_LAA = core.BufferedArray(call_LAA_array, partition.start)
+
+        gt_array = zarr.open_array(
+            store=self.wip_partition_array_path(partition_index, "call_genotype"),
+            mode="r",
+        )
+        alleles_array = zarr.open_array(
+            store=self.wip_partition_array_path(partition_index, "variant_allele"),
+            mode="r",
+        )
+        for chunk_index in range(gt_array.cdata_shape[0]):
+            A = alleles_array.blocks[chunk_index]
+            G = gt_array.blocks[chunk_index]
+            for alleles, var in zip(A, G):
+                j = call_LAA.next_buffer_row()
+                # TODO we should probably compute LAAs by chunk for efficiency
+                call_LAA.buff[j] = compute_laa_field(var, alleles)
+
+        call_LAA.flush()
+        self.finalise_partition_array(partition_index, "call_LAA")
+
     def encode_alleles_partition(self, partition_index):
         array_name = "variant_allele"
         alleles_array = self.init_partition_array(partition_index, array_name)