feat: add optional suppression of allele collection (#545)

* VCF annotator should not collect alleles if no output is requested by
user. This has major implications for memory usage, apparently.
* Provide this in a relatively OOP-friendly way without producing a
breaking change

At the next major version, there is a cleaner way to do this and it
should be implemented at that point

Author: jsstevenson

src/ga4gh/vrs/extras/annotator/vcf.py

@@ -109,6 +109,18 @@ def __init__(self, data_proxy: _DataProxy, **kwargs) -> None:  # noqa: ARG002
         self.data_proxy = data_proxy
         self.tlr = AlleleTranslator(self.data_proxy)
 
+    def should_collect_alleles(self, **kwargs) -> bool:  # noqa: ARG002
+        """Determine whether allele aggregation is necessary.
+
+        This method is called to initialize (or not) an initial allele collection for
+        downstream use. By default, it returns the corresponding class variable, but
+        implementing classes can choose to amend this based on provided annotation
+        arguments.
+
+        :return: ``True`` if alleles should be collected
+        """
+        return self.collect_alleles
+
     @abc.abstractmethod
     def raise_for_output_args(self, output_vcf_path: Path | None, **kwargs) -> None:
         """Raise an exception if no output appears to be configured or declared.
@@ -215,7 +227,11 @@ def annotate(
         else:
             vcf_out = None
 
-        allele_collection = [] if self.collect_alleles else None
+        allele_collection = (
+            []
+            if (self.collect_alleles and self.should_collect_alleles(**kwargs))
+            else None
+        )
         for record in vcf:
             if vcf_out:
                 additional_info_fields = [FieldName.IDS_FIELD]
@@ -265,7 +281,7 @@ def annotate(
         if vcf_out:
             vcf_out.close()
 
-        if self.collect_alleles:
+        if allele_collection is not None:
             self.on_vrs_object_collection(allele_collection, **kwargs)
 
     @abc.abstractmethod
@@ -275,8 +291,8 @@ def on_vrs_object(
         """Perform side-effects (eg additional annotation or storage) or additional
         filtering on VRS alleles as they are constructed during VCF annotation.
 
-        Reimplement in a child class to add custom logic. Otherwise, this method simply
-        passes through ``vrs_allele`` without altering it further or storing it.
+        Reimplement in a child class to add custom logic. Otherwise, simply pass through
+        ``vrs_allele`` without altering it further or storing it.
 
         :param vcf_coords: CHR-POS-REF-ALT from VCF for this allele
         :param vrs_allele: allele translated from coords
@@ -444,6 +460,15 @@ class VcfAnnotator(AbstractVcfAnnotator):
     pkl_arg_name = "output_pkl_path"
     ndjson_arg_name = "output_ndjson_path"
 
+    def should_collect_alleles(self, **kwargs) -> bool:
+        """Inhibit allele collection parameter if no means of output are given.
+
+        :kwparam output_pkl_path: Optional path to output PKL dump of all alleles
+        :kwparam output_ndjson_path: Optional path to output NDJSON dump of all alleles
+        :return: ``True`` if at least one of the output path args is ``True``
+        """
+        return bool(kwargs.get("output_pkl_path") or kwargs.get("output_ndjson_path"))
+
     @use_ga4gh_compute_identifier_when(VrsObjectIdentifierIs.MISSING)
     def annotate(
         self,