Merge pull request #1239 from david4096/va_client_doc

Add sphinx comment for variant annotation search

docs/api.rst

@@ -98,5 +98,6 @@ Client API
         getReadGroupSet, getReadGroup,
         searchDatasets, searchReferenceSets, searchReferences,
         searchVariantSets, searchVariants, searchReadGroupSets,
-        searchReads
+        searchReads, searchVariantAnnotations,
+        searchVariantAnnotationSets
 

ga4gh/client.py

@@ -280,11 +280,29 @@ def searchVariants(
             request, "variants", protocol.SearchVariantsResponse)
 
     def searchVariantAnnotations(
-            self, variantAnnotationSetId, referenceName=None, referenceId=None,
-            start=None, end=None, effects=[]):
+            self, variantAnnotationSetId, referenceName=None,
+            referenceId=None, start=None, end=None, effects=[]):
         """
-        Returns an iterator over the Annotations fulfilling the specified
-        conditions from the specified AnnotationSet.
+        Returns an iterator over the Variant Annotations fulfilling
+        the specified conditions from the specified VariantSet.
+
+        :param str variantAnnotationSetId: The ID of the
+            :class:`ga4gh.protocol.VariantAnnotationSet` of interest.
+        :param int start: Required. The beginning of the window (0-based,
+            inclusive) for which overlapping variants should be returned.
+            Genomic positions are non-negative integers less than reference
+            length. Requests spanning the join of circular genomes are
+            represented as two requests one on each side of the join
+            (position 0).
+        :param int end: Required. The end of the window (0-based, exclusive)
+            for which overlapping variants should be returned.
+        :param str referenceName: The name of the
+            :class:`ga4gh.protocol.Reference` we wish to return variants from.
+
+        :return: An iterator over the
+            :class:`ga4gh.protocol.VariantAnnotation` objects
+            defined by the query parameters.
+        :rtype: iter
         """
         request = protocol.SearchVariantAnnotationsRequest()
         request.variantAnnotationSetId = variantAnnotationSetId
@@ -361,7 +379,7 @@ def searchVariantSets(self, datasetId):
 
     def searchVariantAnnotationSets(self, variantSetId):
         """
-        Returns an iterator over the AnnotationSets fulfilling the specified
+        Returns an iterator over the Annotation Sets fulfilling the specified
         conditions from the specified variant set.
 
         :param str variantSetId: The ID of the