diff --git a/docs/api.rst b/docs/api.rst index cf4515bdb..cfb628c5d 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -98,5 +98,6 @@ Client API getReadGroupSet, getReadGroup, searchDatasets, searchReferenceSets, searchReferences, searchVariantSets, searchVariants, searchReadGroupSets, - searchReads + searchReads, searchVariantAnnotations, + searchVariantAnnotationSets diff --git a/ga4gh/client.py b/ga4gh/client.py index 635325e09..b0435b47c 100644 --- a/ga4gh/client.py +++ b/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