def _readsGeneratorSingle(self, request):
compoundId = datamodel.ReadGroupCompoundId.parse(
request.read_group_ids[0])
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
referenceSet = readGroupSet.getReferenceSet()
if referenceSet is None:
raise exceptions.ReadGroupSetNotMappedToReferenceSetException(
readGroupSet.getId())
reference = referenceSet.getReference(request.reference_id)
readGroup = readGroupSet.getReadGroup(compoundId.read_group_id)
intervalIterator = paging.ReadsIntervalIterator(
request, readGroup, reference)
return intervalIterator
def _readsGeneratorMultiple(self, request):
compoundId = datamodel.ReadGroupCompoundId.parse(
request.read_group_ids[0])
dataset = self.getDataRepository().getDataset(compoundId.dataset_id)
readGroupSet = dataset.getReadGroupSet(compoundId.read_group_set_id)
referenceSet = readGroupSet.getReferenceSet()
if referenceSet is None:
raise exceptions.ReadGroupSetNotMappedToReferenceSetException(
readGroupSet.getId())
reference = referenceSet.getReference(request.reference_id)
readGroupIds = readGroupSet.getReadGroupIds()
if set(readGroupIds) != set(request.read_group_ids):
raise exceptions.BadRequestException(
"If multiple readGroupIds are specified, "
"they must be all of the readGroupIds in a ReadGroupSet")
intervalIterator = paging.ReadsIntervalIterator(
request, readGroupSet, reference)
return intervalIterator