def ga2vcf_run(args):
searchVariantsRequest = RequestFactory(args).createSearchVariantsRequest()
workarounds = getWorkarounds(args)
httpClient = client.HttpClient(args.baseUrl, args.verbose, workarounds,
args.key)
# do conversion
vcfConverter = converters.VcfConverter(httpClient, searchVariantsRequest,
args.outputFile, args.binaryOutput)
vcfConverter.convert()
def run(self):
variantSet = self._httpClient.getVariantSet(self._variantSetId)
iterator = self._httpClient.searchVariants(
start=self._start, end=self._end,
referenceName=self._referenceName,
variantSetId=self._variantSetId,
callSetIds=self._callSetIds)
# do conversion
vcfConverter = converters.VcfConverter(
variantSet, iterator, self._outputFile, self._binaryOutput)
vcfConverter.convert()
def ga2vcf_run(args):
# The factory expects a variantSetIds value rather than a single variant
# set, so we add this in by hand.
args.variantSetIds = args.variantSetId
searchVariantsRequest = RequestFactory(args).createSearchVariantsRequest()
workarounds = getWorkarounds(args)
httpClient = client.HttpClient(
args.baseUrl, args.verbose, workarounds, args.key)
# do conversion
vcfConverter = converters.VcfConverter(
httpClient, searchVariantsRequest, args.outputFile, args.binaryOutput)
vcfConverter.convert()
def ga2vcf_run(args):
# instantiate params
searchVariantsRequest = RequestFactory(
args).createSearchVariantsRequest()
searchVariantSetsRequest = RequestFactory(
args).createSearchVariantSetsRequest()
if args.outputFile is None:
outputStream = sys.stdout
else:
outputStream = open(args.outputFile, 'w')
workarounds = getWorkarounds(args)
httpClient = client.HttpClient(
args.baseUrl, args.verbose, workarounds, args.key)
# do conversion
vcfConverter = converters.VcfConverter(
httpClient, outputStream,
searchVariantSetsRequest, searchVariantsRequest)
vcfConverter.convert()
# cleanup
if args.outputFile is not None:
outputStream.close()
