def getGa2VcfParser():
parser = cli.createArgumentParser((
"GA4GH VCF conversion tool. Converts variant information "
"stored in a GA4GH repository into VCF format."))
cli_client.addClientGlobalOptions(parser)
cli.addOutputFileArgument(parser)
cli_client.addUrlArgument(parser)
parser.add_argument("variantSetId", help="The variant set to convert")
parser.add_argument(
"--outputFormat", "-O", choices=['vcf', 'bcf'], default="vcf",
help=(
"The format for object output. Currently supported are "
"'vcf' (default), which is a text-based format and "
"'bcf', which is the binary equivalent"))
cli_client.addReferenceNameArgument(parser)
cli_client.addCallSetIdsArgument(parser)
cli_client.addStartArgument(parser)
cli_client.addEndArgument(parser)
cli_client.addPageSizeArgument(parser)
return parser
def getGa2SamParser():
parser = cli.createArgumentParser("GA4GH SAM conversion tool")
cli_client.addClientGlobalOptions(parser)
cli_client.addUrlArgument(parser)
parser.add_argument(
"readGroupId",
help="The ReadGroup to convert to SAM/BAM format.")
cli_client.addPageSizeArgument(parser)
cli_client.addStartArgument(parser)
cli_client.addEndArgument(parser)
parser.add_argument(
"--referenceId", default=None,
help="The referenceId to search over")
parser.add_argument(
"--outputFormat", "-O", default="sam", choices=["sam", "bam"],
help=(
"The format for object output. Currently supported are "
"'sam' (default), which is a text-based format and "
"'bam', which is the binary equivalent"))
cli.addOutputFileArgument(parser)
return parser
def getGa2SamParser():
parser = cli.createArgumentParser("GA4GH SAM conversion tool")
cli_client.addClientGlobalOptions(parser)
cli_client.addUrlArgument(parser)
parser.add_argument("readGroupId",
help="The ReadGroup to convert to SAM/BAM format.")
cli_client.addPageSizeArgument(parser)
cli_client.addStartArgument(parser)
cli_client.addEndArgument(parser)
parser.add_argument("--referenceId",
default=None,
help="The referenceId to search over")
parser.add_argument(
"--outputFormat",
"-O",
default="sam",
choices=["sam", "bam"],
help=("The format for object output. Currently supported are "
"'sam' (default), which is a text-based format and "
"'bam', which is the binary equivalent"))
cli.addOutputFileArgument(parser)
return parser