__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "*****@*****.**"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
bcftools_opts = get_bcftools_opts(snakemake)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("bcftools view {bcftools_opts} "
"{extra} "
"{snakemake.input[0]} "
"-o {snakemake.output} "
"{log}")
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2021, Patrik Smeds"
__email__ = "*****@*****.**"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
bcftools_opts = get_bcftools_opts(snakemake, parse_memory=False)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
if len(snakemake.output) > 1:
raise Exception("Only one output file expected, got: " +
str(len(snakemake.output)))
filter = snakemake.params.get("filter", "")
extra = snakemake.params.get("extra", "")
shell("bcftools filter {filter} {extra} {snakemake.input[0]} "
"{bcftools_opts} "
"-o {snakemake.output[0]} "
"{log}")