Configure¶

This function is used for setting all the pipe configures.

Note

Configure or Configure2 should be called before analysis.

Parameters¶

# get configure names
Configure.getConfigs()

# get configure through name
Cinfigure.getConfig(key)

# set configure through name
Cinfigure.setConfig(key, val)

# additional function: check virus genome
Configure.virusGenomeCheck(folder=None, build=False)

# additional function: check SNV reference
Configure.snvRefCheck(folder=None, build=False)

key, val: key and value.
folder: folder path to the virus genome or snv genome files.
build: download and build by cfDNApipe or not.

Example usage:

from cfDNApipe import *
import glob

pipeConfigure(
    threads=60,
    genome="hg19",
    refdir=r"path_to_reference/hg19",
    outdir=r"path_to_output/snv_output",
    data="WGS",
    type="paired",
    build=True,
    JavaMem="10G",
)

Configure.getConfigs()

Cinfigure.getConfig("genome")