Commit 277de0d8 authored by aknecht2's avatar aknecht2
Browse files

Updated samtools filter to write output to bam format.

parent 3f707dfc
......@@ -22,6 +22,10 @@ samtools_filter_bam:
required: false
has_value: true
default: 30
- "-b":
changeable: false
required: true
has_value: false
- "-o":
changeable: false
required: true
import chipathlon.db
import argparse
parser = argparse.ArgumentParser(description="Download target file.")
parser.add_argument("-u", "--url", dest="url", required=True, help="Target url.")
parser.add_argument("-p", "--path", dest="path", required=True, help="Local path to file.")
parser.add_argument("-t", "--url_type", dest="url_type", default="ftp://", help="Type of url to access.")
parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")
parser.add_argument("-n", "--overwrite", dest="overwrite", default=True, action="store_false", help="Dont' overwrite local file if exists.")
parser.add_argument("-m", "--md5", dest="md5", help="Check md5 value against passed value.")
args = parser.parse_args()
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