15877160304

Committed 25 Jun 2025 01:05PM UTC coverage: 86.038% (-0.2%) from 86.224%

Build # 15877160304

Build Type

Pull #1255

github

Committed by

web-flow

Commit Message

Merge 652286d65 into 5e8083eb6

Pull Request Pull Request #1255: Fix bug in processing inframe deletions during aggregation

Run Details

0 of 1 new or added line in 1 file covered. (0.0%)

19 existing lines in 2 files now uncovered.

7863 of 9139 relevant lines covered (86.04%)

4.29 hits per line

Source File
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62.07

/pvactools/tools/main.py

import argparse
import sys
try:
    from importlib.metadata import version
except:
    from importlib_metadata import version
from pvactools.tools import *

def define_parser():
    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    subparsers = parser.add_subparsers()

    #add subcommands
    download_cwls_parser = subparsers.add_parser(
        "download_cwls",
        help="Download pVACtools CWLs for each tool's main pipeline",
        add_help=False
    )
    download_cwls_parser.set_defaults(func=download_cwls)

    download_wdls_parser = subparsers.add_parser(
        "download_wdls",
        help="Download pVACtools WDLs to run the main pVACseq and pVACfuse pipelines",
        add_help=False
        )
    download_wdls_parser.set_defaults(func=download_wdls)

    parser.add_argument(
        "-v", "--version",
        action="store_true",
        help="Display the currently installed pvactools version",
    )
    return parser

def main():
    parser = define_parser()
    args = parser.parse_known_args()
    if args[0].version is True:
        print(version('pvactools'))
    else:
        try:
            args[0].func.main(args[1])
        except AttributeError as e:
            parser.print_help()
            print("Error: No command specified")
            sys.exit(-1)


if __name__ == '__main__':
    main()

1	import argparse	5✔
2	import sys	5✔
3	try:	5✔
4	from importlib.metadata import version	5✔
UNCOV 5	except:	1✔
UNCOV 6	from importlib_metadata import version	1✔
7	from pvactools.tools import *	5✔
8
9	def define_parser():	5✔
10	parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)	5✔
11	subparsers = parser.add_subparsers()	5✔
12
13	#add subcommands
14	download_cwls_parser = subparsers.add_parser(	5✔
15	"download_cwls",
16	help="Download pVACtools CWLs for each tool's main pipeline",
17	add_help=False
18	)
19	download_cwls_parser.set_defaults(func=download_cwls)	5✔
20
21	download_wdls_parser = subparsers.add_parser(	5✔
22	"download_wdls",
23	help="Download pVACtools WDLs to run the main pVACseq and pVACfuse pipelines",
24	add_help=False
25	)
26	download_wdls_parser.set_defaults(func=download_wdls)	5✔
27
28	parser.add_argument(	5✔
29	"-v", "--version",
30	action="store_true",
31	help="Display the currently installed pvactools version",
32	)
33	return parser	5✔
34
35	def main():	5✔
36	parser = define_parser()	×
37	args = parser.parse_known_args()	×
38	if args[0].version is True:	×
39	print(version('pvactools'))	×
40	else:
41	try:	×
42	args[0].func.main(args[1])	×
43	except AttributeError as e:	×
44	parser.print_help()	×
45	print("Error: No command specified")	×
46	sys.exit(-1)	×
47
48
49	if __name__ == '__main__':	5✔
50	main()	×

griffithlab / pVACtools / 15877160304

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