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samparser.py might be using the wrong ArgumentParser #198

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ghost opened this issue Sep 20, 2018 · 1 comment
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samparser.py might be using the wrong ArgumentParser #198

ghost opened this issue Sep 20, 2018 · 1 comment

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@ghost
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ghost commented Sep 20, 2018

When I downloaded the project and ran samparser.py, I got the error that that "the Namespace object has no attribute infile" (line 3800 of samparser.py at if args.infile == args.outfile:).

The problem seems to be that infile is a member of the parsed arguments of the io_parser rather than the argparser, and the problem seemed to be fixed by changing
args = argparser.parse_args()
to
args = io_parser.parse_args()

(It seemed to me that io_parser was in fact supposed to be the main parser, but I don't know enough to know whether that's true)

@ghost
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ghost commented Sep 20, 2018

The issue was that while infile was inherited correctly by both the subparsers, none of them were invoked when samparser.py was invoked with no subcommand.

Fixed by #199

@ghost ghost closed this as completed Sep 20, 2018
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