Dear Maintainer,

Using spades with the --careful flag triggers the following error:

    Traceback (most recent call last):
      File "/usr/libexec/spades/spades.py", line 683, in <module>
        main(sys.argv)
      File "/usr/libexec/spades/spades.py", line 621, in main
        cfg, dataset_data, command_line = parse_args(args, log)
      File "/usr/libexec/spades/spades.py", line 257, in parse_args
        options, cfg, dataset_data = options_parser.parse_args(log, bin_home, spades_home,
      File "/usr/share/spades/spades_pipeline/options_parser.py", line 1157, in parse_args
        add_to_cfg(cfg, log, bin_home, spades_home, options_storage.args)
      File "/usr/share/spades/spades_pipeline/options_parser.py", line 995, in add_to_cfg
        if which("bwa-spades"):
    NameError: name 'which' is not defined

Reproducible with e.g.:

    f="$(mktemp XXXX.fq)"
    echo -e "@a\nA\n+\n!" > "$f"
    spades --careful --12 "$f" -o "/tmp"

The code path related to that flag in options_parser.py has been patched in
Debian to add the call to which():

https://salsa.debian.org/med-team/spades/-/blob/d3c54b2ae8f0ee29a639fe0246d670fcad54b45b/debian/patches/0003_accept-system-bwa.patch#L82-L95

When the patch was initially created in this commit:

https://salsa.debian.org/med-team/spades/-/commit/ac1cfa145bf4066ca7f3af47db1aae6dd28ac5ab

the call and definition of which() were both in spades.py but the call was
later moved to options_parser.py while the definition was left behind unused.
Rather than adding multiple definitions of which() in the patch, the single
version in support.py could be imported wherever it needs to be used.

Hi Carl,

thanks a lot for the analysis of this bug.  I'm unavailable for two days but
I hope some team member will care for the issue quickly.

Kind regards

       Andreas.

We believe that the bug you reported is fixed in the latest version of
spades, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1010788@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Lance Lin <LQi254@protonmail.com> (supplier of updated spades package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Tue, 10 May 2022 20:15:40 +0700
Source: spades
Architecture: source
Version: 3.15.4+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Lance Lin <LQi254@protonmail.com>
Closes: 1010788
Changes:
 spades (3.15.4+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Lance Lin ]
   * d/patches/0003_accept-system-bwa.patch - refactored 'which'
     Closes: #1010788
 .
   [ Andreas Tille ]
   * Review copyright
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