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[augur ancestral] input VCF alignment is often overwritten #1343

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jameshadfield opened this issue Nov 29, 2023 · 0 comments · Fixed by #1344
Closed

[augur ancestral] input VCF alignment is often overwritten #1343

jameshadfield opened this issue Nov 29, 2023 · 0 comments · Fixed by #1344
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bug Something isn't working VCF

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Current Behavior

Providing augur ancestral with a VCF input (--alignment foo.vcf) and not specifying a output VCF will result in the input VCF being overwritten. That's due to this line, which replaces the input alignment's suffix with 'vcf':

augur/augur/ancestral.py

Line 373 in 7cb3848

vcf_fname = '.'.join(args.alignment.split('.')[:-1]) + '.vcf'

Expected behavior

We shouldn't be producing files unless requested to do so. I suggest only exporting a VCF if --output-vcf is provided.

Your environment: if running Nextstrain locally

augur 23.1.1
@jameshadfield jameshadfield added the bug Something isn't working label Nov 29, 2023
@jameshadfield jameshadfield self-assigned this Nov 29, 2023
jameshadfield added a commit that referenced this issue Nov 29, 2023
@jameshadfield
[ancestral] only export VCF if requested
ce7f094 
This is consistent with augur's general behaviour of "request a file for
it to be produced". Moreover, the previous code would ~always result in
the VCF input file being overwritten.

This is potentially a backwards compatible change. The number of users
expected to be affected is minimal (perhaps zero).

Closes #1343.
@jameshadfield jameshadfield mentioned this issue Nov 29, 2023
Merged
jameshadfield added a commit that referenced this issue Dec 4, 2023
@jameshadfield
[ancestral] only export VCF if requested
3ceaad3 
This is consistent with augur's general behaviour of "request a file for
it to be produced". Moreover, the previous code would ~always result in
the VCF input file being overwritten.

This is potentially a backwards compatible change. The number of users
expected to be affected is minimal (perhaps zero).

Closes #1343.
jameshadfield added a commit that referenced this issue Dec 4, 2023
@jameshadfield
[ancestral] only export VCF if requested
0011372 
This is consistent with augur's general behaviour of "request a file for
it to be produced". Moreover, the previous code would ~always result in
the VCF input file being overwritten.

This is potentially a backwards compatible change. The number of users
expected to be affected is minimal (perhaps zero).

Closes #1343.
jameshadfield added a commit that referenced this issue Dec 7, 2023
@jameshadfield
[ancestral] only export VCF if requested
24f1fa0 
This is consistent with augur's general behaviour of "request a file for
it to be produced". Moreover, the previous code would ~always result in
the VCF input file being overwritten.

This is potentially a backwards compatible change. The number of users
expected to be affected is minimal (perhaps zero).

Closes #1343.
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[augur ancestral] arg parsing improvements nextstrain/augur
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