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[augur ancestral] arg parsing improvements #1344

Merged
merged 4 commits into from
Dec 10, 2023
Merged

[augur ancestral] arg parsing improvements #1344

merged 4 commits into from
Dec 10, 2023

Commits on Dec 7, 2023

  1. [ancestral] Check invalid args up-front 

    Check that provided arguments are compatible. Where possible we use
argparse built-ins, but they don't cover everything we want to check.
This checking isn't intended to replace conditional checks in the code
which check for arg existence (as demonstrated by the additional
conditional added here), however by checking for invalid combinations
up-front we can exit quickly.
    @jameshadfield
    jameshadfield committed Dec 7, 2023
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  2. [ancestral] only export VCF if requested 

    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 committed Dec 7, 2023
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  3. [ancestral] use AugurError consistently 

    This is the preferred method rather than printing to STDERR and exiting
    @jameshadfield
    jameshadfield committed Dec 7, 2023
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  4. [ancestral] Mutually exclusive ref/root seq arg 

    For VCF alignments, `--vcf-reference` becomes the 'ref' variable and
for FASTA alignments, `--root-sequence` becomes the 'ref' variable.
If both was provided then (previously) one was silently ignored, but
they are now mutually exclusive.

The argument help messages are also improved.
    @jameshadfield
    jameshadfield committed Dec 7, 2023
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