Specifying --write-pre-masked shouldn't prevent placement

[metasoarous]

Currently, when this flag is specified, pplacer seems to write out the pre-masked alignment, then halt, never going on to actually produce a placefile.

[matsen]

Closed by 480c7ea

[cmccoy]

The old behavior was as-documented:

--write-pre-masked
    Write out the pre-masked sequences to the specified fasta file and exit.

[matsen]

Huh, indeed. Well, the reason I wanted to change it rather than leave it be was to make its operation more consistent with the other masking-writing options.

What do you think-- update docs or back up some commits and forget it entirely?

[cmccoy]

Updating docs sounds good to me.

On Tue, Nov 5, 2013 at 7:02 PM, Erick Matsen [email protected]:

Huh, indeed. Well, the reason I wanted to change it rather than leave it
be was to make its operation more consistent with the other masking-writing
options.

What do you think-- update docs or back up some commits and forget it
entirely?

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[matsen]

Re-closed by eda4442 . Thanks, Connor.