pplacer should warn if there is an all-gap reference after pre-masking

matsen / pplacer

Phylogenetic placement and downstream analysis

http://matsen.fredhutch.org/pplacer/

GNU General Public License v3.0

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Closed matsen closed 13 years ago

matsen commented 13 years ago

That is, if there is a sequence in the reference alignment that is all gaps in the post-pre-masking alignment.

matsen commented 13 years ago

The following would seem quite reasonable:

apply "informative" to each reference sequence to get a binary array of non-gap sites before starting to place sequences
for each query sequence, compute the 'binary and' with the mask_arr already computed as part of placement
raise an error saying that "query XXX has no overlap with reference sequence YYY" if this 'binary and' is all false.

I can't imagine that would slow things down much!