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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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checks on bad subsets are not working #45

Closed roblanf closed 9 years ago

roblanf commented 9 years ago

Hey @brettc, can you take a look at this ASAP? This is a very important check that currently doesn't work.

Previously, we have checked that sites in data blocks are non-overlapping, and also spit a warning for any missing sites.

E.g. with the aminoacid example file:

This is fine ''' [data_blocks] COI = 1-407; COII = 408-624; EF1a = 625-949; '''

This should spit a warning about missing sites 1-3 and 941-949 ''' [data_blocks] COI = 4-407; COII = 408-624; EF1a = 625-940; '''

And this should quit with an error about a site only being allowed to appear in a single data block: ''' [data_blocks] COI = 1-407; COII = 408-624; EF1a = 625-949; OOPS = 1-949; '''

Right now, the second and third options are not behaving properly. No warning, and no error. Can we re-instate these?

brettc commented 9 years ago

Fixed on develop branch 49075e22b049c66cbd9c632b94aa0324fd611dbf with two new tests.