nw_prune exits too early, gives incomplete output

[josephwb]

In trying to prune terminals, a weird result arises: 1) 10 terminals specified to be removed are not, and 2) a root edge length is in the final tree.

Using nw_prune compiled from the master branch. Recreate error:

nw_prune in.tre -f to_drop.txt > nw_out.tre

The original tree has 59 terminals, and 39 are specified to be pruned; so, 20 terminals should remain. However, the tree produced has 30 terminals.

Input tree, file with taxa to be pruned, actual output, expected output, and a list of terminals that we erroneously not removed are attached.

in.tre.txt
list.txt
nw_out.tre.txt
expected.tre.txt
unremoved.txt