macroevolution/bamm — pull request #84 by jonchang (2014-02-20 08:19:41+00:00)
Title: Fix "polytomy" msg for trees with dos line endings

If you have a tree file with dos line endings (`xxd tree.tre` shows `0d0a`), bamm munches the newlines (probably because of `getline` somewhere) and complains about a polytomy, when in fact the parser has been filled with garbage. See the junk in `s` in the debugger below, and how `i` is huge.

```
Breakpoint 1, Tree::buildTreeFromNewickString (this=0x7fffffffd5b0, ts=
"(((Polyodon_spathula:50.7052,Psephur"...) at /home/jonchang/bamm/src/Tree.cpp:791
791 log(Error) << "Tree contains at least one polytomy.\n";
(gdb) info locals
q = 0xc76cf0
s =
"\r", '\000' "\341, \000\000\220\064j", '\000' ...
c =
i = 306328
readingBL =
p =
```