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FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
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pxrr does not work when root edge present #137

Closed josephwb closed 3 years ago

josephwb commented 3 years ago

[Submitted by zhangqiong]

Working with this tree:

((Hsinensis:0.00699791,(Eurya_acuminatissima:0.0835567,(((SCwallichii:0.00136009916772134249,SCsericans:0.00141386)34:0.00815149,(Falatamaha:0.00671644043733485296,(Lgrandis:0.00412921003436183924,Glasianthus:0.01518895745936422147)99:0.00486958391019317802)94:0.00127025718921492943)100:0.01747225291781624376,(((PAmultisepala:0.00365334,Tchampioni:0.00132095)92:0.00185297,Pyoblongicarpa:0.00439602406472616378)99:0.00356576568831727496,(((Paxillaris:0.00330613,Phainanensis:0.0033232)100:0.00478620036552010464,L_fruticosa:0.01591355197683665471)55:0.00077860035722394677,(Aoblata:0.00749197588443350181,((szechuanensis:0.00198329,((amplexifolia:0.00331048293113049433,huana:0.0016512)19:0.00000100000050002909,Cfluviatilis:0.00530477)2:0.00000100000050002909)49:0.000331115,(Cyungkiangensis:0.0053169,tsingpienensis:0.00390286)93:0.00132573824062239909)98:0.00339835620774759121)45:0.00032091731443947716)70:0.00147512627596211102)100:0.02885341291361050511)96:0.00518918801976389534)95:0.01502963600235036543)100:0.00294092040782343656);

Trying to reroot or just unroot gives the error:

./pxrr -t rr.tre -g Eurya_acuminatissima
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 1) >= this->size() (which is 1)

I've gone through previous releases and the same error is always printed.

When I do:

pxcltr -t rr.tre | pxrr -g Eurya_acuminatissima

things work, which makes me think the annotations are to blame. However, when I add annotations to other trees, things work, so I have no idea what is going on...

josephwb commented 3 years ago

Ah ok this tree somehow has a root edge (despite seemingly been reconstructed with RAxML). So, not an issue with annotations: pxcltr removes annotations, knuckles, and root edges all at once. So, bad input, I suppose. But we can deal with this.

josephwb commented 3 years ago

Extended pxcltr to allow specific properties to be removed (not just all) with 67de1ec3de4092a168ef27e876d8a21a15bb568b. I'll put a quick check for a root edge in pxrr so we don't run into this again.

josephwb commented 3 years ago

Check implemented with a0fc9ef9d9e25cb743e79b75fdf0f7083831827f. I suppose we could do this automatically, but really we should not be encountering this type of tree often.