replaceMets.m does not define some outputs

[dimwas]

replaceMets.m is supposed to look like [model, removedRxns, idxDuplRxns] = replaceMets(model, metabolite, replacement, verbose). However, removedRxns and idxDuplRxns are not defined in the function.

[edkerk]

Please check that #755 works.

[dimwas]

Partially. removedRxns is correct, but idxDuplRxns returns not the indices of removedRxns in original model, as the function suggests, but a cell array of character vectors, which contain reaction identifier as in model.rxns for removed reactions and is empty otherwise. Moreover, the reaction identifier is placed in a position of the reaction that remains. Find attached the model.
model.zip

Now, reaction 490 is this one:
'Metname_648[c] + Metname_896[c] + Metname_1096[c] => Metname_549[c] + Metname_894[c]'
Reaction 1122 is this one:
'Metname_648[c] + Metname_896[c] + Metname_1096[c] => Metname_1069[c] + Metname_894[c]'
They will be identical, if we replace Metname_1069[c] with Metname_549[c].

[model, removedRxns, idxDuplRxns]=replaceMets(model,"M_1069","M_549",true,true);

Now, metabolites are replaced, and reaction 1122 is removed. However, idxDuplRxns contains 'R_1122' in position 490.

[edkerk]

Thanks for the detailed reporting, seems like our tests were to simple to notice this deviation. #755 has now been updated and some other spurious bugs came up that are now also fixed.

[dimwas]

Can confirm that it works.