Bug detected in `getSubsetEcModel`

[mihai-sysbio]

Description of the bug:

Initially spotted here, running the last step of the light tutorial triggers an error.

Reproducing these results:

>> ecHT29 = getSubsetEcModel(ecModel,HT29);
Matrix index is out of range for deletion.

Error in removeReactions (line 41)
        reducedModel.rxns(indexesToDelete)=[];

Error in getSubsetEcModel (line 53)
smallEcModel = removeReactions(smallEcModel,~keepRxns, true, true, true);

System information

• Operating system: macOS 13
• MATLAB version: 2021b
• GECKO version: develop

I hereby confirm that I have:

• [x] Tested my code with all requirements for running GECKO
• [x] Done this analysis in the develop branch of the repository
• [x] Checked that a similar issue does not exist already

[mihai-sysbio]

These two lines are identical https://github.com/SysBioChalmers/GECKO/blob/38b6768b2ef9fb801a6739ef653372c3766c9f5a/src/geckomat/utilities/getSubsetEcModel.m#L41 https://github.com/SysBioChalmers/GECKO/blob/38b6768b2ef9fb801a6739ef653372c3766c9f5a/src/geckomat/utilities/getSubsetEcModel.m#L53

but I don't understand how come there is no

smallEcModel = removeReactions(bigEcModel,~keepRxns, true, true, true);

[edkerk]

These two lines are identical

https://github.com/SysBioChalmers/GECKO/blob/38b6768b2ef9fb801a6739ef653372c3766c9f5a/src/geckomat/utilities/getSubsetEcModel.m#L41

https://github.com/SysBioChalmers/GECKO/blob/38b6768b2ef9fb801a6739ef653372c3766c9f5a/src/geckomat/utilities/getSubsetEcModel.m#L53

Line 53 should be deleted.

but I don't understand how come there is no

smallEcModel = removeReactions(bigEcModel,~keepRxns, true, true, true);

That would not make sense. The smallEcModel is starting to get generated in line 26, and then modified in the rest of the function.

https://github.com/SysBioChalmers/GECKO/blob/38b6768b2ef9fb801a6739ef653372c3766c9f5a/src/geckomat/utilities/getSubsetEcModel.m#L26

[edkerk]

Resolved in #331