ozguzMete
commented
2 years ago These are basically missing columns in the example maf file. Interestingly, we got the column names from the file. We merge these column names with the predefined column names list inside MutationRecord. MutationRecord has 36 headers while the maf format has 126 columns in total... These 36 columns look like more "required" than the rest but not soo "required" by your comment
Do we really need to use the predefined column names list inside MutationRecord? If not we can solve the problem by removing this merge operation.
The code gets IllegalArgumentException since a column with the given name is not defined. we can simply suppress this exception since the annotation is "correct" -- or -- instead of logging an error we can log a warning
In both cases, we should be printing a clearer error/warn message when we got the IllegalArgumentException at that point and it should be this: No such column name: XXXXXXXX -- or -- Missing column: XXXXXXX
inodb
Seems like things get annotated correctly but tons of errors about reading fields: