HTSinfer keeps track of common errors and warnings by setting a run state. Depending on the state, after execution a status code of 2 (at least 1 error), 1 (1 or more warnings, but no errors) or 0 (no warnings or errors) is returned.
However, unexpected errors could lead to status codes of 1 being returned, making the above semantics unreliable.
Solution
Catch generic Exceptions in the tool's CLI entry point, log the error and exit with a status code of 2.
Problem
HTSinfer keeps track of common errors and warnings by setting a run state. Depending on the state, after execution a status code of 2 (at least 1 error), 1 (1 or more warnings, but no errors) or 0 (no warnings or errors) is returned.
However, unexpected errors could lead to status codes of 1 being returned, making the above semantics unreliable.
Solution
Catch generic
Exceptions in the tool's CLI entry point, log the error and exit with a status code of 2.