Use wildtype sequence length if it is shorter than desired peptide sequence length

Previously, if the wildtype sequence length was shorter than the desired peptide sequence length, the retrieved sub-sequence array (@wildtype_arr) would be patted with empty array elements. This would lead to warning messages later when the array elements would be joined into a string. This PR will address this by using the wildtype sequence length for retrieval of the sub-sequence if it is shorter than the desired peptide sequence length so that no padding of the array will occur. A new test case was added to cover this change.

This PR also fixes the error message of an else case that was previously based on a wrong assumption.