Cannot detect focal sequence names in summary report if --rename is used

[matt-sd-watson]

In the draft version of the summary report, the txt file or multi-FASTA for both the focal and background sequences are read in for summary statistics. If any of the sample names in the tree match to the focal sequence list, they will be categorized as "focal", or "background" otherwise.

Currently this breaks if --rename is used, as the focal and background names are read from the files before the renaming, so a mismatch will occur and no focal sequences will be detected.