Help understanding outputs of PIT:FASTA_ORFS_2

I’m interested in using FASTA_ORFS_2 in the PIT Workflow because I want the longest ORFS, but also would like to know which transcripts do not have a stop codon, etc. However, I do not understand:

  1. Why does this software have to change the name of the transcripts (prefix)?
  2. In the output file titled “renamed_transcripts_strand_corrected_if_needed” what is it correcting in the transcript?

Thank you!