Suggestion: for establishing transcripts file identity

[NDHall]

First of all, this has been a great pipeline. I appreciate the obvious thought and work you have already invested in it.
While working with the code I go this error:

Loaded degradome density data from file Some.fa_dd.txt
	Transcriptome: ppv01_70/Those_transcripts.fasta
Loaded GSTAr alignment file Query.fasta_GSTAr.txt
	Transcriptome: Those.fasta
	Queries: Query.fasta
	Ranked by: MFEratio

FATAL: Transcriptome has to be the same for the degradome density file and the GSTAr alignment file!

I appreciate the spirit of Error, but in this case both files were the same even though their relative paths were different. I was able to fix this without re-running the GSTAr step, but it occurs to me that this problem could be side stepped entirely by using MD5 Checksum values. If implemented, when transcriptomes are processed they would be fed to MD5 Hash, Digested and the resulting values printed back to the header. The Transcripts field would then read

# Transcripts: 202cb962ac59075b964b07152d234b70

since the hash is created from file contents it frees the program to take in correct transcript files no matter where they are stored.

Again, great program! Keep up the good work.