Are only filtered reads in $DIR/$SAMPLENAME_$TRANSLATEDALIGN_aligned.tsv file?

[Joe Piechura]

Hello!

I am wondering if the alignments reported in the temp file $DIR/$SAMPLENAME_$TRANSLATEDALIGN_aligned.tsv are ALL alignments, or only those alignments that pass the e value threshold, the translated query coverage threshold, and map to proteins that pass the translated subject coverage threshold. 

Thanks very much for sharing this pipeline, it is very helpful!

Joe