To align with the rust files, I had to re-add the missing RNAs.fasta file to the fixtures directory and update the filename in the python count script from RNAseqs.fasta to RNAs.fasta.

Super naive implementation of feature to report total hit counts added. For each search result reported, it now also prints out the running total of hits for each DCE. This is accomplished by adding a "hits" field to the CompressedSeq struct, making the needle mutable, and incrementing its hits number every time there is a match while searching.
Adaptations are still required to create results matching the python version, i.e. writing out to a results file that contains the name of each DCE that had >= 1 hit, and the total number of hits it had.

This is a "functioning" version with the input arguments and print to file features added, but it is incredibly slow and total hits count doesn't work properly with the way main iterates through the sequences.