feat: write a custom collapsing script

[deliaBlue]

Right now, the workflow uses FASTX Toolkit to collapse the reads. In this processes, the names are changed by numbers but there's no track of which reads belong to which number.

Create a custom script that not only collapses reads, but also a lookup table that lists the new name for each read. In addition, this table can then be used during the uncollapsing step sam_uncollapse.pl to change the read names back to the original ones. Finally, in the step that converts the FASTQ into a FASTA one, names are changed by numbers due to the -r option; this option will have to be removed in order to avoid the issue described here.