Type for Paired-end Reads about biosequences.jl HOT 2 CLOSED

BioSequence{DNAAlphabet{2}} does not allow gaps but BioSequence{DNAAlphabet{4}} does. Why do you want gaps for paired end reads?

I do have a plan for dealing with reads in a better manner - especially for assembly and mapping: I'm going to implement "read-datastores", which can be built using FASTQ files, and act as efficient binary datastores for read datasets - reusable for all BioJulia projects. When we have those, it might be cool to have some kind of type like PairedReads, or even just Pair{DNASequence,DNASequence}. After we have PE I'll look at getting us Long Reads (PacBio and Nanopore) and TaggedReads (10X) datastores. For paired reads I don't know if I would use gaps. I think I would just map the two reads from a pair to the graph individually, if everything (reads + graph) make sense, then we would expect the two reads to map nearby to each other in the graph, and we would expect the distance between them to be close to the average insert size of the library that was prepared for sequencing.

from biosequences.jl.

My initial plan was to embed the average insert size information to a paired-end read by putting gaps between the two reads. For now, I also represent paired-end reads as a tuple (sequence1,sequence2,expected insert size). I think the approach you describe is more clean than inserting gaps which would take unnecessary space.

from biosequences.jl.