Use "chromosome" instead of "contig" throughout the user interface

[armish]

The term contig is really not well-known to biologists and therefore might be confusing for many of the Cycledash users. I suggest we use chromosome instead of contig throughout the user interface and also in the CQL before it gets being used by researchers.

This is also relevant to pileup.js terminology.

What do people think?

Here are some relevant tools and use cases for better comparison:

• This is the default BED file format from Genome Browser:
• This is a screenshot from the browser itself:
• These are from IGV:
• And this is Cycledash:

[ihodes]

Something worth some further user-validation @jaclynperrone

I think the reason I changed it to/settled on contig was because we're not just dealing with chromosomes; we're working with many unmapped contigs, bacterial contigs, mitochondrial DNA, etc.

[danvk]

My 2¢: "contig" is more general and more correct, but 99% of the time people are going to be dealing with true chromosomes, particularly when they're working with human DNA. I don't think we'd lose much by using the term "chromosome". Even mitochondrial DNA is referred to as a "bacterial chromosome" and is often marked as chrM in VCFs and BAMs.

[armish]

I didn't even know that Cycledash could handle assemblies other than human. In that sense, I agree that contig is the right term to use, but it is one of those things people get quite confused about. Might make sense to wait until @jaclynperrone validates my assumption with the upcoming interviews.

[ihodes]

@armish yeah I think we're confining ourselves to human DNA for the time being, but we often see contigs other than the 23 + M chromosomes in human DNA. Can't pull up Cycledash (DNS!) to get an example now, though.