Decide how to separate modules

[magicDGS]

First proposal, taking the last commont of @tfenne in samtools/htsjdk#896:

• htsjdk-core: common code, interface/api definitions for things and then the implementations of most things that don't include significant dependencies. Suppor for SAM/BAM, VCF.
• htsjdk-cram: support for CRAM (requires a lot of external libraries)
• htsjdk-sra: support for SRA (requires the ngs-java, which downloads native libraries)
• htsjdk-jexl: for expressions, because it is not a core dependency for just reading/writing VCFs

Is this ok for you, @samtools/htsjdk-next-maintainers?

We should also decide for the naming scheme:

Maven artifactId	Folder name	Package name
htsjdk-module	htsjdk-module	org.htsjdk.htsjdk_module
htsjdk-module	htsjdk-module	org.htsjdk.module
module	module	org.htsjdk.module

[lbergelson]

I think might actually split sam/bam out of core and have core be JUST be the API and the machinery for loading plugins.

I would advocate for:

Maven artifactId	Folder name	Package name
htsjdk-module	module	org.htsjdk.module

[magicDGS]

Let's go for that one if @tfenne and @jacarey agree!

[magicDGS]

By the way - if we split a sam/bam out of core, we should also split vcf (and maybe other locatable implementations). Is that ok for you? And where the FASTQ will live (sam/bam, or a new module), if we opt to implement as a Read?

[lbergelson]

I'm not sure exactly how finely we want to subdivide things, maybe it makes sense to leave sam/vcf/fasta in core.