Full analysis pipeline

[standage]

At the moment, MicroHapulator users are expected to invoke the entire 4+ stage analysis pipeline in a step-wise fashion. While it will always be important to support step-wise execution, it would be very helpful to provide a standard automated pipeline that can be invoked with a single command. The current docs and demo provide the basis of that pipeline, but performing a bit of additional QA/QC would be warranted as well. Here is what I see as the contours of that pipeline.

• [x] Snakemake workflow implementation
  • [x] validate marker references and marker definitions
  • [x] core pipeline: merge, map, type, filter
  • [x] QA/QC
    • [x] plot read length distribution of unmerged paired-end reads (#125)
    • [x] merging rates
    • [x] plot read length distribution of merged reads (#125)
    • [x] mapping rates vs MH references
    • [x] mapping rates vs chromosome (GRCh38) references (#116, #124)
    • [x] typing rates (#126)
    • [x] plot interlocus balance
    • [x] plot heterozygote balance
• [x] Sample name driven FASTQ file discovery a la MAnaT
• [x] Report generation using Jinja2

[standage]

We'll also want to include length distribution of the unmerged reads.