[ADAM-1853] Various improvements to readthedocs documentation.

[heuermh]

Fixes #1853.

[coveralls]

Coverage decreased (-0.1%) to 82.564% when pulling a806e5c on heuermh:doc-fixes into adff336 on bigdatagenomics:master.

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[heuermh]

Updated checkboxes at #1853 to show what this pull request addresses.

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[fnothaft]

Nice! Are you still working on the issues left in #1853, or is this as far as you're getting?

[heuermh]

Are you still working on the issues left in #1853, or is this as far as you're getting?

Let's see ... these ones need help/feedback from you

• RI inline doc refers to s(i) but I don't see it in the equation
• Left margin in BQSR read ←the read to observe block looks incorrect
• Figures on http://adam.readthedocs.io/en/latest/benchmarks/algorithms/ should use GATK4 as a label
• Is it "GATK" or "the GATK"?
• GATK in "...more performant than the same algorithms implemented in the GATK. ADAM outperforms the GATK when running..." should be GATK4
• GATK4 comparison is missing in INDEL Realignment figure

I tried messing around with the CSS but couldn't find a easy way to make code blocks wider without completely overhauling the layout (everything uses static widths).

This one I'll add soon in a separate PR along with new pages for homebrew, conda, and docker

• Add deploying on EMR doc with example config

[fnothaft]

GATK4 comparison is missing in INDEL Realignment figure

GATK4 drops the INDEL realigner.

Otherwise, I'll PR the others over to you shortly.

[fnothaft]

RE: Is it "GATK" or "the GATK"?

We're consistently using the GATK:

$ cd docs
$ grep GATK -R . | grep -v "the GATK"
./algorithms/reads.rst:   implementation is fully concordant with the Picard/GATK duplicate

[fnothaft]

@heuermh I think all of the ones that needed action from me will be resolved after you merge heuermh#6.

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