Add support transforming sample indices.

[roryk]

This also simplifies the fastqtransform options, removing the
--umi-only and --dual-index options by detecting them from the
regex. Ran tests and diffed the results and they are identical
to the master branch.

Addresses @qfwills comment at COMBINE-lab/salmon#93 about
having everything in one file.

Tagging @vals for a heads up before merging since this removes a couple command line options.

[roryk]

Attached a couple other commits to this one:

1. Added examples for the Broad's DGE scheme, SCRB-seq
2. Added support for 4 fastq files, some schemes use the i5 and i7 read.
3. Added an example from the Klein group that has the 4 fastq scheme.
4. Don't report 0 reads processed when running bamtag.