Annotate output matrices with salmon effective length

[mdshw5]

DESeqDataSetFromTximport requires both counts and effective length. While PISCES uses effective length internally for DESeq2, it does not write out the values for use in downstream analysis.

[mdshw5]

@lucamarrocco - it looks like I already implemented this feature as part of 9f7ba0e, and I just need to do integration testing and push a new release.

[mdshw5]

@carloravagli I see that I should add the weighted gene-level effective length matrices as well. The tximport package provides summarizeToGene() for this purpose, which internally weights the lengths by abundance and takes an average:

https://github.com/mikelove/tximport/blob/b54bdbd2072c49043fc5834ca0500ecb214c6147/R/summarizeToGene.R#L90-L95

It can replace any problematic rows with a simple geometric mean as well. PISCES uses tximport internally so I will just write out the one extra gene-level length matrix.