Take parameters for setDadaOpt from the command line

[wbazant]

This change allows running the pipeline on 454 data, issue #6.

I've tested the whole pipeline by:

• running a small test run on the current version
• running the same run on the changed version and verifying errorsF.RDS and seqtab_original.RDS are the same
• specifying slightly different alignment parameters (--dadaOpt.GAP_PENALTY -10 \ etc.) and verifying errorsF.RDS and seqtab_original.RDS have slightly changed

For the mad optparse + eval line added to R scripts, I've checked that the following program works:

#!/usr/bin/env Rscript
suppressPackageStartupMessages(library(dada2))
suppressPackageStartupMessages(library(optparse))
option_list = list(
    make_option(c("--dadaOptStr"), type="character", default='', help="values for setDadaOpt passed as one string")
)
opt <- parse_args(OptionParser(option_list=option_list))
eval(parse(text=paste0("setDadaOpt(", opt$dadaOptStr, ")")))
getDadaOpt()

[cjfields]

Hi @wbazant I will merge this into a branch for now to work around some issues with pull requests failing CI (unrelated to this specific request; seems to be happening to all prior submitted requests as well).

[cjfields]

Thanks @wbazant ! I'll also add you to the contributing/authors list