dada2_fun changes

See merge request !4

dada2: add cutadapt to trim primers for all type of data
fixes

when some samples don't pass filters

asvenn no need to specify levels when <= 7
dada fix single end mode orient sequences / search primers on reverse complement
dada fix output name of filterandtrim step
beta fix interpretation of factor to test

doing multiple plot.

add extension argument to inform R1 R2 pattern for paired data
change amplicon argument to "cutadapt". set to TRUE and inform sequence primers to trim primers with cutadapt.
add cutadapt step in singleend SOP (illumina/torrent).

fix message at ranomaly startup
add message when no significant features in aggregate

update

See merge request !3

bars: allow to keep sample order given by metadata
alpha: suppress fdr for pairwise wilcox and legend display
beta: plotly output

add secondary plot when cov argument is used

stats was done on raw table inducing NAs.

replace Fact argument by sample_labels boolean, allow user to display sample ids rather than group they belong for non splitted plot.
autoorder argument to apply or not automatic ordering of groups.

add aggregate_top_taxa

debug coercing combination in to factor