Update description to reflect scritp
Stop keeping track of locations and reads, they are cumbersome to handle
Move method index_annotated_reads from calculate_diff_mirna to AnnotatedReads
Add option to create index without subdics
Init commit: merges data for deseq analysis
init commit: run deseq on merged samples
Write missing values to 0 rather than "NA".
initial commit: t-test deseq
Track offset optionally
Calculate pairwise fold change
Write table as CSV, with an empty string at far left corner.
Run annotate aligned reads with explicit offset, offset tracking off.
Run annotate reads with explicit offset, offset tracking off
Init commit: adjust pvalues by BH method