Restarting repository anew; this time with Makefile to have a more reproducible pipeline

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
First working version of new miRNA-Tools pipeline

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
...

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Added script to produce graph for GenomeMapping step

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Added a Hairpin Alignment module

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Utility/miRNA_align.cpp: Corrected a bug caused by the same buffer being used twice that caused out_of_range error

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Added modules for Length Distribution Analysis and for Contribution Analysis

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Cleaned RawSequenceFiltering module

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Added a namespace to variables in template to avoid name clash

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Cleaned pipeline

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Corrected a bug in init where incorrect path to trimmed fasta file was given to some makefile configuration files

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
New version of the pipeline

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>