New features

• added new script SCRIPTS/make_ref.py to build references from multiple source (gencode, ensembl, refseq). See wiki page Creating a manual reference.
• added new statistics in logs created by SCRIPTS/count.py to visualize the number of reads aligned on too many transcripts and reads containing too many mismatches.
• added logs in many secondary analysis scripts.

Bug fix

• fixed multiqc reports when analyzing a high number of sample (many plates).
• made the new SCRIPTS/make_multiplates_config script backward compatible with ancient configuration files.
• fixed bug in README files.