Major refactoring

[lsantuari]

• integration of brentp's code in the refactor branch;
• fix the bug that leads to the generation of multiple windows for the same positions;
• move the run.sh script to the svchannels folder and adapt it to run the scripts:

1. extract_signals.py
2. generate_channels.py

• add vcf2bedpe.R to the run.sh script;
• copy the label_windows.py to the svchannels folder;
• simplify the I/O of the label_windows.py script. It should take in input the file for the positions (BEDPE1) and the file with the truth set positions (BEDPE2) and output a file (BEDPE3) with the positions from BEDPE1 labelled as either DEL or REF;
• add script for training (optimize);
• add script to generate predictions (predict);
• add bedpe_to_vcf to generate the final VCF output;