Technology migration for better restartability

Version 2.0 of the EVA pipeline will move from Luigi to Spring Batch. Instead of tracking progress of steps as a whole (done / not done), Spring Batch splits the work in chunks of configurable size. This way, if a step has processed millions of variants before failing, it will be resumed from that point instead of completely restarted.

The functionality implemented for this first beta includes:

• Normalization of variants reported in a VCF file
• Storage of variants in MongoDB
• Calculation of allele frequencies and other statistics for all the samples in a VCF file
• Annotation using Ensembl Variant Effect Predictor

Future beta releases will include support for population statistics via a PED file and improved usability.