V-pipe 2.0: Benchmark functionalities

• simBench and testBench modules added to simulated reads from virus populations and evaluate read alignment bias and SNV calls, respectively
• vpipeBench allows automated execution of the benchmark, from the generation of the in silico virus population to the evaluation of SNV calls
• vpipeBenchRunner enables simultaneous execution of multiple pipeline configurations

This version of V-pipe was used to run computations reported in Posada-Céspedes et al (doi:10.1101/2020.06.09.142919)

NOTE: During the Gibbs sampling performed by ShoRAH, several clusters may generate the same haplotype representative. Such collisions result in inflated posterior values. Also, the averaging of the haplotype abundances across iterations can be affected by floating-point precision problems. Fortunately, ShoRAH also reports the number of reads assigned to each haplotype per iteration which we use to correct the aforementioned quantities in post-processing. We are currently implementing the changes required to resolve these issues in future releases of ShoRAH.