Improve Testing and CLI

[timothymillar]

• Multi-chain MCMC simulation (convergence metric not needed when calling posterior mode with high probability) #16
• Use and recording of random seed in output VCF file #23
• Correctly zero-pad date #37
• Added filter based on read count #38
• Correction for NS info field#39
• Changed code for phenotype field #40
• Changed code for phenotype SNV position field
• Record SNV positions using 1-based indexing #46
• Merge duplicate SNPs in input VCF #41
• Much improved testing
• Use single CLI entry point
• Add filter PASS code header to VCF output