V2.0.0 bug fixes/improvements

[martinghunt]

Changes:

• report het snps for noncoding sequences
• add plasmidfinder
• write all assemblies to a single file at the end
• better naming of clusters when using argannot

Bug fixes:

• off by one error in ref and contig positions of variants in some report lines
• samtools/bcftools parameters changed for snp calling. Diploid assumption was making some Q scores zero, so got filtered out when they shouldn't have
• cluster naming fixed (was getting broken by vfdb)
• catch when no proper pairs mapped and nothing gets assembled. Writes empty report instead of crashing.