Merge pull request #72 from cboursnell/master

Everything ready for next release
use new bindeps method to check deps at every run
need to call missing with deps hash
remove express dependency
v0.3
add citation to README
fix overwriting of contigs by adding assembly name to file
bump patch version for bugfix
update README with doi for v0.3.1
update bin test to reflect new csv naming
add samtools to binary dependencies
add edit distance and mapq score metrics
updated test to take into account new way that bcftools calculates coverage.
mpileup counts coverage if the read goes over the base.
bcftools counts coverage if the read actually maps to that base.