update status badges to use http://shields.io/
Merge pull request #87 from cboursnell/master

Massive speed up of bcf file parsing using C
Merge pull request #89 from cboursnell/master

Actual read length used for effective length calculations
Merge pull request #90 from cboursnell/master

use SNAP aligner
reduce snap class complexity, add more arguments to snap cmds
temporary deps for osx builds
make help test less fragile by regex-testing content rather than length
add eXpress and bam-split
incorporate proportion of fragments that mapped plausibly into assembly score
incorporate eXpress, bam-split, update metric names and reporting
restore merged_bam name
cache contig scores
comment up the read metrics run method
add count of good contigs to read metrics
add bam-split to deps
remove bowtie2
merge from blahah master
remove bcf parsing code from c extension