changed sam parsing with bettersam to bam parsing with bamtools c++
bump version
read count with wc now handles comma separated list of fastq files
added proportion of good mappings to individual contig
add bam-read to dependencies
Merge remote-tracking branch 'blahah/master'

Conflicts:
	lib/transrate/contig.rb
output all metrics involved in contig score
alter tests to match new metrics output
transrate assembly score is now geometric mean of all contig scores
fixed score so individual metrics can't be NaN
fixed error with proportion of uncovered bases not being a float
renamed method to generate bcf file
parse bcf file in c extension
add to tests to check new c extension
bump version to 0.3.3
fixed error from missing contigs in bcf file
fixed array index error
save read count in a text file for later use
try to make the c less leaky
fixed some more memory leaks