Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	lib/transrate/assembly.rb
	lib/transrate/comparative_metrics.rb
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.
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.
Merge branch 'master' of github.com:cboursnell/transrate

is necessary,
added low uniqueness bases metric to individual contigs
added tests for above #69
add mean mapq and proportion of low uniqueness bases to reads stats output
missing comma in hash
adding coverage variance calculation
Added calculation for variance over contig effective length
add c ext build artefacts to gitignore
parse stderr from bowtie to capture number of read pairs
add support for comma separated list of fastq files as input
bump bindeps dependency version to get bzip2 support
bump bettersam version number
changed samtools download to an archive that contains the binaries
fixed link to samtools to be to raw file
fixed reference coverage calculation; bumped crb-blast version in gemspec
fixed error caused by variable not being set