transrate: v1.0.0 alpha 3

Some minor changes and bug-fixes:

• avoid re-running stages of the read-processing if their output files already exist
• add timestamp to logger #94
• print help message when transrate is run with no arguments #93
• transrate now reports the version number for missing dependencies
• fix samtools sort threads argument #96
• help message updated to include transrate score example and both authors
• updated coverage calculation
• fix a segfault in bam-read (https://github.com/cboursnell/transrate-bam-read/commit/8fec0e9fe1fd49878a644fd1755ebd97e4bc1931, #98)