use relative paths for trinity contig dir
allow velvet-style contig names for coverage computation
count the number of actual bases/sites interrogated for differences or informative status
make adjustments for fasta reads
add abyss and velvet (non velvet optimiser) code
changes fastq/fq to reads and use common read finder
return None when unsetting singleton reads
fix field numbering problem
allow inputs of difference case in config files
add lowercase degen bases
sorted output from match contigs
add a velvet option
add a generic option (rather than just Trinity)