speedseq installs lumpy-sv-0.2.1, with product-base evidence aggregation and better trim thresholds
removed GSL prerequisite from lumpy. also, updated README.md to use sambamba 0.4.6 (deals with empty bams gracefully)
speedseq README now reflects that it pulls a tagged version of samblaster (0.1.14) rather than the latest on git
added lumpy exclude bed file. this is the same as the freebayes exclude file except that it additionally excludes the mitochondrial chromosome
updated readme with lumpy exclude info
updated lumpy example
removed gsl req from readme
bumped to bwa 0.7.8
fixed manual installation freebayes instructions
updated readme
fixed bug in lumpy module that affected output file name when not provided by -o flag