reverted vcfToAlignment because the results had no longer worked. added in numCpus to launch_vcfToAlignment.
I wanted to get this faster version running. It is not producing correct results yet
removed SGELK
can now send options to qsub using -q; can also set the number of cpus for launch-smalt
added a second intermediate file to freebayes so that it doesn't look complete until the final file is actually there
commiting whatever changes I've made
init
switched over to launch_smalt.pl
removed smalt bash script
Random changes over the last week
added alphabetical order within each row
I initilized each sequence with lowercase so that I do not have to do lowercase for each pairwiseDistance subroutine call
added a new logmsg for smalt. Changed the way progress is done internally in pairwiseDistances.pl
added the pairwiseTo2d script
added fst stuff
Merge branch 'master' of https://github.com/lskatz/lyve-SET into HEAD
added the low mem vcf to alignment module
random fixes
project directory creation script
moving 'bad sites' to just masking them