v1.1.4 - unstable

• Edit, 2015-08-28 A bug was found where multiple contigs in the reference genome will cause race conditions. Therefore, please instead download v1.1.4b or a newer version.
• SNP annotation with SnpEff (still kind of experimental; thanks to @teishi for the main script)
• Multithreaded mpileup and VCF merging, ie, faster SNP calling
• To multithread and find equally sized regions, there is now the helper script makeRegions.pl.
• SNPs-only VCF is created for viewing purposes. However it is not used for downstream analysis and so SNP calls have not been changed.
• Fixed a problem where /tmp/ is used at one point for a really large file; it is not used anymore and so you aren’t limited by space anymore
• Perl libraries are now discoverable; no need to change PERL5LIB in your environment. Only PATH.
• Clade distances script - find distances between output clades. Still kind of experimental; thanks to @andrewdhuang
• Can now use shuffleSplitReads.pl to shuffle a whole set of paired-end reads; makes it easier to start off a Lyve-SET project.
• Main output files are put into the main Lyve-SET directory as symlinks.
• set_diagnose.pl: helps you start investigating if anything went wrong in your Lyve-SET run. I think there is a lot of potential to put more things in this script; suggestions welcome.
• Employs samtools v1.2 instead of v1.1
• Easier-to-look at log folder. Timestamps are now shown for start/stop in the log. All options that were used are now shown in the log.
• Many, many bug fixes