Sailfish v0.7.6

This release addresses a few issues and adds a significant new feature:

Fixes:

• Fixed an issue where argument validation could cause Sailfish to fail to process certain single-end libraries.

New features and changes:

• New: Added the ability to compute bootstrap samples using either the Variational Bayesian or normal EM algorithm. Providing the option --numBootstraps k, where k is some integer greater than 0 will cause Sailfish to compute k bootstrap samples. Bootstraps are computed in parallel using the number of threads normally provided to Sailfish via the --threads option. The bootstraps themselves are computed in parallel, each making use of a single thread. The results are saved in the quantification directory to a file called quant_bootstraps.sf. The format of the file is comment lines (starting with a #), followed by a header line listing the transcript ids, followed by k lines, each of which gives the bootstrap values for each transcript, under each bootstrap. The order of the values in a line is the same as the order of the transcripts in the header.
• New: Added a new method for adjusting for effective length that is less "aggressive" with non-standard fragment length distributions. The previous behavior can be enabled with --unsmoothedFLD.
• Removed the --useGSOpt flag since it was somewhat redundant. Now, simply providing a number greater than 0 to --numGibbsSamples will enable the posterior Gibbs sampler.