Version 0.6.3

@kingsfordgroup kingsfordgroup released this Mar 11, 2014 · 401 commits to master since this release

  • Now handles the presence of 'N' characters in the reference transcripts. Currently, these k-mers are just discarded and the effective length of the reference transcripts are adjusted accordingly.
  • Fixed numerical instability caused by very small probabilities that would sometimes lead to NaNs in quantification.
  • Interface Change: Changed the specification of read files to the quant phase of Sailfish. The user must now provide a library format string (the specification of which is described in the README and the manual). The format string informs Sailfish about e.g. the relative orientation of the reads. While not all of this information is currently used, this change was made in anticipation of an upcoming feature, which will allow Sailfish to perform very rapid quantification of abundance using read alignments, if the user already has these available or needs to compute them anyway for other analyses.
  • Significant speed improvements to the optimization procedure during the quant phase. This allows one to perform many more EM steps in substantially less time.
  • Changed the default convergence criterion to be data-based rather than a fixed number if iterations. The old behavior (a fixed number of iterations) can be mimicked by setting the -i option with the desired number of iterations and setting the -m option to 0. However, the new default convergence criteria is generally recommended.
  • Fixed a bug in the computation of the read counts of bias-corrected quantification estimates.
  • Added a new output type, the estimated number of k-mers. This is like the estimated number of reads originating from a transcript, but is somewhat more natural for Sailfish as it reports the number of k-mers, which are the fundamental unit of coverage.
  • Added initial logging support, which is part of an ongoing effort to improve error handling and messages in Sailfish (this is currently only activated under Linux, until I can figure out how to get g2log to work with g++ under OSX).

There are a number of important improvements and bug-fixes in this release, and we strongly encourage all users to upgrade to version 0.6.3 at this time. There are also some new features, which are close to completion, and we anticipate the time between this release and 0.6.4 to be much smaller than the time between 0.6.2 and 0.6.3.