Sailfish v0.7.2

Changes: v0.7.2 adds the ability to select the Variational Bayesian EM algorithm for optimization in place of the "regular" EM algorithm. This mode is selected by passing --useVBOpt to sailfish's quant command.

Note: v0.7.1 introduces no new features over v0.7.0 but fixes some build issues on OSX.

This release brings some long-standing bug-fixes and some substantial improvements to Sailfish. The code is also being cleaned up and trimmed down. There is no longer a dependency on Shark, so building should be easier than before. A number of header-only external dependencies have been included in the source tree to further ease build issues. Sailfish now adopts Salmons library format strings, reducing the need for difficult escape sequences when placing these strings in shell scripts. This new version of Sailfish also adopts the quasi-mapping approach from RapMap to provide transcripts and position hits for reads, leading to a substantial reduction in runtime and an improvement in accuracy under a number of scenarios.

NOTE: Since v0.7.0 the format of the output (the quant.sf file) written by Sailfish has changed. The RPKM, KPKM and EstNumKmers columns are no longer present. The output format is now equivalent to that of Salmon, and reports, for each record, (1) Transcript Name, (2) Transcript Length, (3) TPM, (4) Estimated Number of Reads. Please be aware of this to make the appropriate changes for tools that perform downstream processing with Sailfish's output.