Sailfish Changelog

v0.1.0

Date: June 19, 2013

Speed improvements in "quant" phase -- Substanially improved the speed of direction-aware kmer counting. In most cases, it should now be almost as fast as counting kmers with the "canonical" flag set. Also improved the speed of the EM proceedure by consildating non-dependent computations into the same loops so that fewer passes over the data are required.
Fixed bug in computation of the log-likelihood function. The SQUAREM procedure now acts upon (and prints out) the expected per-transcript log-likelihood rather than the log-likelihood for all transcripts. The value is more reasonable and works better for the SQUAREM step-size selection procedure.
Build improvements
- Removed build dependency on libprofiler (thanks to Chirs Hill for mentioning this dependency).
- Fixed std::this_thread dependence that would lead to compilation problems on versions of GCC built without "--enable-libstdcxx-time" (thanks to Chirs Hill for the suggested fix).

Moved computation of k-mer equivalence classes to the index-building phase. This substantially reduces the memory usage during estimation as well as the size of several of the stored indexes. The algorithm used to compute the equivalence classes was also changed from a parallel-hashing based algorithm to a divisive partition refinement algorithm. This latter algorithm is more suitable to the per-transcript processing that happens during the indexing phase.
Implemented reading from named pipes and input redirection. Sequencing reads can now be streamed in from a named pipe (e.g. using process substitution syntax.)
Implemented direction-aware k-mer counting. If the directionality (sense / anti-sense) for a set of reads is known (e.g. as the result of a direction-aware protocol), it can now be specified on the command line. Thus, there are conceptually 3 "classes" of reads; forward/sense, reverse/anti-sense and undirected.
The estimated number of reads originating from each transcript is now written to the output file. This may be useful for differential-expression tools which are based on read counts.
Fixed oversight in bias-correction phase where only RPKM estimates (and not e.g. TPMs) were corrected. Now all different estimates are corrected during the bias-correction phase.