Version 0.6.2

• 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.)
• The indexing phase now uses the streaming read parser instead of the mem-mapping parser. This now allows the entire pipeline to be run without using the mem-mapping parser (which may cause issues on a small number of systems). To force usage of the streaming read parser during quantification, just create a named pipe to stream in the reads. For example, if the reads are in the files reads1.fq and reads2.fq, you can create a named-pipe to stream in all of the reads by passing <(cat reads1.fq reads2.fq) to the -r option. This will trigger usage of the streaming read parser instead of the mem-mapping parser.
• 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.