Sailfish v0.9.1

This release provides some performance improvements and bug-fixes over v0.9.0. It also provides some new features:

• The ability to write out the equivalence classes and their counts. The --dumpEq flag will write out a file in the auxiliary directory called eq_classes.txt. This file has the following format:

N (num transcripts)
M (num equiv classes)
tn_1
tn_2
...
tn_N
eq_1_size t_11 t_12 ... count
eq_2_size t_21 t_22 ... count

That is, the file begins with a line that contains the number of transcripts (say N) then a line that contains the number of equivalence classes (say M). It is then followed by N lines that list the transcript names --- the order here is important, because the labels of the equivalence classes are given in terms of the ID's of the transcripts. The rank of a transcript in this list is the ID with which it will be labeled when it appears in the label of an equivalence class. Finally, the file contains M lines, each of which describes an equivalence class of fragments. The first entry in this line is the number of transcripts in the label of this equivalence class (the number of different transcripts to which fragments in this class map --- call this k). The line then contains the k transcript IDs. Finally, the line contains the count of fragments in this equivalence class (how many fragments mapped to these transcripts). The values in each such line are tab separated.

• The ability to select the "auxiliary" directory where information such as bootstrap estimates, gibbs samples, and auxiliary parameters are stored. The default sub-directory of the quantification directory is aux, but it can be changed with --auxDir. This original name is apparently a conflict on systems based on cygwin where aux is a reserved directory name. Even if you're not using this feature, it's recommended to upgrade for the performance improvements and bug fixes.