Numerous bug fixes and significant performance improvements in Cufflinks and Cuffdiff. Note that some the formats of some files have changed. Other changes:

• Expression values were not being reported for a small number of genes when using certain annotation files.
• Fixed a divide-by-zero error in Cuffdiff
• Various GTF parser fixes.
• .expr files produced by Cufflinks now contain FPKM confidence interval columns
• Isoform filtering was being innappropriately applied when working with annotation in Cufflinks (via –GTF)
• The .tmap files reported by Cuffdiff contained zero in FPKM field.
• New command line options –num-importance-samples and –max-mle-iterations allow advanced users to influence of the transcript abundance estimation.