cufflinks accepting BAM files as input???

[PFS]

After the recent changes in TopHat's output format (BAM instead of SAM), I remember reading here that cufflinks would naturally accept BAM as input.

However, when I tried it today I did not succeed.

Do I have to convert the BAM file into SAM? That does not make much sense, given that TopHAt and Cufflinks are part of the same suite ... am I missing something here?

[patternist]

Starting release 0.9.0, Cufflinks and Cuffdiff support both BAM and SAM files. Both file types require that the chromosome names in header @SQ records, if present, must be sorted in the same order as the reads.

http://cufflinks.cbcb.umd.edu/