On Sat, Jun 9, 2012 at 12:09 AM, Charles Plessy <[email protected]> wrote: > Le Fri, Jun 08, 2012 at 11:33:46AM -0400, Carlos Borroto a écrit : >> >> I intent to work on updating Cufflinks to 2.0.0. I see Charles Plessy >> imported upstream 2.0.0 already but master is still on 1.3.0. Should I >> merge master and upstream branches and start working? Charles how did >> you import the new upstream version into upstream but kept master >> untouched? I normally do a "git-import-orig >> /path/to/<packagename>-<verionnumber>.tar.gz" which do both things. >> >> Finally is there a reason why we haven't updated to 2.0.0? > > Hi Calros, > > I imported version 2.0.0 when we worked on #672744, as I wanted to see if > 2.0.0 > solved it. But upstream, 2.0.0 is marked beta, so unless there are good > reasaons, > I would prefer to keep 1.3.0 in Wheezy and provide later versions as > backports. In > the meantime, it is always possible to upload 2.0.0 to Experimental if you > want. > > Have a nice week-end, >
Hi Charles, I'm happy to leave it UNRELEASED for now. Would having 2.0.0 on the master branch make harder to maintain 1.3.0? Is there a way to keep working with 1.3.0 if that would be necessary before the 2.0.0 line gets ready for prime time? Regarding Debian Med's PPA in Launchpad. Would it be OK to upload 2.0.0 there? I having some issues with 1.3.0 and I'm not the only one[1]. [1]http://seqanswers.com/forums/showthread.php?t=17662 Even upstream acknowledged there are issues with 1.3.0 in 2.0.0's changelog[2]. [2]http://cufflinks.cbcb.umd.edu/ "Some users were reporting a high FAIL rate on gene and transcripts quantification. This has been resolved according to a battery of tests using real and simulated data. The root cause was that in conditions with substantial overdispersion across replicates, the FPKM variance-covariance matrices produced by the Cuffdiff model were not always positive-definite. Cuffdiff was detecting this, and marking those genes as having unreliable confidence intervals. Prior to 2.0.0, the model contained a heuristic approximation of the covariances between assigned fragment counts (which are necessary for calculating the variance on each gene's expression level), and this approximation was producing poorly conditioned matrices. We have replaced the heuristic approximation with a direct sampling approach, in effect "simulating" the assignment of fragments to each isoform many times for each gene. By simulating fragment generation and assignment to each transcript, we are reconstructing variance-covariance matrices for assigned fragment counts that are always properly condition. This sampling approach produces more accurate estimates of variance and covariance as well, improving accuracy of transcript and gene level differential analysis. Users should expect more accurate quantification and shorter, more conservative lists of differentially expressed genes and trasncripts." Best, Carlos -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/cabgghblnlgniaehquxovo-sgnhudhhu6jhnn383y9lq6egn...@mail.gmail.com
