Hi Angie On Nov 6, 2009, at 6:36 PM, Angie Hinrichs wrote:
> Hi Davide, > > You haven't missed any email -- BAM support is unannounced because > it is incomplete and still under development. When do you have time > to read our code diffs? :) > Well, I did that after reading this: http://genome-test.cse.ucsc.edu/builds/versions-all/v218-preview.html and this: http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables#USE_BAM > Indeed we currently use samtools-c's support for ftp and http. I > would prefer to use our own network code because it supports https > and its local-disk caching is more sophisticated. samtools-c > doesn't have a simple interface to plug in some other data source -- > it wants either local file paths that it can open, read etc., or URLs. Yep, I've been using samtools to view remote bam files... Actually I've asked if there will be SSL support... > > There is still a lot of polishing and documentation left to do, in > addition to making udcFuse fast and stable. And it's not the only > thing on my plate, so I make no promises for the formal announcement > before 'early next year'. > No problem, I understand that. > I would be happy to hear any other feedback you have about our BAM > display. > Actually it works quite well, when it does. I mean, sometimes it cannot open a bam, although I can dislpay bam files which are in the same directory (and with a bai index). When a track is loaded I don't have any performance issue, I can browse the genome quite fast. I would like to load PE data (to see if the paired reads are somehow connected with a line...) but I wasn't able to load. d _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
