Hey Saatvik, I can confirm that the summary table is not accessed if you specify "wigMaf" as your track type and load it using the -custom option to hgLoadMaf. I hadn't anticipated this particular combination, but I can see why you need to do it this way since you're overwriting your extFile table with UCSC's whenever you update your mirror.
For the moment I guess you're stuck with either having base-level (with type wigMaf) or summary-level (with type maf). Sorry about that. I'll fix this problem in our source in the next day or two, but it'll be a couple of weeks before this makes it into our standard distribution. I'll send you a note off-list with the details of the fix so you can rebuild the binaries if you want to take that course. Alternately, you can change a single line in kent/src/hg/hgTracks/mafTrack.h to make it so the browser never goes into summary view (which will make your browser really slow if you have a lot of data). #define MAF_SUMMARY_VIEW 100000000 Thanks a bunch for reporting these problems. We depend on our users to help us make the product better. brian On Tue, Mar 23, 2010 at 12:16 PM, Saatvik Agarwal <[email protected]> wrote: > Hi Brian, > > I had tried changing the type to wigMaf based on a colleague's suggestion. > The problem with that is that when I am completely zoomed out in full > display mode, I don't see any elements in my track but if I zoom into the > specific region of the alignment then I see the exact alignment. Strangely > enough, this is not a problem in dense mode, i.e. it looks fine both zoomed > out and zoomed in. I tried changing windowingFunction but that did not help. > > Other than that, changing the type to wigMaf is fine by me, but I would > ideally like to see all the elements in full mode. Can you reproduce this > behavior on your end? > > Thanks, > Saatvik > > On Tue, Mar 23, 2010 at 3:39 PM, Brian Raney <[email protected]> wrote: >> >> Hey Saatvik, >> >> I'm able to replicate your error here. The problem is our support for >> tracks of type "maf" don't support the use of the trackDb variable >> "mafFile" properly. A work-around for this problem is to make the >> type of your track "wigMaf" in the trackDb entry (see README in >> kent/src/hg/makeDb/trackDb for details). >> >> I hope this resolves your error. If not, please respond to this >> message cc'ing the mail list. >> >> brian >> >> On Thu, Mar 18, 2010 at 2:48 AM, Saatvik Agarwal >> <[email protected]> wrote: >> > Hello, >> > >> > I am trying to display pairwise alignments generated by BLAT (Genbank >> > sequences to hg18) using the MAF format. I like the MAF format since it >> > is >> > pretty close to the UCSC cgi custom track for blat results in that it >> > shows >> > gaps and mismatches graphically. Now if I upload my MAF track (attached) >> > as >> > a custom track, it works fine, but if I load it into our mysql database >> > (we >> > run a personal browser mirror) using hgLoadMaf and add it to my >> > trackDb.ra >> > entry it doesn't work properly. It looks fine when you're zoomed out but >> > when I zoom in (to the point where it would normally show the seq. ident >> > plot) the browser crashes and just gives me a completely blank webpage. >> > It's >> > obviously this track because if I turn it off everything else works >> > fine. >> > >> > Any thoughts on what I might be doing wrong? All the examples I saw in >> > the >> > kent src doc were multiple alignments to reference genomes. My MAF >> > aligns >> > short sequences from Genbank to a reference genome. >> > >> > My commands for loading the MAF looks like this: >> > >> > hgLoadMaf hg18 bejsaGenbankBLAT >> > -pathPrefix=/cluster/u/curator/tracks/hg18 -custom >> > -loadFile=genbankBLAT.maf >> > hgLoadMafSummary -minSize=50 -mergeGap=500 -maxSize=50000 hg18 >> > bejsaGenbankBLATSummary /cluster/u/curator/tracks/hg18/genbankBLAT.maf >> > >> > and my hg18 trackDb.ra entry is as follows: >> > >> > track bejsaGenbankBLAT >> > shortLabel Endogenous enhancers >> > longLabel Endogenous (same species) enhancers BLAT >> > color 0,255,0 >> > priority 1000 >> > group regulation >> > visibility dense >> > mafDot on >> > type maf >> > mafFile /cluster/u/curator/tracks/hg18/genbankBLAT.maf >> > summary bejsaGenbankBLATSummary >> > >> > Thanks, >> > Saatvik >> > >> > _______________________________________________ >> > Genome maillist - [email protected] >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
