Dear Angie, many thanks for your detailed reply.
In case you're wondering, the overlap is supposed to be a "reverse frame-shift". I admit that it is weird and perhaps evolutionarily nonsensical. For what it's worth, though, there is precedent for alignments like that: http://scholar.google.com/scholar?cluster=18267901163676215671 http://www.ncbi.nlm.nih.gov/pubmed/9403055 (FASTX) http://song.sourceforge.net/gff3.shtml ("the gap attribute") Have a nice day, Martin On Mon, Nov 15, 2010 at 04:29:51PM -0800, Angie Hinrichs wrote: > Dear Martin, > > I believe you have found a bug -- thank you for the report. > > In case you're interested in the details, the failing line of PSL has a small > overlap on the target (reference) between the third and fourth blocks: 3rd > block end 182000 + 24*3 = 182072; 4th block start 182071. Our custom track > importer has a bit of code that bumps the 4th block start to 182072 to get > rid of the overlap, but it makes no adjustment to the 4th block size, and > then the end of the 4th block 182072 + 3*275 = 182897, one greater than the > size of chr7_gl000193_random, 182896. Then, since strand is +-, we reverse > the blocks on the reference and subtrack block ends from tSize to get the new > start coords on the positive strand of the reference. 182896 - 182897 is how > we get -1 there. > > We are discussing the best way to fix this. > > Thanks, > Angie > > > ----- "Martin Frith" <[email protected]> wrote: > > > From: "Martin Frith" <[email protected]> > > To: [email protected] > > Sent: Sunday, November 14, 2010 5:29:33 PM GMT -08:00 US/Canada Pacific > > Subject: [Genome] track load error: 0 coordinate -> -1 > > > > Dear genome folks, > > > > if I try to upload this PSL line as a custom track for hg19: > > > > 294 61 0 0 2 3 2 0 +- > > UniRef90_P56545 445 3 361 > > chr7_gl000195_random 182896 0 1065 4 49,7,24,275, 3,54,62,86, > > 181831,181978,182000,182071, > > > > I get this error message: > > Error track load error (track name='ct_UserTrack_3545'): > > start -1, end 1065 out of range in findBin (max is 512M) > > > > It looks like the (0, 1065) start and end coordinates are somehow > > getting changed to (-1, 1065). Is this a bug? > > > > Strangely, the problem does not occur for the following PSL line, > > which has coordinates (0, 111): > > > > 32 5 0 0 0 0 0 0 +- > > UniRef90_UPI0001D62716 354 0 37 > > chrUn_gl000229 19913 0 111 1 37, 0, 19802, > > > > > > Have a nice day, > > Martin Frith > > http://www.cbrc.jp/~martin/ > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
