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
