From: James C. <ca...@gm...> - 2010-01-12 10:29:09
|
I have the following file: """ ##gff-version 3 ##sequence-region CYP2C8 1 36725 CYP2C8 src Feature 4100 4291 . - . ID=37 CYP2C8 src Feature 6125 6213 . - . ID=38 CYP2C8 src Feature 8093 8330 . - . ID=39 CYP2C8 src Feature 11013 11204 . - . ID=40 CYP2C8 src Feature 23538 23764 . - . ID=41 CYP2C8 src Feature 20003 20213 . - . ID=42 CYP2C8 src Feature 32411 32944 . - . ID=43 CYP2C8 src Feature 34400 35725 . - . ID=44 """ Running "flatfile-to-json.pl --gff /tmp/e.gff --tracklabel 'feature' --cssclass feature --out browsers/human-gene-test --type Feature" produces the following track: "featureNCList":[[4099,4291,-1,"37"],[6124,6213,-1,"38"],[8092,8330,-1,"39"],[11012,11204,-1,"40"],[23537,23764,-1,"41"]] You can see that everything above 30,000 bases is ignored. Changing the sequence-region pragma to be a larger region fixes the problem: ##sequence-region CYP2C8 1 46725 What is going on here? Why do I not get all the features I declared? thanks, James |