Bug #5903
closed
[gff2fj] Does not correctly label no-calls at end of cytogenetic band
Description
68fe4db9013109327ebf52cadcd09435+4522998/hu016B28.fj/213.fj.gz on tb05z is missing it's last tile. On further inspection, the last portion of the GFF has no entry (therefore a 'no-call') for GFF position chr11:134946116 onwards. This lands in the middle of the next to last tile (213.00.41d8). The resulting 213.00.41d8 tile only has 261 base pairs out of the reference 463. Further, the hu016B28 213.00.41d8 tile does not have any other indel or no-call information.
The proper behavior is to explicitly fill in no-calls till the end and have the last tile full of no-calls.
Updated by Abram Connelly over 9 years ago
- Project changed from Arvados to 39
- Category deleted (
Lightning)
Updated by Sarah Guthrie about 9 years ago
- Project changed from 39 to Lightning
Possibly fixed with introduction of PASTA
Updated by Sarah Guthrie about 9 years ago
- Target version set to Future sprints (Lightning)
Updated by Abram Connelly over 8 years ago
- Status changed from New to Closed
The pasta tools implement this functionality and make this bug obsolete. Testing is provided in the pasta repo that does a "round-trip" conversion, from a random sequence, to GFF then back again to make sure the conversion to and from are working.