Bug #5903

[gff2fj] Does not correctly label no-calls at end of cytogenetic band

Added by Abram Connelly about 4 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
-
Start date:
05/04/2015
Due date:
% Done:

0%

Estimated time:
Story points:
-

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.

History

#1 Updated by Abram Connelly about 4 years ago

  • Category set to Lightning

#2 Updated by Abram Connelly about 4 years ago

  • Project changed from Arvados to Curoverse Science
  • Category deleted (Lightning)

#3 Updated by Sarah Guthrie almost 4 years ago

  • Project changed from Curoverse Science to Lightning

Possibly fixed with introduction of PASTA

#4 Updated by Sarah Guthrie almost 4 years ago

  • Target version set to Future sprints (Lightning)

#5 Updated by Abram Connelly almost 3 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.

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