Story #5904

[gff2fj] Add in error checks to check common errors and do sanity checks on resulting FastJ files

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

gff2fj or the pipeline that uses it, should have some basic error checking to make sure the resulting tiles make sense. Some common errors are:

  • Tiles at the end of paths or cytogenetic bands sometimes don't appear
  • Tiles at the end of paths or cytogenetic bands don't have proper no-call information

History

#1 Updated by Sarah Guthrie over 3 years ago

  • Tracker changed from Feature to Story
  • Project changed from Curoverse Science to Lightning

Tile loss has not occurred after introduction of PASTA.

#2 Updated by Sarah Guthrie over 3 years ago

  • Target version set to Future sprints (Lightning)

#3 Updated by Abram Connelly almost 3 years ago

  • Status changed from New to Closed

The pasta tools implement GFF conversion:

https://github.com/abeconnelly/pasta

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