AGP Validation

Files structure and content can be validated at two different levels:

• File content and structure
• Overlap and swith point validation

I. File content and structure

program: agp_validate

parameters:

purpose: this program checks for text formatting and consistency (as defined by the AGP Specification). It also prints the following statistics for components, gaps, scaffolds and objects.

Error level violations:

• Incorrect number of columns (excluding comments): There should be 9 tab-separated columns; the first 8 should not be emtpy.
• Non-positive integers in the following columns:
  • 2: object_beg
  • 3: object_end
  • 4: part_num
  • 6b: gap_length
  • 7a: component_beg
  • 8a: component_end
• Objects have ranges that are non-sequential and/or overlapping.
• object_beg is greater than the object_end.
• component_beg is greater than the component_end.
• The length of the span specified for the component (in column 7a and 8a) does not match the length of the span specified for the object (in column 2 and 3).
• An object not having an object_beg coordinate of 1.
• An object not having a part_number of 1.
• The value of column 4 (part_number) not equal to the previous part_number + 1.
• Invalid terms or symbols in the following columns:
  • 5: component_type
  • 7b: gap_type
  • 8b: linkage
  • 9a: orientation
• 0 or na component orientation used for a non-singleton scaffolds
• Objects with non-sequential lines and/or lines mixed with other objects.

Warning level violations:

• A gap at the beginning or the end of an object
• Consecutive gap lines of the same type
• Linkage=yes with a gap_type other than fragment, clone or repeat.
• Overlapping spans used for a given component_id.
• Non-draft component_id used more than once.
• Non-draft component spans out of order.
• Extra tab character at the end of the line.

II. Overlap and switch point validation

This is currently unavailable. Support for this may be added in the future.