Database Checks

• Number of contigs used is <= number allocated
• Disk and memory values for "number of contigs" are consistent
• Number of readings used is <= number allocated
• Disk and memory values for "number of readings" are consistent
• Disk and memory values for "actual database size" are consistent
• Actual database size <= maximum size
• Data_class is either DNA(0) or protein(1).
• Number of free annotations >= 0 and <= number allocated
• Contig order is consistent
• Number of free notes >= 0 and <= number allocated
• First note has prev_type as GT_Database
• Detect note loops

Contig Checks

• Has a left reading number
• Has a right reading number
• The left reading has no left neighbour
• The right reading has no right neighbour
• Chain right to
  • check loops
  • check holes
  • flag a reading as used
• When finished chaining
  • check length is correct
  • check right reading number is correct
• Reference only valid reading numbers
• Chain left to
  • check loops
  • flag readings as used, if not done so in right chaining;
• When finished chaining, check left reading number is correct
• Chain along annotation list to
  • flag as used
  • detect annotation loops
  • annotation is within the contig
  • annotation is rightwards of previous
• First note has prev_type as GT_Contigs
• Detect note loops

Reading Checks

• Memory and disk values tally for
  • left neighbour
  • right neighbour
  • relative position
  • length + sense
• Left neighbour is a valid reading number
• Right neighbour is a valid reading number
• Reading is not used zero times
• Reading is not used more than once
• Hand holding: (lnbr[rnbr[reading]] == reading)
• Relative position of reading >= position of left neighbour
• Length != 0
• Used sequence length == "right clip position" - "left clip position"
• Has valid strand (0 or 1)
• Has valid primer
• Has valid sense (0 or 1)
• Chain along annotation list to
  • flag as used
  • detect annotation loops;
  • annotation is rightwards of previous
• First note has prev_type as GT_Readings
• Detect note loops

Annotation Checks

• No loops in free annotation list
• Is neither used nor is on the free list
• Annotation is not used more than once
• Is used, yet is still on the free list
• Length >= 0
• Has valid strand (0 or 1)

Note Checks

• No loops in free note list
• Is neither used nor is on the free list
• Hand holding: (note->next->prev == note)
• Note is not used more than once
• Is used, yet is still on the free list

Template Checks

• Minimum insert length <= maximum insert length
• Has valid vector
• Has valid clone
• Has valid strand

Vector Checks

• Level > 0
• Level <= MAX_LEVEL (MAX_LEVEL currently is 10; a "feasibility" check)

Clone Checks

• Has valid vector