Identifying elemental genomic track types and representing them uniformly

BMC Bioinformatics

Table 3 Overview of the reserved columns in the GTrack format and their associations to track type

Core property:			Gaps	Lengths	Values			Interc.
GTrack column(s):	genome	seqid	start	end ¹	value	strand	id	edges ²
Type of column:	N	N	C	C	C	N	N	C
Track type
Points (P)	?	!	✓	.	.	?	?	.
Segments (S)	?	!	✓	✓	.	?	?	.
Genome Partition (GP)	?	!	.	✓	.	?	?	.
Valued Points (VP)	?	!	✓	.	✓	?	?	.
Valued Segments (VS)	?	!	✓	✓	✓	?	?	.
Step Function (SF)	?	!	.	✓	✓	?	?	.
Function (F)	?	!	.	.	✓	?	?	.
Linked Points (LP)	?	!	✓	.	.	?	✓	✓
Linked Segments (LS)	?	!	✓	✓	.	?	✓	✓
Linked Genome Partition (LGP)	?	!	.	✓	.	?	✓	✓
Linked Valued Points (LVP)	?	!	✓	.	✓	?	✓	✓
Linked Valued Segments (LVS)	?	!	✓	✓	✓	?	✓	✓
Linked Step Function (LSF)	?	!	.	✓	✓	?	✓	✓
Linked Function (LF)	?	!	.	.	✓	?	✓	✓
Linked Base Pairs (LBP)	?	!	.	.	✓	?	✓	✓

C Core reserved column (defines track type)
N Non-core reserved column (reserved, but does not define track type)
✓ Column is mandatory
? Column is optional
. Column is not allowed
! Property must be present, either as a column or in a bounding region specification
¹ The length is the difference between the end and the start position, or, if the start column is not present, the difference between the current end position and the previous.
² The non-core reserved column id is required when the edges column is present.

ISSN: 1471-2105