gvtrack.iterator: Defines modification rules for a one-dimensional iterator in...

In misha: Toolkit for Analysis of Genomic Data

Defines modification rules for a one-dimensional iterator in a virtual track

Description

Defines modification rules for a one-dimensional iterator in a virtual track.

Usage

gvtrack.iterator(vtrack = NULL, dim = NULL, sshift = 0, eshift = 0)

Arguments

vtrack	virtual track name
dim	use 'NULL' or '0' for 1D iterators. '1' converts 2D iterator to (chrom1, start1, end1) , '2' converts 2D iterator to (chrom2, start2, end2)
sshift	shift of 'start' coordinate
eshift	shift of 'end' coordinate

Details

This function defines modification rules for one-dimensional iterator intervals in a virtual track.

'dim' converts a 2D iterator interval (chrom1, start1, end1, chrom2, start2, end2) to a 1D interval. If 'dim' is '1' the interval is converted to (chrom1, start1, end1). If 'dim' is '2' the interval is converted to (chrom2, start2, end2). If 1D iterator is used 'dim' must be set to 'NULL' or '0' (meaning: no conversion is made).

Iterator interval's 'start' coordinate is modified by adding 'sshift'. Similarly 'end' coordinate is altered by adding 'eshift'.

A shifted interval that runs past a chromosome boundary is clamped to it. If nothing is left of it - it falls entirely outside the chromosome, or the shifts collapse it to zero length - the virtual track returns 'NaN'.

Value

None.

See Also

gvtrack.create, gvtrack.iterator.2d

Examples

gdb.init_examples()

gvtrack.create("vtrack1", "dense_track")
gvtrack.iterator("vtrack1", sshift = 200, eshift = 200)
gextract("dense_track", "vtrack1", gintervals(1, 0, 500))

gvtrack.create("vtrack2", "dense_track")
gvtrack.iterator("vtrack2", dim = 1)
gextract("vtrack2", gintervals.2d(1, 0, 1000, 1, 0, -1),
    iterator = "rects_track"
)

misha documentation built on Aug. 24, 2026, 5:14 p.m.