sgkit.window_by_interval#

sgkit.window_by_interval(ds, *, variant_contig='variant_contig', variant_position='variant_position', interval_contig_name='interval_contig_name', interval_start='interval_start', interval_stop='interval_stop', merge=True)#

Add window information to a dataset, using arbitrary intervals.

Intervals are defined using the variables interval_contig_name, interval_start, and interval_stop, where the start and stop range acts like a Python slice, so the start position is inclusive, and the stop position is exclusive.

Windows are defined over the variants dimension, and are used by some downstream functions to calculate statistics for each window. Windows never span contigs.

Parameters:
ds Dataset

Genotype call dataset.

variant_contig Hashable (default: 'variant_contig')

Name of variable containing variant contig indexes. Defined by sgkit.variables.variant_contig_spec.

variant_position Hashable (default: 'variant_position')

Name of variable containing variant positions. Must be monotonically increasing within a contig. Defined by sgkit.variables.variant_position_spec.

interval_contig_name Hashable (default: 'interval_contig_name')

Name of variable containing interval contig names. Defined by sgkit.variables.interval_contig_name_spec.

interval_start Hashable (default: 'interval_start')

Name of variable containing interval start positions. Defined by sgkit.variables.interval_start_spec.

interval_stop Hashable (default: 'interval_stop')

Name of variable containing interval stop positions. Defined by sgkit.variables.interval_stop_spec.

merge bool (default: True)

If True (the default), merge the input dataset and the computed output variables into a single dataset, otherwise return only the computed output variables. See Dataset merge behavior for more details.

Return type:

Dataset

Returns:

: A dataset containing the following variables: