Documentation for CNVRegionAnnotation

chr: str instance-attribute

Chromosome of the CNV region in the format like chr1

cnv_type: enums.CNVType instance-attribute

Type of the CNV region

cytogenetic_position: str instance-attribute

Cytogenetic position of the CNV region, e.g.: q15.1

end: int instance-attribute

End position of the CNV region

genomic_coord: str property

Genomic coordinates in the format chr:start-end

is_duplication: bool property

Check if the CNV region is a duplication

length: int instance-attribute

Length of the CNV region

name: str instance-attribute

Name of the CNV region given as {chr}_{start}_{end}_{cnv_type}

start: int instance-attribute

Start position of the CNV region

get_overlap_with_region(target_start, target_end)

Get the number of overlapping bases with another interval.

has_end_in_region(target_start, target_end)

Check if the CNV region has its end in the target region

has_start_in_region(target_start, target_end)

Check if the CNV region has its start in the target region

is_overlapping(target_start, target_end, overlap)

Check if the CNV region overlaps with another region in the specified manner

is_position_inside(position)

Check if the position is inside the CNV region

matches_cnv_type_or_both(benign_cnv_type)

Check whether benign_cnv matches the CNV type or is a combination of both

Parameters:

Name	Type	Description	Default
benign_cnv_type	str	Type of CNV as given by entry in benign CNV DB	required

Returns:

Type	Description
bool	True if benign_cnv_type matches the CNV type or is a combination of both, False otherwise

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