viola.Bedpe.merge

Bedpe.merge(ls_bedpe: list, ls_caller_names: list, threshold: float, linkage='complete', str_missing=True)

Return a merged bedpe object from mulitple caller’s bedpe objects in ls_bedpe

Parameters

• ls_bedpe (list) – A list of bedpe objects to be merged, which are the same order with ls_caller_names

• ls_caller_names (list) – A list of names of bedpe objects to be merged, which should have self’s name as the first element

• threshold (float) – Two SVs whose diference of positions is under this threshold are cosidered to be identical.

• linkage ({‘complete’, ‘average’, ‘single’}, default=’complete’) – The linkage of hierarchical clustering. To keep the mutual distance of all SVs in each cluster below the threshold, “complete” is recommended.

• str_missing (boolean, default="True") – If True, all the missing strands are considered to be identical to the others.

Return type

A merged bedpe object