The function assign_cn_to_ssm currently only works with battenberg outputs. As we now have merges available for all the things, it needs to be reorganized to support other CNV callers. In addition, the seg file should be obtained through the get_sample_cn_segments instead of reading individual file from its location on the drive.
The function
assign_cn_to_ssmcurrently only works with battenberg outputs. As we now have merges available for all the things, it needs to be reorganized to support other CNV callers. In addition, the seg file should be obtained through theget_sample_cn_segmentsinstead of reading individual file from its location on the drive.