##07/29/2019
##@@author: Simon (Chong) Chu, DBMI, Harvard Medical School
##@@contact: chong_chu@hms.harvard.edu

#Given reference genome, and rmsk annotation file (for specific repeat type), check whether there is deletion happen

#make sure the module can be easily extend to call other non-TE deletions

#what about homozygous/heterzygous deletion???????????????

class xTERefDel():
    def __init__(self):
        return

    def call_TE_deletion(self, sf_ref, sf_rmsk, sf_bam, sf_rslt):
        return

    #