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file1=cnv file
start   stop  size(in bp) 
5389769  98256008  3567
7452344  871875466 64547

file2=genelist1
name start stop
BRCA1 41196312   41277500
TP53   7571720    7590863

file3=genelist3
name start stop
OMG  29621668   29624380
NR3C1  142657496..142815077

 !/usr/bin/perl
    
...
    }
    close(OUT);

gene name  size  start stop 
xyz         5464 83654272 6735353
...
...