Input

<chr##>  <label> <start>   <end>  

ie.

chr02  CR         39673000   39673200
chr02  PS39673005 39673005   39673085  
chr02  PS39673086 39673086   39673098  
chr02  PS39673005 39673099   39673191

If a region is covered by CR and by another sequence then the other sequence takes precedence

Graphical representation

Turns this:

|------------CR------------|
|-----1-----|  
    |--2--| 
            |--3--|
                |--4--|

Into this:

|-1-|       
    |--2--| 
          |1| 
            |-3-|
                |--4--|
                       |-CR-|