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chrM:307    0    AGCGGGGA    129
chrM:307    0    AGCGGGGA    130
...
chrM:309    1    TCAGGGTG    106
chrM:309    2    TCAGGGTG    130
chrM:309    2    TCAGGGTG    129

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chrM:307    0    AGCGGGGA    130     #-->Line1
chrM:307    0    TCAAAATG    130     #-->Line2
...
chrM:307    0    TCAGCCTG    129     #-->Line8
chrM:307    2    TCAGGGTG    129     #-->Line9
chrM:307    1    TCAGGGTG    106     #-->Line10

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CLUSTER
chrM:307    0    AGCGGGGA    130     #--> Select, first line sorted by
+ col3, col2, col4(rev sort)    # Line1
...
chrM:307    0    TCAGCCTG    129     #--> Now selected, line#8 sorted 
+by col3, col2, col4(rev sort)      #Line8, make single line cluster
CLUSTER
....and so on for next chr positions...

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CLUSTER
chrM:307    1    TCAGGGTG    106
...
chrM:309    0    AGCGGGGA    130
chrM:309    0    AGCGGGGA    129
CLUSTER

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#!/usr/bin/env/perl

...
close $OFILE;
close DATA;