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#!/usr/bin/env perl -l

...
    }
    close $gen_fh;
}

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$ cat pm_1079751_reference.csv
34787638,A,C
34787800,A,G

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$ cat pm_1079751_source1.gen 
C1, M1, 99999999, A, C, ... source1 info ...
C1, M2, 34787638, A, G, ... source1 info ...
C1, M3, 34787800, A, C, ... source1 info ...
C1, M4, 34787800, A, G, ... source1 info ...

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$ cat pm_1079751_source2.gen 
C1, M1, 99999999, A, C, ... source2 info ...
C1, M2, 34787638, A, G, ... source2 info ...
C1, M4, 34787800, A, G, ... source2 info ...
C1, M3, 34787638, A, C, ... source2 info ...

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34787800,A,G
    found in 'pm_1079751_source1.gen':
...
34787638,A,C
    found in 'pm_1079751_source2.gen':
        C1, M3, 34787638, A, C, ... source2 info ...