Why is the code you've posted so completely broken?

Did you think that you could fool us by sticking use strict; use warnings; at the top and declaring some of the variables with my, and get us to solve your problems that you've failed to solve?

Tip: If you strict and warnings from the get go, you'd find it far easier to get your code right as you go, rather than painting yourself into a corner of undeclared and uninitialised variables.

I have a 25 line solution to what I interpret from your description to be correct. It produces this output from your samples: 

C:\test>819005
c1      100     12000   11901   +       AT
c1      100     12000   11901   +       AT
c1      100     12000   12989   +       AT
c1      100     12000   13901   +       AT
c1      19800   20000   206     -       AG
c9      10078   14008   3931    -       AG
c9      1078    10008   9109    -       TA

[download]

But I cannot check whether that is correct because your code doesn't produce anything for me to compare it against :(

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
"I'd rather go naked than blow up my ass"

In reply to Re^3: Data munging by BrowserUk
in thread Data munging by umasuresh

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