Added gzip support to plain text tools addressing #91 #143
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Adding a checkbox to the window was surprisingly fun
Added makeReader(File f) and makePrintStream(File o, Boolean gzip), and replaced redundant if - else statements
And added GZip output to FilterbyProximity and PeakAligntoRef' also cleaned up code
and cleaned up code
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accidentally was on sort-by-ref branch when making documentation, so I rewrote some tools and it turned out to be better than the code on this branch
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And made checkbox UI more consistent
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Format gzip output flag to use consistent syntax and usage info
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