correcting function prototypes
Adding a method for breaking up very large cacti.
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Moving to 64-bit integers for all
More 64bit changes (Changing INT32 constants to INT64 ones)
Changing intTuple syntax
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Fixed filtering function
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Adding function to shift ordering of segments in block
Fix to assert
Fixing small memory leak
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Fixed to scaling issue
Performance tweaks
Small efficiency improvements
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Adding in bones of function to collapse reverse tandem duplications
properly within chains.
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Basic function for removing reversals finished, but not yet tested or
properly documented.