changes to support large index files #603
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Part of #550
This PR contains changes to start to support the index files for > 2 GB.
In this PR I switch to using bareadl() instead of baread() for the ixgb2() subroutine. To maintain backward compatibility I introduce a new ix2gb2() subroutine, which will accept the index version as a parameter. Calling ixgb2() will call ix2gb2() with an index version of 1 (i.e. legacy behavior). But ix2gb2() can be used on files larger than 2 GB.
I would like to merge these changes incrementally, rather than as one giant PR. The changes in this PR have no effect on functionality at the moment, but allow for the next version of the index to be supported in future PRs.