Always include third-party
Generate the small/large index binaries and added the first version of wrappers.
Made binaries wrapper aware.
Made sure we properly check the size.
In work. From this point we temporarly break bowtie functionality.
more work for lfs.
Added all code coresponding to bowtie2 for LFS.
Some more adjustments.
More work. Code compilable now.
Fixed warnings.
test updates
Fixed the index build
Just a temporary change
Another lfs adjustment.
These still needs review.
more changes. Still not done yet.
many changes that fix LFS bugs and make implicit casts explicit
Updated the test scripts to include large index testing as well.
Added the big ref test.
Added the large index test.