Merge pull request #1096 from RosettaCommons/roccomoretti/valgrind_fixes
A bundle of fixes for Valgrind issues.
1. Don't access off the end of a string in PoseFromSFRBuilder, for mmcif_IO
2. Better checking of out-of-range access in DeNovoUtilTests
3. (slightly) Better input checking in residue_io, to catch badly formatted params files, for ProteinUpstreamBuilderTests
4. Don't wrap a stack-allocated object into an OP, for AntibodyDesignOptions
5. Increase stack size, for fragment integration tests (At some point we may want to figure out what's taking up so much stack space in these tests, and see if we can flatten the call stack, or move some object allocation to the heap.)
I turned off the bulk of DeNovoUtilTests:test_bulge_strandpairing, as there was a hidden bug that, once properly checked for, makes the unit test now perma-fail. (The ss parameter given is not long enough to cover the segment.) Someone who knows the test should probably look into why that is, and what should be done to properly correct it.