do inlining of EndaCounts method
bug 24128

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 128920]
Fix bug in SparseMatrix copy constructor, and add some regression tests.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129161]
Simplify RangeUnion business

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129221]
Be more careful about the boundary condition for mutation scoring

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129398]
few updates to Edna/ConsensusCore API to fix .net/C++ memory management bug
bug 24128

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129433]
not sure why instrument linux build doesn't like this... see if this helps?
bug 24128

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129438]
Update to numpy.i from numpy 1.8.

 This fixes the SWIG compiler warnings.

(I hope this doesn't break Py3K)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129462]
Fix the numpy_typemaps

ToHostMatrix has been broken for a while because of the DOUBLE typemap
that was in there.  Stick to single precision, since we're doing log
domain math anyhow.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129463]
Fix SWIG memory leak in UsedRowRange

TODO: Unify Interval, IntervalS types

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129465]
This should fix jenkins failure 2/3

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129475]
Comment this EDNA stuff out till we can discuss on monday

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129504]
Add asserts in SparseMatrix

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129559]
Unify Interval types

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129604]
Appease jenkins

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 129610]
bug 24050 - remove all pip related conditionals from the master Makefile
pbcore/GenomicConsensus/kineticsTools/pbaha/pbalign/pbbarcode/pbh5tools/pbsamtools

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130184]
Bounds check in uses of Matrix::UsedRange

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130221]
Cleanly support mutation scoring at ends

Now no convergence failures on fluidigm data test case

Breaks multibase scoring, needs structural fix

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130222]
Remove broken unused code

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130223]
Split up mutation scorer tests more naturally

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130224]
Remove chatty comments

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 130225]