Make inactive reads with NULL when accessed via Read(int)
[tracking bug 24908]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138874]
Hide this state-checking behind NDEBUG
[tracking bug 24908]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138980]
Additional state checks in MultiReadMutationScorer::CheckInvariants
[tracking bug 24908]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138981]
Fix and simplifications resolving [bug 25619]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 139196]
Fix MappedConsensus slowness.  Quiver and MC are now about the same speed on a cmp.h5.

The slowness was due to the huge bands used by LAA and
CCS (ScoreDiff=18) vs Quiver (ScoreDiff=6).  I would really like all
of our code to be using the same banding but that is risky for 2.3.
We will revisit post 2.3.

This required adjusting ConsensusCore API and I brought method names
in the class up to Pascal-case standard (style guide) while in there,
so I will have to fix GenomicConsensus in a subsequent checkin.

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 139279]
Attempt to fix AlphaBetaMismatch for Edna
[tracking bug 25680]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 140350]
Bug 23016

Fixed relative path for swigwin in windows build.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 140960]
Allow cross platform compilation for consensuscore (Bug 25700)

The following changes were made to allow compilation on windows: 
* Avoid naming conflict in DELETE definition from windowsnt.h
* Avoid naming conflict in max function in windows.h
* Upgrade to boost 1.55
* Comment out unused function that throws errors
* Change path to new swig location.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 140985]
Missed file in windows compatability commit (Bug 25700) 

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 140986]
Fix a goof

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 140987]