Fix jenkins tests

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124832]
Disable diploid tests for the moment

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 124833]
consensus: bug 23171: fixing the primary build

The assumption that the primary build did not call the csharp-pacbio
target was incorrect, so the primary build was breaking trying to
point to the new multi-os version of swig for the smrtanalysis build.

We now detect if we are running a smrtanalysis build (by the existance
of the software/smrtanalysis directory) and set the location of
the swig binary and libs accordingly.

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125017]
consensus: bug 23171: fixing whitespace

A copy/paste inserted whitespace at the end of some make variables
causing the build to fail.  Removing all whitespace at the 
end of variable assignments.

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125022]
Update mutation test order for diploid

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125869]
Remove assertion that Mutation::NewBases is in [ACGT]*

Diploid quiver is using IUPAC codes behind the scenes

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125870]
Clean up formatting

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125941]
Add AlignAffineIupac for diploid support

BACKWARDS-INCOMPATIBLE CHANGE: some functions have been renamed

Bumping version to 0.6.2

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125942]
Refactor AlignAffine

This also removes the function pointer---fixing jenkins---and fixes a
memory leak

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/common/ConsensusCore/": change = 125955]