Initial import of //depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/ from the state at revision #head

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138416]
MultiReadMutationScorer now works on a Read instead of a naked sequence features

This enables us to give better diagnostic log messages

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138451]
Fix build

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138454]
bug 25426 - getting rid of ThirdParty path from bioinformatics

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138468]
Handling for alpha-beta mating failures

When we can't mate alpha and beta, blacklist the read, excluding it
from scoring consideration.  Also log the occurrence of the mating
failure.

Excessive alpha-beta mating failures may be symptomatic that he
banding is too stingy, so should be monitored.

NB:

1. I am not entirely convinced this is the best solution to the
   problem at hand.  For example, mating failures in a window could
   correlate with a structural variant, if the banding is too stingy.
   A better solution might be to make a last-ditch effort to do the
   mating by doubling the allowed bandwidth.

2. The solution here and (1) are not mutually exclusive

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138527]
Version 0.8.8

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138528]
Move off of easylogging onto cpplog (https://github.com/andrew-d/cpplog)

(MIT-licensed; imported at revision 1a51f681f07ea32ab004182551085d634c3b6b2b)

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138529]
Add checksumming capability

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138799]
Add ToString() methods for MMS and classes it uses

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138800]
Get rid of C# compilation warning on new ToString()

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138801]
Add read length to the diagnostic output

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/ConsensusCore/": change = 138803]