Make AllQVsMergingByChannelModel available

[Bug 22969]
prop:S2.0

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122018]
Remove XL-C2 Quiver training, which seemed to cause issues on GC-rich genomes

[Tracking bug 22690]
prop:S2.0

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122341]
WIP on fancy chunking

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122483]
More refactoring

* Some option names have changed:
    - mapQvThreshold             -> minMapQV     (will require change in smrtpipe module!)
    - variantCoverageThreshold   -> minCoverage
    - variantConfidenceThreshold -> minConfidence
* Make plurality go through the same configure() dance, getting it to
  stop calling into options.  Now very testable.
* Plurality defaults changed:
    - default max coverage now 100 (more than adequate for haploid calling);
    - min coverage now 5 and sites calling below this min are no-called
    - min confidence default now 40

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122484]
QuiverConfig() should have a usable ConsensusCore parameter set.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122485]
Fix failing jenkins test

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122537]
Enable fancy chunking by default, and revise Ecoli test

Fancy chunking enables correct behavior in amplicons workflows.

The revised Ecoli test uses a newer dataset with a larger insert size.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122657]
Fix Eichler BAC test

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122674]
Fix remaining issues in Eichler BAC test

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122710]
Add --quiet option to disable warnings

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122715]
Use the right fastadiff

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122716]
Add test for new adaptive windowing/amplicons support

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122717]