ConsensusCore Mutation API changes

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122965]
Fix tests

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122974]
Fix incorrect handling of dinucleotide repeats, add test

Was previously not keeping track of the running length diff.  Also the
pattern match was broken.  Basically it was only working in scenarios
where a single dinucleotide repeat block needed correction in a
window.  This is the most common case, but I am sure we were still
seeing errors because of this.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 122988]
Require ConsensusCore 0.6.1

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123009]
"Fix" the plurality variant scores, using a kludgy binomial tail probability

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123200]
Fix test failures resulting in slight changes to plurality.

Also now truncate plurality confidences at 40.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123237]
Add new QuiverParameters.ini with P4-C2 training to the
GenomicConsensus distribution, for GitHub users

[Bug 23151]
prop:S2.0

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123246]
Fix the logic for determining whether all the QVs are loaded

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123378]
Move allQVsLoaded

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123419]
Fix typo

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123420]
Add QuiverConsensus class

QuiverConsensus class adds the ConsensusCore mms object. Enables
post-hoc diploid/sample mixture investigation

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123421]
Capture readName in MappedRead

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123422]
Remove the "domain" function

good riddance to an odious piece of code

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123423]
Whitespace

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123424]
Resurrect --dumpEvidence

Now the h5 file gets the Scores matrix dataset and also RowNames,
ColumnNames companion datasets.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123425]
Move filterAlnsForQuiver into utils, for reuse by DumbView

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123463]