Dead code removal and refactoring

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129031]
Clean up sorry star-import situation in quiver.py

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129032]
Preserve backwards-compatibility for "--referenceWindow"

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129033]
Improve the windowing scheme.

Now whenever possible, our window boundaries are "snapped to
grid"---formerly when there were coverage dropouts, the window
boundaries would drift out of phase with the round-numbered 500bp
windows.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129034]
Fix Eichler BAC test (windowing change)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129064]
Partial fix for frequent convergence failures at low coverage

If we are about to apply a set of mutations that would
introduce a cycle (revisiting a template we've already seen),
apply a subset of the mutations instead.  The code as I've
written it could still actually run into a cycle but it is
unlikely.

This fixes about 50% of the convergence failures I have been
observing on the 10x human dataset.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129083]
Revision to previous change: don't give up on score decrease

Score decreases seem to be recoverable, so don't give up so easily.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129089]
Add an *unsupported* "--fast" mode

(Cuts some corners to run faster)

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 129093]