Add --simpleChunking option to disable fancy chunking

       [Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123508]
Fix buggy kCoveredIntervals implementation

There were at least two bugs in this short function---
  - min could be called on an empty list
  - 0 and None both evaluate to False

and a third potential bug could have arisen if it was ever
used without winStart, winEnd set.

Fix is to make winStart, winEnd non-optional

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123652]
Add 'tags' make target

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123661]
Shorten some long, redundant function names

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123662]
Fold interval length filter into kSpannedIntervals

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123669]
Clean up quiver.model API

Provide a higher-level API for loading parameter sets

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 123670]