Move the actual body of variantCaller.py into GenomicConsensus/main.py

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120694]
Remove unneeded version checking code

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120695]
Grand version unification---version maintained in one place now.

(Version bumped to 0.6.1)

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120696]
General housekeeping

1) Move executables into bin/ directory;
3) Make ConsensusCore an install dependency and remove some version checking logic

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120699]
Move remaining vestiges of training-specific code into separate quiver training package

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120815]
Need to de-numpy-ify window bounds

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 120951]
Document the list of QV tracks required for best results.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121425]
Add interval logic for dealing with amplicons workflows

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121730]
Some refactoring

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121731]
More shuffling

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121732]
Remove extraneous Window class

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121733]
Sort of working.  Coverage, quality not passed through yet.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121734]
Even more sort-of-working.  Runs through fluidigm amplicons, giving a consensus FASTA

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121735]
Make parallelism overrideable for lambda test job

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121736]
Plumb coverage level through to variants

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121737]
Make lambda test more precise

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121738]
Fix underflow problem in kSpannedIntervals

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121739]
Plumb options into QuiverConfig

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121740]
Add shebangs for more reliable execution.

For some reason bash on OS X hits an error sometimes when shell
scripts lack a shebang.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121741]
Add back the filter for stumpy reads.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 121742]