Resolve coordinate drift in heterozygous variants reported

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126023]
Make variantCaller.py default to quiver, not plurality.

This shouldn't affect anything in SMRTportal as we are always explicit
in the algorithm there.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126029]
Retune plurality for diploid.

The EPS was too high for detecting heterozygous variants with any reliability.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126055]
Version 0.7.0 for 2.1 release

Update CHANGELOG as well

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126057]
Fix for bug 23238

No-call windows where MLE search fails to converge.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126063]
Fix jenkins tests for Eichler BAC, M.Ruber

For future reference: these tests contain regions where convergence to MLE fails.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126104]
Diploid plurality: explicitly filter out mixed-length heterozygous variant calls

(These are almost always false positives in my experience)

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126134]
Add cram test for diploid plurality.

(Quiver test to follow)

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126136]
Set up a properly calibrated unknown.NoQVsModel, overwriting old one.

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126148]
Diploid quiver: default to unknown.NoQVsModel under --diploid

This is a stopgap until I can recalibrate all the models to work with
diploid (this should in theory just involve a rescaling).

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126149]
Add quiver diploid test

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126150]
Explicitly request unknown.NoQVsModel here

The cmp.h5 *has* the QV tracks, but they are fake data

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126151]
Add note about HDF5 leak fix to changelog

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126152]
Restore the cram test for tiny coverage windows

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 126213]