Formatting changes only
Add support for BCF2 files

Still not extensively tested, shouldn't be released yet
Add FeatureCodecDecoder, wrapper for FeatureCodecs for reading from command line.
Not tested. May be used for BCF2
Prevent accumulation of SpliceJunctions

We store the SpliceJunctionHelper.LoadOptions in the AlignmentDataManager, and give each AlignmentInterval its own SpliceJunctionHelper instance. The SpliceJunctionHelpers store the accumulated results, so we want new ones each time data is loaded.
Preload data for SashimiPlot

Accomplish this by using MemoryAlignmentDataManager, which just takes initial AlignmentIntervals and recalls them as necessary. Current implementation is not done yet
Merge branch 'SpliceJunctionCounting' into SashimiNoDataManager

Conflicts:
	src/org/broad/igv/ui/SashimiPlot.java
Finish decoupling of SashimiPlot from AlignmentDataManager

We now make copies of AlignmentDataInterval and containing SpliceJunctionHelper data fields
Have AlignmentTrack reload/clearCaches when preferences change.

We want AlignmentTracks to reload but not SpliceJunctionFinderTracks. Believe that has been accomplished in this commit.
Add test for making sure alignment tracks are updated when preferences changed
Add ability to override preference via batch command

Syntax:

preference <key> <value>

Preference does not persist
Merge in branch SashimiNoDataManager

Preload data for SashimiPlot.  Accomplish this by using MemoryAlignmentDataManager, which just takes initial AlignmentIntervals and recalls them as necessary.

Prevent accumulation of SpliceJunctions. We store the SpliceJunctionHelper.LoadOptions in the AlignmentDataManager, and give each AlignmentInterval its own SpliceJunctionHelper instance.

Add test for making sure alignment tracks are updated when preferences changed
Formatting changes, typo fixes, deletion of some commented code
Improve CommandExecutorTest.testMaxPanelHeight, so that it's better named and limits set better

Was consistently failing on our test runner
Add test for "preference" batch command