Fix round-off bug in IGVFeatureRenderer.
Fix minor bug with feature overlap test.  End coordinate is not part of interval,  so feature (0,1) does not overlap feature (1,2).
Cursor updates, many bug fixes
Cusor updates
Force gene track to load synchronously in SashimiPlot

This is important to set the height correctly before constructing the window

IGV-2074
Merge branch 'master' of github.com:broadinstitute/IGV
Properly increment redirectCount
Have getChromosomeLength behave as expected

getChromosomeLength(String chrName) was just returning the chromosome for the ReferenceFrame, rather than the chromosome which was named in the input. We make this method static so it's explicitly not the current ReferenceFrame, have an instance method getChromosomeLength()
Improve searching for DownsampledInterval so it can't get caught in infinite regress

IGV-2075
IGV-2076 - A "404" should not count as a failed HEAD request for purposes of retrying with GET.  The GET will also fail with a 404.
Cursor bug fixes
Rename goby & batik jars to include version numbers
Cursor updates.  Add ability to switch signal column (score, signals, pvalue, qvalue) for encode peak tracks.
Enable downloading sequence in production
Reduce memory warning threshold from 600mb to 400mb
Fix script - batik & goby jar names
Fix typo in batik-codec file name

Make batik and goby file names properties for easier reuse
Add error dialog if alignments cannot be output

IGV-2077
Add more info to alignment writing error message

IGV-2077
Change sort order in fileHeader on SAM/BAM export

This is largely to work around the fact that many files seem to have "sorted" as an SO attribute, which causes picard to choke.

IGV-2077