Have SamAlignment set mate start as 0-based
Downsample read pairs together

Not quite done yet. Don't calculate downsampled intervals at all

Known weakness (may never be fixed): We operate by read name mostly, if a primary alignment is removed it will also remove all secondary alignments. We preserve the primary requirement that if a read is kept, it's mate is also kept

IGV-2065
Calculate downsampledintervals (not efficiently)

IGV-2065
Refactor/cleanup

IGV-2065
Look for DownsampledIntervals by binary search

IGV-2065
Finish AlignmentTile on cancel

clear indexingmap used for downsampling on finish

IGV-2065
Additional downsampling unit tests
Test that we don't downsample when limit set high, and also do another keep-pair test with a different file

IGV-2065
Add ability to export alignments using picard to UI

Still in development mode only

IGV-2070
Merge remote-tracking branch: upstream/master