Remove mismatch block logic

If an AlignmentBlock has no mismatches to reference, don't store bases
Update AlignmentUtils so a null reference is treated as a match

Previously would throw a NullPointerException. If the sequence cannot be retrieved then showMismatches will show nothing, showAllBases will show all bases.
Have IGV fail faster when trying to load a VCF file when it can't access the index file

Previously would need to time out a few times, now it only times out once (with a 10 second timeout)
Properly set Chromosome index in ChromSizesParser
Merge remote-tracking branch upstream/$:{upbranch}