Add hack in loading coverage track to deal with su2c
Modify HttpUtils.parseQueryString so it splits only on 1st equal sign

This was causing a problem if there were parameters with equal signs in them
Remove warning re fasta index modified date
IGV-2004  gtf parsing issues
Add back in getting/setting of mate sequence, so unmapped mates are shown in tooltip

IGV-2002
Merge remote-tracking branch: upstream/master