adding documentation for db.neverLocal
Fixing link to information on PSL format, refs #11307
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Release log update
Encode release log update
Adding a frameshift SNP to pgSNP format example per request of Bob
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
cleaning up the commonNames.sh name listing refs #10272
add an option to pslCDnaFilter to treat matches in repeats the same as
matches that aren't.
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent

Conflicts:
	src/hg/pslCDnaFilter/usage.txt
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
added the panTro2 to panTro4 over chains as a separate track as requested by Adam/David, they want to compare the assemblies
Oops, forgot to correct test file after fixing intron off-by-one in 099102d.  Too bad I didn't notice it in the test file to begin with...
Fixing bug reported by user in MLQ #11775: VCF that is sorted by
start position might not be sorted by UCSC-start position, specifically
when at the same VCF start position there is an indel followed by a
substitution.  VCF start coords for indels are actually one base to
the left of the actual inserted or deleted bases.  So we internally
adjust those to be one base to the right, which can make them out-of-order
when followed by a non-indel variant.

To restore sorting order, indels are now saved aside in a queue until
we know it's safe to let them out because either
a) we got a substitution whose start is greater than the indel start
b) we got an indel whose start is greater than the queued indel start
c) we hit EOF.
When condition (a) or (b) is met, we have to do something with the
new record while the indel queue drains, so it's saved aside in the
nextPosQ (which never holds more than one row).  If it's (b), then
when indelQ is empty, we move the nextPosQ indel to indelQ because
we can't let that indel out until one of the 3 conditions is met.

fixes #11787
Made some changes to conditions.html per ref #8699. Also removed some duplicate info from indexInfo.html, but not all of it. This will improve once we revamp the static pages, but I think it's OK for now.
Release log update
Encode release log update
Merge remote-tracking branch: upstream/master