Program to help revoke files mistakenly imported into ENCODE3 seems to work.
Program to rerun conversion of gtf files to bigBed seems to work.
Program to cope with files renamed in ENCODE2 is functional.
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Program to rename submitFileName of spikins is done.
Release log update
Encode release log update
avoid duplicate definition of this structure from src/hg/lib/fullBed.as
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Fix segfault in databases with no snpNNN tables.
now allow bash scripts in auto jobs and construct bigBed files for repeat masker result refs #11681
Program that depricates replaced files in ENCODE2 and tries to connect them to their replacement seems to work.  Was run at any rate.
Fixed doctor to add in dummy gene_id if not present since gffToBed requires this tag.
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
User request from Case: don't truncate alt allele column so readily.
Updating reference for dbNSFP.
Updating test file to match new understanding of NMD_transcript_variant
(should have been part of 4c4eb6b4f0) refs #12205
Adding entry for 100way. refs #11808
Merge remote-tracking branch: upstream/master