Release log update
Encode release log update
include localEnvironment.mk so that a local make will work in userApps build refs #9149
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Changing reference link to point to the free abstract per Code Review, refs #12135
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
fixup correct expected test result refs #9149
running any test that can be found refs #9149
Two new tracks for Locus Reference Genomic (LRG) (#11863) with custom
handlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence.  They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly.  Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info.  hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code.  (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
do not need the OK message on the testAll procedure refs #9149
adding utils directory to the test targets refs #9149
adding more tests when they can be found refs #9149
Made changes suggested by Donna in code review (redmine #12134)
Merge branch 'master' of hgwdev.sdsc.edu:/data/git/kent
document finish of genscan2 refs #7272
new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
Fixed output of extraneous blank lines refs #12159
Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
Release log update
Encode release log update