Commits for hiram

v328_base to v329_preview (2016-02-08 to 2016-02-15) v329

• refGene in new composite needs to be release alpha refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text
• fixup ncbiRef gene tracks to have the correct labels on the track longLabels refs #refs #13673
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text
• print out position links for ncbiRefSeq item refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 54, context: html, text, full: html, text
• ok to use showGenePos for ncbiRef tracks refs #refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 18, context: html, text, full: html, text
• ok to use showGenePos for ncbiRef tracks refs #refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 4, context: html, text, full: html, text
• adding UI for refSeqComposite refs #13673
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 17, context: html, text, full: html, text
• adding UI for refSeqComposite refs #13673
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 25, context: html, text, full: html, text
• cleaning up the ncbiRefSeq composite refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 108, context: html, text, full: html, text
• need to make hte protein click links for the ncbiRefSeq resf #13673
  
  • src/hg/hgc/hgc.c - lines changed 19, context: html, text, full: html, text
• adding some searches for refSeqComposite refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 16, context: html, text, full: html, text
• fixup correct From: and Cc: email addresses refs #16802
  
  • src/utils/qa/weeklybld/sendLogEmail.pl - lines changed 2, context: html, text, full: html, text
• Added rheMac8 - Rhesus refs #16744
  
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 2, context: html, text, full: html, text
• adding rheMac8 rules refs #16744
  
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• correct spelling code review refs #16795
  
  • src/hg/lib/ncbiRefSeqLink.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.sql - lines changed 2, context: html, text, full: html, text
• code review clean up refs #16795
  
  • src/hg/hgc/hgc.c - lines changed 14, context: html, text, full: html, text
• code review fixups refs #16795
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 3, context: html, text, full: html, text
• fixup search rules for refSeqComposite refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 13, context: html, text, full: html, text
• need release alpha in all stanzas to quite release beta make refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 7, context: html, text, full: html, text
• adding rheMac8 chain net definitions refs #16744
  
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRheMac3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRheMac8.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac8.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 212, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 151, context: html, text, full: html, text
• adding rheMac8 chain net definitions refs #16744
  
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 1, context: html, text, full: html, text
• protect omim button on refSeq UI refs #13673
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 14, context: html, text, full: html, text
• adding chain net overrides
  
  • src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.chainNet.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra - lines changed 8, context: html, text, full: html, text
• rheMac8 in the pushQ refs #16744
  
  • src/hg/makeDb/doc/rheMac8/initialBuild.txt - lines changed 357, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac8/lastzRuns.txt - lines changed 51, context: html, text, full: html, text
• add pep table for ncbiRefSeq refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text
• pepTable belongs on the PSL track refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 3, context: html, text, full: html, text
• manage the case of existing refGene track in new composite without the new tables refs #13673
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 7, context: html, text, full: html, text
• lift overs to rheMac8 refs #16744
  
  • src/hg/makeDb/doc/rheMac2.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 19, context: html, text, full: html, text
• lastz chain net to rheMac8 refs #16744
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 56, context: html, text, full: html, text
• manage existing refGene tracks without the refSeqComposite refs #13673
  
  • src/hg/makeDb/trackDb/baboon/papAnu2/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papHam1/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro3/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/trackDb.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg16/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm7/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm8/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe2/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn3/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/defaultPriority.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/defaultPriority.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra - lines changed 13, context: html, text, full: html, text
• add references to papers describing chrom naming schemes refs #16744
  
  • src/hg/makeDb/trackDb/rhesus/rheMac8/description.html - lines changed 50, context: html, text, full: html, text
• v329 preview1 refs #16669
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text