Commits for braney

v317_preview to v317_preview2 (2015-05-18 to 2015-05-25) v317

• if hideTracks is on the command line, set the visibilities of the other
  tracks based on URL even if they are the default visibilities in
  trackDb refs #15299
  
  • src/hg/hgTracks/hgTracks.c - lines changed 4, context: html, text, full: html, text
• loaded the blastTabs on the other species for mm10 ucsc genes refs
  
  • src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh - lines changed 16, context: html, text, full: html, text
• take out spurious printf #15399
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
• add NCBI metadata to NCBI RefSeq track ( refs# 13673)
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 90, context: html, text, full: html, text
  • src/hg/inc/ncbiRefLink.h - lines changed 67, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/ncbiRefLink.as - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/ncbiRefLink.c - lines changed 150, context: html, text, full: html, text
  • src/hg/lib/ncbiRefLink.sql - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer10/ncbiGene.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/ncbiGene.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/rn6.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 19, context: html, text, full: html, text
• make sure that chroms are sorted in a case-sensitive manner in
  bedToBigBed because otherwise the indexes don't work #15400
  
  • src/lib/bbiWrite.c - lines changed 6, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/expected/notSorted.err - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/notSorted.bed - lines changed 3, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/notSorted.chrom.sizes - lines changed 3, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/makefile - lines changed 7, context: html, text, full: html, text
• get GENCODE ID from knownGene table if Gencode models #14639
  
  • src/hg/hgGene/hgGene.c - lines changed 5, context: html, text, full: html, text
• make sure tests are run out of ${BINDIR} in bedToBigBed #15400
  
  • src/utils/bedToBigBed/tests/makefile - lines changed 2, context: html, text, full: html, text