File Changes for braney

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

• src/hg/hgGene/hgGene.c
  • lines changed 5, context: html, text, full: html, text
    get GENCODE ID from knownGene table if Gencode models #14639
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    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/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    take out spurious printf #15399
    
  • lines changed 10, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/hgc/hgc.c
  • lines changed 90, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/inc/ncbiRefLink.h
  • lines changed 67, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.as
  • lines changed 9, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.c
  • lines changed 150, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.sql
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/danRer10/ncbiGene.txt
  • lines changed 14, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/hg38/ncbiGene.txt
  • lines changed 16, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh
  • lines changed 16, context: html, text, full: html, text
    loaded the blastTabs on the other species for mm10 ucsc genes refs
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 19, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/lib/bbiWrite.c
  • lines changed 6, 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/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, 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/utils/bedToBigBed/tests/expected/notSorted.err
  • lines changed 1, 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/utils/bedToBigBed/tests/input/notSorted.bed
  • lines changed 3, 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/utils/bedToBigBed/tests/input/notSorted.chrom.sizes
  • lines changed 3, 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/utils/bedToBigBed/tests/makefile
  • lines changed 7, 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
    
  • lines changed 2, context: html, text, full: html, text
    make sure tests are run out of ${BINDIR} in bedToBigBed #15400