File Changes for hiram

v261_preview to v261_preview2 (2011-12-13 to 2011-12-20) v261

• src/hg/hgTracks/netTrack.c
  • lines changed 3, context: html, text, full: html, text
    fixup color problem for chain net caePb3 tracks on ce10
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fixup color problem for chain net caePb3 tracks on ce10
• src/hg/htdocs/images/phylo/ce10_7way.png
  • lines changed 0, context: html, text, full: html, text
    7-way diagram for ce10 multiz
• src/hg/makeDb/doc/ce10.txt
  • lines changed 833, context: html, text, full: html, text
    running a 7-way alignment to eliminate the two broken genomes
  • lines changed 12, context: html, text, full: html, text
    entering pushQ
  • lines changed 53, context: html, text, full: html, text
    adding frames creation to the 7-way
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1030, context: html, text, full: html, text
    version 65 update done
  • lines changed 13, context: html, text, full: html, text
    version 65 update dateReference updated
  • lines changed 16, context: html, text, full: html, text
    indicate which assemblies are updated in v65
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding gorilla to the xrg definition
  • lines changed 17, context: html, text, full: html, text
    adding ce10 and related nematodes
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 103, context: html, text, full: html, text
    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 107, context: html, text, full: html, text
    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
• src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
  • lines changed 306, context: html, text, full: html, text
    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
  • lines changed 3, context: html, text, full: html, text
    fixup errors in the type chain specifications
  • lines changed 51, context: html, text, full: html, text
    adding entry for ce10 chain net
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 182, context: html, text, full: html, text
    adding v65 definitions
  • lines changed 3, context: html, text, full: html, text
    there is a new panTro4 for v65
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 4, context: html, text, full: html, text
    eliminate wget warning: timestamping does nothing in combination with -O. See the manual
  • lines changed 1, context: html, text, full: html, text
    update to Ensembl peptide fasta header syntax parsing
• src/hg/utils/genomeQuality/genomeQuality.pl
  • lines changed 300, context: html, text, full: html, text
    initial source