hiram: changes by file

review to branch (2009-05-05 to 2009-05-12) v206

• src/hg/hgTracks/hgTracks.c
  • 1.1564 lines changed: 8, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/hgc/hgc.c
  • 1.1536 lines changed: 8, context: html, text, full: html, text
    Allow click through to NCBI entrez search for Contig names on ctgPos tracks
• src/hg/hgc/hgc.h
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Allow click through to NCBI entrez search for Contig names on ctgPos tracks
• src/hg/inc/ensFace.h
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Properly lift to Ensembl haplotype coordinates for Blue bar click through
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/lib/ensFace.c
  • 1.11 lines changed: 28, context: html, text, full: html, text
    Properly lift to Ensembl haplotype coordinates for Blue bar click through
  • 1.10 lines changed: 28, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/makeDb/doc/hg18.txt
  • 1.360 lines changed: 39, context: html, text, full: html, text
    Add UCSC to Ensembl chrom name translation and haplotype lift tables for Blue Bar Ensembl click through
• src/hg/makeDb/doc/hg19.txt
  • 1.11 lines changed: 74, context: html, text, full: html, text
    Running Mouse Mm9 and Dog CanFam2 blastz
  • 1.10 lines changed: 230, context: html, text, full: html, text
    Document ctgPos table build, done with STS Markers, BAC Ends, and now working on FISH Clones
  • 1.9 lines changed: 1065, context: html, text, full: html, text
    STS Markers track done
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • 1.1 lines changed: 28, context: html, text, full: html, text
    Assembly description for hg19 is different
• src/hg/pslFilterPrimers/pslFilterPrimers.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    The line files need to be opened with zTerm and the split is on tab
• src/hg/stsMarkers/epcrToPsl
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Proper size on target chromosome
  • 1.4 lines changed: 103, context: html, text, full: html, text
    This functioned OK on hg19
• src/hg/stsMarkers/fixPrimersQueryGaps.pl
  • 1.1 lines changed: 62, context: html, text, full: html, text
    Initial source rescued from /cluster/bin/scripts
• src/hg/stsMarkers/liftFromSpec.pl
  • 1.1 lines changed: 60, context: html, text, full: html, text
    Initial source, worked with the ePCR results for hg19
• src/hg/utils/automation/HgAutomate.pm
  • 1.26 lines changed: 2, context: html, text, full: html, text
    Do not check swarm for workhorse idle machines, and add orfeomeGenes to genbank list of tables for makePushQSql.pl
  • 1.25 lines changed: 11, context: html, text, full: html, text
    Adding encodek and disable sanvol1
• src/hg/utils/automation/makePushQSql.pl
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Do not check swarm for workhorse idle machines, and add orfeomeGenes to genbank list of tables for makePushQSql.pl