hiram: changes by commit

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

• The line files need to be opened with zTerm and the split is on tab
  • src/hg/pslFilterPrimers/pslFilterPrimers.c 1.5 - lines changed: 3, context: html, text, full: html, text
• Initial source, worked with the ePCR results for hg19
  • src/hg/stsMarkers/liftFromSpec.pl 1.1 - lines changed: 60, context: html, text, full: html, text
• This functioned OK on hg19
  • src/hg/stsMarkers/epcrToPsl 1.4 - lines changed: 103, context: html, text, full: html, text
• Initial source rescued from /cluster/bin/scripts
  • src/hg/stsMarkers/fixPrimersQueryGaps.pl 1.1 - lines changed: 62, context: html, text, full: html, text
• Proper size on target chromosome
  • src/hg/stsMarkers/epcrToPsl 1.5 - lines changed: 6, context: html, text, full: html, text
• STS Markers track done
  • src/hg/makeDb/doc/hg19.txt 1.9 - lines changed: 1065, context: html, text, full: html, text
• Allow click through to NCBI entrez search for Contig names on ctgPos tracks
  • src/hg/hgc/hgc.c 1.1536 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.46 - lines changed: 2, context: html, text, full: html, text
• Allow hg19 to click through to pre.ensembl.org with chr name translation
  • src/hg/hgTracks/hgTracks.c 1.1564 - lines changed: 8, context: html, text, full: html, text
  • src/hg/inc/ensFace.h 1.7 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/ensFace.c 1.10 - lines changed: 28, context: html, text, full: html, text
• Properly lift to Ensembl haplotype coordinates for Blue bar click through
  • src/hg/inc/ensFace.h 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/ensFace.c 1.11 - lines changed: 28, 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/hg18.txt 1.360 - lines changed: 39, context: html, text, full: html, text
• Assembly description for hg19 is different
  • src/hg/makeDb/trackDb/human/hg19/ctgPos.html 1.1 - lines changed: 28, context: html, text, full: html, text
• Document ctgPos table build, done with STS Markers, BAC Ends, and now working on FISH Clones
  • src/hg/makeDb/doc/hg19.txt 1.10 - lines changed: 230, context: html, text, full: html, text
• Adding encodek and disable sanvol1
  • src/hg/utils/automation/HgAutomate.pm 1.25 - lines changed: 11, 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
  • src/hg/utils/automation/HgAutomate.pm 1.26 - lines changed: 2, context: html, text, full: html, text
  • src/hg/utils/automation/makePushQSql.pl 1.24 - lines changed: 1, context: html, text, full: html, text
• Running Mouse Mm9 and Dog CanFam2 blastz
  • src/hg/makeDb/doc/hg19.txt 1.11 - lines changed: 74, context: html, text, full: html, text