Commits for hiram

v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266

• updated to new assemblies
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 6, context: html, text, full: html, text
• updated with reference to one single html page
  • src/hg/makeDb/trackDb/mouse/mm10/chainNet.html - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra - lines changed 1, context: html, text, full: html, text
• changed name of file
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra - lines changed 162, context: html, text, full: html, text
• update reference to html file
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 1, context: html, text, full: html, text
• loading up the first 60-way result
  • src/hg/makeDb/doc/mm10.txt - lines changed 173, context: html, text, full: html, text
• initial look at the 60way alignment
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 195, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 2, context: html, text, full: html, text
• first pass an a 60-way tree diagram
  • src/hg/htdocs/images/phylo/mm10_60way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• fixup Glire group display and treeImage
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 5, context: html, text, full: html, text
• added windowMasker track
  • src/hg/makeDb/doc/hg19.txt - lines changed 65, context: html, text, full: html, text
• the multiz60waySummary table is loaded and fix a bunch of broken path names
  • src/hg/makeDb/doc/mm10.txt - lines changed 65, context: html, text, full: html, text
• adding cpgIsland and genscan tracks
  • src/hg/makeDb/doc/fr3.txt - lines changed 157, context: html, text, full: html, text
• UCSC source from CVS source tree 2005 version
  • src/utils/cpgIslandExt/README - lines changed 26, context: html, text, full: html, text
  • src/utils/cpgIslandExt/cpg.c - lines changed 174, context: html, text, full: html, text
  • src/utils/cpgIslandExt/cpg_lh.c - lines changed 200, context: html, text, full: html, text
  • src/utils/cpgIslandExt/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/cpgIslandExt/readseq.c - lines changed 191, context: html, text, full: html, text
  • src/utils/cpgIslandExt/readseq.h - lines changed 9, context: html, text, full: html, text
• fixup compile errors with modern environment
  • src/utils/cpgIslandExt/cpg_lh.c - lines changed 12, context: html, text, full: html, text
  • src/utils/cpgIslandExt/makefile - lines changed 21, context: html, text, full: html, text
  • src/utils/cpgIslandExt/readseq.c - lines changed 2, context: html, text, full: html, text
• masking and cpg operation are now kluster jobs to take care of the gigantic contig count genomes
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 156, context: html, text, full: html, text
• correctly specify paraHub for the doCpg script
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 1, context: html, text, full: html, text
• add run time calculation
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 11, context: html, text, full: html, text
• add featureBits measurement of result
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 2, context: html, text, full: html, text