Commits for hiram

v239_base to v240_preview (2010-08-31 to 2010-09-07) v240

• comment about deprecated type wig to type bigWig types
  • src/hg/makeDb/trackDb/README - lines changed 3, context: html, text, full: html, text
• loading the hg19Patch2 sequences as psl tracks
  • src/hg/makeDb/trackDb/human/altSeqComposite.html - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19Patch2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• make the altSeqComposite be a view in the middle composite
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 23, context: html, text, full: html, text
• added blat server and lastz to hg19
  • src/hg/makeDb/doc/hg19Patch2.txt - lines changed 103, context: html, text, full: html, text
• attempting to baseColor altSeq
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding PSL configuration for multi-views
  • src/hg/inc/hui.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 57, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text
• adding base coloring options to altSequence
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 14, context: html, text, full: html, text
• need to remove destination before moving to destination
  • src/hg/encode/mkEncodeFrameset/makefile - lines changed 2, context: html, text, full: html, text
• consolidate the baseColor drop down box code to a single instance
  • src/hg/lib/hui.c - lines changed 58, context: html, text, full: html, text
• first pass at a handler for the altSequence hg19Patch2 PSL track
  • src/hg/hgc/hgc.c - lines changed 52, context: html, text, full: html, text
• update hChromSize call to use database
  • src/hg/hgTracks/oneTrack.c - lines changed 1, context: html, text, full: html, text
• adding chain net tracks to the altSeqComposite
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 66, context: html, text, full: html, text
• no need for the URL to the otherDb
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
• disable the debug printouts
  • src/hg/hgc/hgc.c - lines changed 6, context: html, text, full: html, text
• removing experiments testChainHg19Patch2 and patch2Psl
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 22, context: html, text, full: html, text
• add the business to construct the altSequence chains and nets and PSL track
  • src/hg/makeDb/doc/hg19Patch2.txt - lines changed 140, context: html, text, full: html, text
• changing track name
  • src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/hg19ContigDiff.html - lines changed 31, context: html, text, full: html, text
• changing track name
  • src/hg/makeDb/trackDb/human/hg19/hg18ContigDiff.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19ContigDiff.html - lines changed 31, context: html, text, full: html, text
• hg19ContigDiff changing track name and becomes itemRgb
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 6, context: html, text, full: html, text
• hg18ContigDiff changing track name and becomes itemRgb
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 6, context: html, text, full: html, text
• finishing off the hg18 and hg19 ContigDiff tracks
  • src/hg/makeDb/doc/hg18.txt - lines changed 221, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
• add table of color and score to indicate category of change
  • src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19ContigDiff.html - lines changed 16, context: html, text, full: html, text
• do not need ccds genes for hg19Patch2
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• Added ce9 C. elegans WS120
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text