braney: changes by commit

branch to review (2009-08-04 to 2009-08-10) v212

• properly deal with the N word
  • src/hg/encode/validateFiles/validateFiles.c 1.22 - lines changed: 3, context: html, text, full: html, text
• fixed publication date
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html 1.9 - lines changed: 2, context: html, text, full: html, text
• changed red to orange for methyl calls
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html 1.10 - lines changed: 1, context: html, text, full: html, text
• changed first person to passive voice. English teachers everywhere feel a tremour in the force.
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html 1.11 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html 1.10 - lines changed: 26, context: html, text, full: html, text
• make Human Proteins track. Needs re-doing to deal with chrUn correctly
  • src/hg/makeDb/doc/tetNig2.txt 1.4 - lines changed: 166, context: html, text, full: html, text
• added some HudsonAlphaCNV stuff... not quite done but need to test something
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.477 - lines changed: 36, context: html, text, full: html, text
• have everything right (methinks) except dates and dataType for HA CNV tracks
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.478 - lines changed: 12, context: html, text, full: html, text
• changes from Kate
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html 1.2 - lines changed: 35, context: html, text, full: html, text
• add options to ignore N's in mismatching and to deal more efficiently with sorted files (assuming there are a lot of records)
  • src/hg/encode/validateFiles/validateFiles.c 1.23 - lines changed: 47, context: html, text, full: html, text
• fix up dates for HudsonalphaCnv track. Also change dataType to CNV
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.479 - lines changed: 6, context: html, text, full: html, text
• oops... fix a typo in dataSubmitted and dataRestricted
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.480 - lines changed: 6, context: html, text, full: html, text
• another typo.... darned Mondays
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.481 - lines changed: 6, context: html, text, full: html, text
• more mismatch tweaks
  • src/hg/encode/validateFiles/validateFiles.c 1.24 - lines changed: 14, context: html, text, full: html, text
• add some tests
  • src/hg/encode/validateFiles/makefile 1.2 - lines changed: 8, context: html, text, full: html, text
• change printf to verbose
  • src/hg/encode/validateFiles/validateFiles.c 1.25 - lines changed: 1, context: html, text, full: html, text