mikep: changes by commit

branch to review (2009-03-31 to 2009-04-07) v203

• temporary fix to avoid bug with scoreMax being set to anything but 1000
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.230 - lines changed: 4, context: html, text, full: html, text
• recovered two wiggle tracks for Affy
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.231 - lines changed: 39, context: html, text, full: html, text
• making code easier to read
  • src/hg/encode/validateFiles/validateFiles.c 1.14 - lines changed: 7, context: html, text, full: html, text
• validation of fasta files (single-line of sequence, no quality)
  • src/hg/encode/validateFiles/validateFiles.c 1.15 - lines changed: 43, context: html, text, full: html, text
• fix warning on comparison with undefined; add fasta file validation by validateFiles program
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.171 - lines changed: 26, context: html, text, full: html, text
• option for quick checking of files (1000 lines of each)
  • src/hg/encode/validateFiles/validateFiles.c 1.16 - lines changed: 26, context: html, text, full: html, text
• add quick option to validateFiles
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.172 - lines changed: 7, context: html, text, full: html, text
• GIS RNAseq initial load
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.236 - lines changed: 133, context: html, text, full: html, text
• GIS RNAseq extra views
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.237 - lines changed: 1, context: html, text, full: html, text
• GIS gDNA PET alignments overflow the 4GB table
  • src/hg/lib/encode/pairedTagAlign.sql 1.3 - lines changed: 4, context: html, text, full: html, text
• first 3 projects of GIS DNA PET
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.238 - lines changed: 71, context: html, text, full: html, text
• try and avoid mysql timeout errors for stuff that takes 14,000 seconds or more
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.61 - lines changed: 8, context: html, text, full: html, text
• validate csfasta and csqual files with validateFiles prog
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.173 - lines changed: 46, context: html, text, full: html, text
• some RNA files are > 4gb
  • src/hg/lib/encode/broadPeak.sql 1.3 - lines changed: 4, context: html, text, full: html, text
• useing ssl stuff
  • src/utils/qa/weeklybld/coBranch.csh 1.5 - lines changed: 1, context: html, text, full: html, text
• adding comments about symlinks in htdocs
  • src/utils/qa/weeklybld/buildCvsReports.csh 1.19 - lines changed: 5, context: html, text, full: html, text
• v204 preview
  • src/utils/qa/weeklybld/buildEnv.csh 1.53 - lines changed: 2, context: html, text, full: html, text