tdreszer: changes by commit

branch to review (2010-05-25 to 2010-06-01) v233

• Added mdb.txt file for metadata lines
  • src/hg/utils/automation/Encode.pm 1.66 - lines changed: 1, context: html, text, full: html, text
• Added origAssembly to help distinguish hg18 to hg19 datasets.
  • src/hg/encode/encodeValidate/config/fields.ra 1.32 - lines changed: 5, context: html, text, full: html, text
• Added origAssembly metadata term. Moved metadata lines from trackDb.ra and fileDb.ra to mdb.txt
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.226 - lines changed: 21, context: html, text, full: html, text
• Make sure therre are tabls and dummy up one experiment
  • src/hg/encode/DAFs/2.0/renSample.ddf 1.2 - lines changed: 6, context: html, text, full: html, text
• Minor touch-ups
  • src/hg/encode/DAFs/2.0/renMm9Tfbs.daf 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/renSample.ddf 1.3 - lines changed: 6, context: html, text, full: html, text
• Validate atleast 1000 on fastqs. I am not 'quick' works on fastq.
  • src/hg/encode/DAFs/2.0/renMm9Tfbs.daf 1.3 - lines changed: 1, context: html, text, full: html, text
• Forgot to load Yale PolyA into the mdb earlier
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra 1.1 - lines changed: 327, context: html, text, full: html, text
• Removed an object that didn't belong
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra 1.2 - lines changed: 18, context: html, text, full: html, text
• At Venkat's urging, added useful comment to trackDb entry with subId
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.227 - lines changed: 12, context: html, text, full: html, text
• A lot of 'organism Human' lines were missing from cells
  • src/hg/encode/encodeValidate/config/cv.ra 1.241 - lines changed: 20, context: html, text, full: html, text
• Empty selection is invalid fro filterBy. Force it to 'All' when this case happens.
  • src/hg/js/hui.js 1.57 - lines changed: 4, context: html, text, full: html, text
  • src/hg/js/ui.dropdownchecklist.js 1.8 - lines changed: 19, context: html, text, full: html, text
• Extended to allow requesting a comma separated list of terms or tags
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c 1.32 - lines changed: 78, context: html, text, full: html, text
• Fixed bug wherre instance was referenced when it was null
  • src/hg/js/ui.dropdownchecklist.js 1.9 - lines changed: 2, context: html, text, full: html, text
• Fix for memory overrun when many classes are being selected via filterBySet()
  • src/hg/hgTracks/simpleTracks.c 1.142 - lines changed: 4, context: html, text, full: html, text
• Split HAIB TFBS out of trackDb.wgEnocde.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.989 - lines changed: 3639, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra 1.1 - lines changed: 3188, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra 1.1 - lines changed: 457, context: html, text, full: html, text
• Split Yale TFBS out of trackdDb.wgEnocde.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.990 - lines changed: 2377, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.ra 1.1 - lines changed: 2381, context: html, text, full: html, text
• Split Open Chromatin out of trackdDb.wgEnocde.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.991 - lines changed: 2185, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.ra 1.1 - lines changed: 2188, context: html, text, full: html, text
• Split Broad Histone out of trackdDb.wgEnocde.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.992 - lines changed: 1623, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra 1.1 - lines changed: 1626, context: html, text, full: html, text
• Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.993 - lines changed: 4785, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra 1.1 - lines changed: 2613, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra 1.1 - lines changed: 241, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra 1.1 - lines changed: 1938, context: html, text, full: html, text
• Rearranged some files due to Katrina's careful QA work
  • src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt 1.7 - lines changed: 45, context: html, text, full: html, text
• Fix for '(null)' showing up in sortColumn header
  • src/hg/lib/hui.c 1.296 - lines changed: 3, context: html, text, full: html, text
• Improvements needed for passing list of terms: support control terms mixed with Antibodies
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c 1.33 - lines changed: 35, context: html, text, full: html, text
• Oops. Lost them all.
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c 1.34 - lines changed: 3, context: html, text, full: html, text