tdreszer: changes by commit

branch to review (2010-04-19 to 2010-04-27) v230

• Fixed Haib Inputs (I hope)
  • src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra 1.3 - lines changed: 5592, context: html, text, full: html, text
• Fixed Haib Inputs further by adding inputType variable allowing pairing of exp.inputType = inp.inputType
  • src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra 1.4 - lines changed: 1383, context: html, text, full: html, text
• Fixed Yale Inputs to match the HAIB model allowing pairing of exp.inputType = inp.inputType
  • src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra 1.4 - lines changed: 2951, context: html, text, full: html, text
• added inputType into the sort order
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 1.35 - lines changed: 1, context: html, text, full: html, text
• First mm9 ENCODE track added
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra 1.1 - lines changed: 61, context: html, text, full: html, text
• First mm9 ENCODE track added (included)
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.90 - lines changed: 1, context: html, text, full: html, text
• First mm9 ENCODE track added and metadata
  • src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.txt 1.1 - lines changed: 1, context: html, text, full: html, text
• Unloader can now handle bigWigs
  • src/hg/encode/encodeLoad/doEncodeUnload.pl 1.7 - lines changed: 25, context: html, text, full: html, text
• Chaged input:yes/no to setType:input/exp
  • src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra 1.5 - lines changed: 1383, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra 1.5 - lines changed: 2147, context: html, text, full: html, text
• Added setType and inputType ddf fields
  • src/hg/encode/encodeValidate/config/fields.ra 1.31 - lines changed: 10, context: html, text, full: html, text
• Back to the roundly hated, rudely arcane and vulgarly capitalized wgEncode prefix.
  • src/hg/utils/automation/Encode.pm 1.64 - lines changed: 1, context: html, text, full: html, text
• Added setType and inputType to allowable ddf terms
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.220 - lines changed: 2, context: html, text, full: html, text
• Changed the sort order once again to handle setType and inputType
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 1.36 - lines changed: 1, context: html, text, full: html, text
• Initial definition of .slantUp,.slantDn,.hintCol,.hintRow classes
  • src/lib/cheapcgi.c 1.134 - lines changed: 9, context: html, text, full: html, text
• Change ENCODCE metdata sort order. Initial check in of both Slant cols and hint cols and rows (both ifdefed out for now).
  • src/hg/lib/hui.c 1.276 - lines changed: 144, context: html, text, full: html, text
• Added defaulting of setType and inputType which are needed for ChIPseq submissions.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.221 - lines changed: 41, context: html, text, full: html, text
• Fixed a couple of bugs from the last checkin
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.222 - lines changed: 9, context: html, text, full: html, text
• Demoted 'input' to 'control'
  • src/hg/encode/encodeValidate/config/cv.ra 1.230 - lines changed: 8, context: html, text, full: html, text
• Unlink bigWig gbdb files as well.
  • src/hg/encode/encodeLoad/doEncodeUnload.pl 1.8 - lines changed: 1, context: html, text, full: html, text
• Make mdb table queries go to the right db.
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 1.37 - lines changed: 2, context: html, text, full: html, text
• Added control term for Yale because it's experiments must be defined by 4 terms
  • src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra 1.6 - lines changed: 1074, context: html, text, full: html, text
• Adding Uw Histone metadata into mdb
  • src/hg/makeDb/trackDb/human/hg18/mdbUwHist.ra 1.1 - lines changed: 11674, context: html, text, full: html, text
• Adding Uw DNase metadata into mdb
  • src/hg/makeDb/trackDb/human/hg18/mdbUwDnase.ra 1.1 - lines changed: 7608, context: html, text, full: html, text
• Adding Uw DGF metadata into mdb
  • src/hg/makeDb/trackDb/human/hg18/mdbUwDgf.ra 1.1 - lines changed: 469, context: html, text, full: html, text
• Handle '#' comments more gracefully and include quotes in non-RA style printing
  • src/hg/lib/mdb.c 1.4 - lines changed: 42, context: html, text, full: html, text
• Made RA style the default output
  • src/hg/makeDb/mdbUpdate/mdbPrint.c 1.2 - lines changed: 17, context: html, text, full: html, text
• Making -ra the default resulted in erroneous usage message
  • src/hg/makeDb/mdbUpdate/mdbPrint.c 1.3 - lines changed: 3, context: html, text, full: html, text
• Straightened out Yale K562/None/SETDB1/MNase at last
  • src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra 1.7 - lines changed: 19, context: html, text, full: html, text
• Changed labeling of Yale/K562b/MNase/SETDB1
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.956 - lines changed: 4, context: html, text, full: html, text
• Extended setType and inputType to Broad
  • src/hg/makeDb/trackDb/human/hg18/mdbBroad.ra 1.3 - lines changed: 1099, context: html, text, full: html, text
• Extended setType and inputType to UW Histones
  • src/hg/makeDb/trackDb/human/hg18/mdbUwHist.ra 1.2 - lines changed: 1123, context: html, text, full: html, text
• Extended setType and inputType to Open Chromatin
  • src/hg/makeDb/trackDb/human/hg18/mdbOpenChrom.ra 1.3 - lines changed: 866, context: html, text, full: html, text
• Fixed labVersions with leading blank that were screwing up MAGIC
  • src/hg/makeDb/trackDb/human/hg18/mdbOpenChrom.ra 1.4 - lines changed: 1, context: html, text, full: html, text
• Show plurals properly
  • src/hg/makeDb/mdbUpdate/mdbPrint.c 1.4 - lines changed: 3, context: html, text, full: html, text
• Fixed some minor wording and replaced an unknown with Percent Tags in Hotspots ~40pct
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html 1.6 - lines changed: 8, context: html, text, full: html, text
• Removed not ready for prime time 'slant titles', 'hint cols and rows' and 'scrolling table'. Added tooltip for each matrix cell.
  • src/hg/lib/hui.c 1.279 - lines changed: 166, context: html, text, full: html, text
• Added tooltip for each matrix cell, so moved 3rd state matrix CB hint to CB only.
  • src/hg/js/hui.js 1.51 - lines changed: 8, context: html, text, full: html, text