tdreszer: changes by file

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

• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.37 lines changed: 2, context: html, text, full: html, text
    Make mdb table queries go to the right db.
  • 1.36 lines changed: 1, context: html, text, full: html, text
    Changed the sort order once again to handle setType and inputType
  • 1.35 lines changed: 1, context: html, text, full: html, text
    added inputType into the sort order
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Unlink bigWig gbdb files as well.
  • 1.7 lines changed: 25, context: html, text, full: html, text
    Unloader can now handle bigWigs
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.222 lines changed: 9, context: html, text, full: html, text
    Fixed a couple of bugs from the last checkin
  • 1.221 lines changed: 41, context: html, text, full: html, text
    Added defaulting of setType and inputType which are needed for ChIPseq submissions.
  • 1.220 lines changed: 2, context: html, text, full: html, text
    Added setType and inputType to allowable ddf terms
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.230 lines changed: 8, context: html, text, full: html, text
    Demoted 'input' to 'control'
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.31 lines changed: 10, context: html, text, full: html, text
    Added setType and inputType ddf fields
• src/hg/js/hui.js
  • 1.51 lines changed: 8, context: html, text, full: html, text
    Added tooltip for each matrix cell, so moved 3rd state matrix CB hint to CB only.
• src/hg/lib/hui.c
  • 1.279 lines changed: 166, 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.
  • 1.276 lines changed: 144, 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/mdb.c
  • 1.4 lines changed: 42, context: html, text, full: html, text
    Handle '#' comments more gracefully and include quotes in non-RA style printing
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Show plurals properly
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Making -ra the default resulted in erroneous usage message
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Made RA style the default output
• src/hg/makeDb/trackDb/human/hg18/mdbBroad.ra
  • 1.3 lines changed: 1099, context: html, text, full: html, text
    Extended setType and inputType to Broad
• src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra
  • 1.5 lines changed: 1383, context: html, text, full: html, text
    Chaged input:yes/no to setType:input/exp
  • 1.4 lines changed: 1383, context: html, text, full: html, text
    Fixed Haib Inputs further by adding inputType variable allowing pairing of exp.inputType = inp.inputType
  • 1.3 lines changed: 5592, context: html, text, full: html, text
    Fixed Haib Inputs (I hope)
• src/hg/makeDb/trackDb/human/hg18/mdbOpenChrom.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed labVersions with leading blank that were screwing up MAGIC
  • 1.3 lines changed: 866, context: html, text, full: html, text
    Extended setType and inputType to Open Chromatin
• src/hg/makeDb/trackDb/human/hg18/mdbUwDgf.ra
  • 1.1 lines changed: 469, context: html, text, full: html, text
    Adding Uw DGF metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbUwDnase.ra
  • 1.1 lines changed: 7608, context: html, text, full: html, text
    Adding Uw DNase metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbUwHist.ra
  • 1.2 lines changed: 1123, context: html, text, full: html, text
    Extended setType and inputType to UW Histones
  • 1.1 lines changed: 11674, context: html, text, full: html, text
    Adding Uw Histone metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra
  • 1.7 lines changed: 19, context: html, text, full: html, text
    Straightened out Yale K562/None/SETDB1/MNase at last
  • 1.6 lines changed: 1074, context: html, text, full: html, text
    Added control term for Yale because it's experiments must be defined by 4 terms
  • 1.5 lines changed: 2147, context: html, text, full: html, text
    Chaged input:yes/no to setType:input/exp
  • 1.4 lines changed: 2951, 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/trackDb.wgEncode.ra
  • 1.956 lines changed: 4, context: html, text, full: html, text
    Changed labeling of Yale/K562b/MNase/SETDB1
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.6 lines changed: 8, context: html, text, full: html, text
    Fixed some minor wording and replaced an unknown with Percent Tags in Hotspots ~40pct
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.txt
  • 1.1 lines changed: 1, context: html, text, full: html, text
    First mm9 ENCODE track added and metadata
• 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
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.90 lines changed: 1, context: html, text, full: html, text
    First mm9 ENCODE track added (included)
• src/hg/utils/automation/Encode.pm
  • 1.64 lines changed: 1, context: html, text, full: html, text
    Back to the roundly hated, rudely arcane and vulgarly capitalized wgEncode prefix.
• src/lib/cheapcgi.c
  • 1.134 lines changed: 9, context: html, text, full: html, text
    Initial definition of .slantUp,.slantDn,.hintCol,.hintRow classes