File Changes for vsmalladi

v264_preview to v264_preview2 (2012-02-21 to 2012-02-28) v264

• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release2.notes
  • lines changed 8, context: html, text, full: html, text
    Updated release notes. Redmine #4145.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCshlLongRnaSeq.release1.notes
  • lines changed 610, context: html, text, full: html, text
    Added release 1 notes for track. Redmine #5986.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 67, context: html, text, full: html, text
    Added 4 cell lines for mouse.
  • lines changed 21, context: html, text, full: html, text
    Fix errors in vendorNames.
  • lines changed 1, context: html, text, full: html, text
    Fixed file name since you can't have / in filenames.
  • lines changed 1, context: html, text, full: html, text
    Added missing type to antibody registration.
  • lines changed 5, context: html, text, full: html, text
    Updated targets to remove vendorId and removed redudant labels for CycT1 and HMGN1 stating the target twice. Redmine #7060.
  • lines changed 14, context: html, text, full: html, text
    Changed var 'geo' for seqPlatform and platform to geoPlatformName to be more descriptive. Redmine #5111.
  • lines changed 19, context: html, text, full: html, text
    Added 3 new differentation treatments. Also updated labels to be consistent on the diffProtA treatments.
  • lines changed 3, context: html, text, full: html, text
    Forgot type treatment.
  • lines changed 36, context: html, text, full: html, text
    Removed duplicate key and re-made NHLF stanza.
  • lines changed 15, context: html, text, full: html, text
    Added 3 new differentiation treatments.
  • lines changed 1, context: html, text, full: html, text
    Fixing label for Spikeins to be Spike-ins. Redmine #5986.
  • lines changed 34, context: html, text, full: html, text
    Added 2 new cell lines for Ren lab.
  • lines changed 1, context: html, text, full: html, text
    Misspelled category.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 125, context: html, text, full: html, text
    Remove duplicate comments that should only be at the end of the stanza. Redmine #7078.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 458, context: html, text, full: html, text
    Fixes for Redmine #4145 1. Updated Cell line sorting to be by tier 2. Removed treatment on sortable columns as treatment is only in release 3 3. Updated ENCODE data freeze from post ENCODE Jan 2011 Freeze -> Mar 2012 Freeze Redmine #6581
  • lines changed 459, context: html, text, full: html, text
    Fixes in Redmine 4145. 14. Fixes typo in restricted until states '2001-10-09' instead of '2009-10-09' 15. Left off 'Freeze' when updating freeze date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 58, context: html, text, full: html, text
    Changed post ENCODE Jan 2011 Freeze to ENCODE Mar 2012 Freeze. Redmine #6581.
  • lines changed 58, context: html, text, full: html, text
    Fixed typo in previous commit with change of ENCODE freeze data, left off Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 453, context: html, text, full: html, text
    Changed post ENCODE Jan 2011 Freeze to ENCODE Mar 2012 Freeze. Redmine #6581.
  • lines changed 453, context: html, text, full: html, text
    Fixed typo in previous commit with change of ENCODE freeze data, left off Freeze. Redmine #6581.
  • lines changed 3137, context: html, text, full: html, text
    Added 25 submissions. Redmine #4486.
  • lines changed 3, context: html, text, full: html, text
    Fixed typo in dataVersion found by cronjob.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 2361, context: html, text, full: html, text
    Added 10 experiments for track. Redmine #5697.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 39, context: html, text, full: html, text
    Changed post ENCODE Jan 2011 Freeze to ENCODE Mar 2012 Freeze. Redmine #6581.
  • lines changed 39, context: html, text, full: html, text
    Fixed typo in previous commit with change of ENCODE freeze data, left off Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added release 2 of track. Redmine #5697.
  • lines changed 2, context: html, text, full: html, text
    Renmaed wgEncodeDukeAffyExon.new.ra -> wgEncodeDukeAffyExon.release3.ra and fixed naming of wgEncodesydhHistone.release3.ra -> wgEncodeSydhHistone.release3.
  • lines changed 1, context: html, text, full: html, text
    Updated release 2 from new to release naming. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 54, context: html, text, full: html, text
    Fixes in track Description for Redmine #4145 1. Updated sentence from "One to 10 nangograms" -> "A quantity of 1-10 ng" 2. Added phrase 'were added' after "except '-C 11' and '-H output_file'" 3. Added 'was' to phrase "....except for '-e' set to extend..." 4. Changed 'Accession' -> 'UCSC Accession' 5. Addded comma before 'e.g' 6. italicized 'e.g' 7. Changed link to Bernsetin lab to be https 8. Moved Contact to end of credits section and removed period 9. Made journal links to pubmed 10. Updated Data Release Policy to Track Standard
  • lines changed 3, context: html, text, full: html, text
    Fixes in Redmine #4145 1. Changed "A quantity of 1-10 ng of DNA were..." -> "A quantity of 1-10 ng of DNA was" 2. Added phrase 'were added' after "except '-C 11' and '-H output_file'" 3. Changed setence to "...except for '-e' which was set to extend..."
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
  • lines changed 193, context: html, text, full: html, text
    Fixes for Redmine #4145 1. Updated Cell line sorting to be by tier 2. Removed treatment on sortable columns as treatment is only in release 3 3. Updated ENCODE data freeze from post ENCODE Jan 2011 Freeze -> Mar 2012 Freeze Redmine #6581
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 191, context: html, text, full: html, text
    Fixes for Redmine #4145 1. Updated Cell line sorting to be by tier 2. Removed treatment on sortable columns as treatment is only in release 3 3. Updated ENCODE data freeze from post ENCODE Jan 2011 Freeze -> Mar 2012 Freeze Redmine #6581
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 5901, context: html, text, full: html, text
    Updated release 2 from new to release naming. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 175, context: html, text, full: html, text
    Updated release 2 from new to release naming. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 5902, context: html, text, full: html, text
    Updated release 2 from new to release naming. Redmine #4486.
  • lines changed 1041, context: html, text, full: html, text
    Added 25 submissions. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html
  • lines changed 185, context: html, text, full: html, text
    Added release 2 of track. Redmine #5697.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 179, context: html, text, full: html, text
    Added release 2 of track. Redmine #5697.
  • lines changed 467, context: html, text, full: html, text
    Added 10 experiments for track. Redmine #5697.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 7, context: html, text, full: html, text
    Added md5sum's. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 143, context: html, text, full: html, text
    Updated md5sum's. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 59, context: html, text, full: html, text
    Added md5sum's to tracks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 62, context: html, text, full: html, text
    Added md5sum's to tracks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 153, context: html, text, full: html, text
    Removed submission 4921, as this duplicated files in 4853 but with incorrect meta-data. Also fixes colliding md5sum issue. Redmine #5397.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 61, context: html, text, full: html, text
    Loaded replaced peaks and hotspots for 18 data sets. At the same time reloaded the Signal tables using the correct View name. Redmine #4468. Note #12.
  • lines changed 720, context: html, text, full: html, text
    Added 6 new submissions. Redmine #4468.
  • lines changed 67, context: html, text, full: html, text
    Updated md5sum's for track. Redmine #4468.
  • lines changed 90, context: html, text, full: html, text
    Updated object name to include age immortalized for cell lines. Error uncovered by Mike Pazin.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 239, context: html, text, full: html, text
    Added 2 more experiments. Redmine #4469.
  • lines changed 11, context: html, text, full: html, text
    Added md5sum's for track. Redmine #4469.
  • lines changed 77, context: html, text, full: html, text
    Updated object name to include age immortalized for cell lines. Error uncovered by Mike Pazin.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Updated file names to new release naming structure. Redmine #4468.
  • lines changed 1, context: html, text, full: html, text
    Renamed new.ra to release naming schema.
  • lines changed 1, context: html, text, full: html, text
    Renamed files from new to release naming schema. Redmine #5696.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.new.ra
  • lines changed 668, context: html, text, full: html, text
    Renamed files from new to release naming schema. Redmine #5696.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.release2.html
  • lines changed 154, context: html, text, full: html, text
    Renamed files from new to release naming schema. Redmine #5696.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.release2.ra
  • lines changed 669, context: html, text, full: html, text
    Renamed files from new to release naming schema. Redmine #5696.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Fixed incorrect species name referenced in track description. Redmine #5986.
  • lines changed 2, context: html, text, full: html, text
    Making links relative. Redmine #5986.
  • lines changed 20, context: html, text, full: html, text
    Fixes for Redmine #5986 5. Changed sentence from "ENCODE Constoria" -> "ENCODE Consortium" 6. Italicized i.e. 7. Updated last sentence in Tissue Samples to state : "Whenever possible biological replicates were obtained from litermates." Litermates is 1 word 8. Updated .9 -> 0.90 9. Redid citations with qaAddTrackReferences
  • lines changed 1, context: html, text, full: html, text
    7b. Added comma after possible and spelled littermates correctly. Redmine #5986.
  • lines changed 1, context: html, text, full: html, text
    Removed m from 'possible'. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    Fixes found in Redmine #5986 2. Fixed ordering of Subcutaneous Fat Pad after Stomach 4. Fixed colors of Kidney to be the same color
  • lines changed 8, context: html, text, full: html, text
    2b. Fixed ordering of Subcutenous Fat Pad in the subTrack list. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
  • lines changed 173, context: html, text, full: html, text
    Renamed new.ra to release naming schema.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra
  • lines changed 18, context: html, text, full: html, text
    Removed submission 4921, as this duplicated files in 4853 but with incorrect meta-data. Also fixes colliding md5sum issue. Redmine #5397.
  • lines changed 969, context: html, text, full: html, text
    Renamed new.ra to release naming schema.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html
  • lines changed 173, context: html, text, full: html, text
    Renamed new.ra to release naming schema.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 969, context: html, text, full: html, text
    Renamed new.ra to release naming schema.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.html
  • lines changed 112, context: html, text, full: html, text
    Updated file names to new release naming structure. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
  • lines changed 68, context: html, text, full: html, text
    Loaded replaced peaks and hotspots for 18 data sets. At the same time reloaded the Signal tables using the correct View name. Redmine #4468. Note #12.
  • lines changed 2634, context: html, text, full: html, text
    Updated file names to new release naming structure. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.html
  • lines changed 112, context: html, text, full: html, text
    Updated file names to new release naming structure. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 2634, context: html, text, full: html, text
    Updated file names to new release naming structure. Redmine #4468.
  • lines changed 428, context: html, text, full: html, text
    Added 6 new submissions. Redmine #4468.
  • lines changed 49, context: html, text, full: html, text
    Added replicate 13 and 14 to attic. Redmine #4468.
  • lines changed 10, context: html, text, full: html, text
    Updated object name to include age immortalized for cell lines. Error uncovered by Mike Pazin.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 73, context: html, text, full: html, text
    Added 2 more experiments. Redmine #4469.
  • lines changed 49, context: html, text, full: html, text
    Updated object name to include age immortalized for cell lines. Error uncovered by Mike Pazin.