Commits for vsmalladi

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• Added in full set of files for track from submission 5451. Redmine #225
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra - lines changed 773, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra - lines changed 55, context: html, text, full: html, text
• Commented out color and type lines for wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalMinusRawRep1 which seem to be comming from subId 4061. The lines were breaking the make. Redmine #1634.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 2, context: html, text, full: html, text
• Resolved merge conflict.
• Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra - lines changed 180, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra - lines changed 4206, context: html, text, full: html, text
• Added in metadata and objects that were removed using old revoke policy to follow new revoke policy. Also updated md5sums. Redmine #4145, note #26.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 1141, context: html, text, full: html, text
• Updated Release notes for track. Redmine #4145.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html - lines changed 12, context: html, text, full: html, text
• Updated fileName to have .bai file and added md5sums. Redmine #4145.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 227, context: html, text, full: html, text
• Fixed DAF for bedRnaElements to have sql table reference for loading purposes. Redmine #5986.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• Added expId's and accessioned experiments new for release 2. Redmine #4145.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 577, context: html, text, full: html, text
• Added release 2 notes for track. Redmine #4145.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release2.notes - lines changed 2511, context: html, text, full: html, text
• Updated the scoreFilter to be default 0. Redmine #225.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra - lines changed 1, context: html, text, full: html, text
• Updated longLabels to fix inconsistency found in QA process. Redmine #110.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra - lines changed 41, context: html, text, full: html, text
• Added cv items for new repli-seq data from Gilbert lab. Also took the first stab at a DAF for the Human data set. Redmine #6627, #6626.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 70, context: html, text, full: html, text
• Fixed example DDF entry. Redmine #6626.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf - lines changed 1, context: html, text, full: html, text
• Updated bam validation to be 99.0%. Redmine #5697.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf - lines changed 1, context: html, text, full: html, text
• Added control specific terms for the eGFP antibodies. Redmine #5697.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 75, context: html, text, full: html, text
• Forgot to increment the DAF version to 1.4 in previous commit: f84df47051abb23f950f4583df4dffaaa983edf7.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf - lines changed 1, context: html, text, full: html, text
• Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 902, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 162, context: html, text, full: html, text
• Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 239, context: html, text, full: html, text
• Updated daf to use 98% bam pass rate and require replicates being tracked for Signal and Peak views. Redmine #5697.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf - lines changed 4, context: html, text, full: html, text
• Removed incorrect 2 on long label.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra - lines changed 1, context: html, text, full: html, text
• Forgot submittions 5439 in data load. Redmine #5986.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra - lines changed 27, context: html, text, full: html, text
• Fixes for Redmine #4577 1. Changed alphabetical order of HeLa-S3 and HepG2 2. Changed alphabetical order of BJ and BGO2ES
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 1, context: html, text, full: html, text
• Added in treatment subGroups for track that were missing in commit: 840a873d9180863c4a6a015cf33d8b8c52b50a10. Redmine #4143.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 33, context: html, text, full: html, text
• Fixes for Redmine #4577 4. Replaced semicolon with comma between cell line and replicate 5. Replaced comma with semicolon before G1/G1b list in description section 6. Removed comma after G2 in description section 7 .Removed comma after Percetage-Normalized Signal in descrption section 8. Removed comma after Peaks in description section 9. Removed comma after Valleys in description section 10. Removed hyphen between weighted average 11. Italicized in vivo 12. Removed semicolons and made 3 seperate sentences in long section of first paragrah in methods section 13 Broke up long on going sentence in last paragraph of Methods section 15. Updated references to be to NCBI Pubmed. 16. Updated Long labels to be consitent and use Repli-seq instead of Replication Timing
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 32, context: html, text, full: html, text
• Fixed issues in Redmine #4577 18. Fixed spelling of header in hgFileUi for Phase from Hase
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 1, context: html, text, full: html, text
• Fixed hardcoded link to relative link. Redmin #6526.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html - lines changed 1, context: html, text, full: html, text