Commits for kate

v278_preview to v278_preview2 (2013-01-08 to 2013-01-15) v278

• Starting V2 of ENCODE Regulation (#7526)
  • src/hg/makeDb/doc/hg19.txt - lines changed 89, context: html, text, full: html, text
• Added histones and TFBS, retrieving from EBI
  • src/hg/makeDb/doc/hg19.txt - lines changed 67, context: html, text, full: html, text
• Merge branch 'master' into reg
• Cluster DNase and load track
  • src/hg/makeDb/doc/hg19.txt - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c - lines changed 9, context: html, text, full: html, text
• Merge branch 'master' into reg
• Start TFBS
  • src/hg/makeDb/doc/hg19.txt - lines changed 55, context: html, text, full: html, text
• Merge branch 'master' into reg
• Finish formatting of RNA signal. Add to trackDb in Txn track
  • src/hg/makeDb/doc/hg19.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra - lines changed 100, context: html, text, full: html, text
• Add HeLa and HepG2 to Txn
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra - lines changed 16, context: html, text, full: html, text
• Merge branch 'master' into reg
• Merge branch 'master' into reg
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 14, context: html, text, full: html, text
• 1. Add 10th cell type to Txn (HMEC). 2. Fix corrupt HepG2 Txn 3. Create track for Uniform DNase. #7526: ENCODE Regulation (V2)
  • src/hg/makeDb/doc/hg19.txt - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnase.ra - lines changed 894, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra - lines changed 15, context: html, text, full: html, text
• Experiment with small RNA and FAIRE as potential tracks for ENCODE Regulation V2
  • src/hg/makeDb/doc/hg19.txt - lines changed 55, context: html, text, full: html, text
• Tune configuration
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnase.ra - lines changed 390, context: html, text, full: html, text
• Fixing merge conflict
  • src/hg/makeDb/doc/hg19.txt - lines changed 705, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 14, context: html, text, full: html, text
• Cluster TFBS from 2012 freeze
  • src/hg/makeDb/doc/hg19.txt - lines changed 196, context: html, text, full: html, text
  • src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/wgEncodeRegTfbsDedupeHelp.c - lines changed 71, context: html, text, full: html, text
• Add experimental short RNA and Transfac/Jaspar motif tracks to look at in context of integrated regulatory track update
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra - lines changed 126, context: html, text, full: html, text
• Tools updates for next iteration of Integrated Regulatory track
  • src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c - lines changed 21, context: html, text, full: html, text
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 11, context: html, text, full: html, text
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c - lines changed 32, context: html, text, full: html, text
• Start Mouse Integrated Regulatory track
  • src/hg/makeDb/doc/mm9.txt - lines changed 13, context: html, text, full: html, text
• Merge branch 'master' into reg
• Back out mm9 changes for now
  • src/hg/makeDb/doc/mm9.txt - lines changed 14, context: html, text, full: html, text
• Backing out for now
  • src/hg/makeDb/doc/mm9.txt - lines changed 1, context: html, text, full: html, text
• Add make docs for ENCODE Regulation tracks (some pulled from hg18.txt)
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 793, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeRegMm9.txt - lines changed 15, context: html, text, full: html, text
• Move ENCODE Reg to its own make doc
  • src/hg/makeDb/doc/hg19.txt - lines changed 790, context: html, text, full: html, text
• Fix merge
  • src/hg/makeDb/doc/hg19.txt - lines changed 335, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 8, context: html, text, full: html, text
• Use AWG Dnase from new Uniform track as basis of Clustered DNase
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra - lines changed 2, context: html, text, full: html, text
• Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 163, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeAwgHg19/.awg.txt.swp - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/encodeAwgHg19/awg.txt - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnase.ra - lines changed 911, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniPk.html - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 911, context: html, text, full: html, text
• Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 2, context: html, text, full: html, text
• Corrections to pubs section of track description. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 11, context: html, text, full: html, text
• Corrections to pubs section of track description. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnase.ra - lines changed 1854, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 1854, context: html, text, full: html, text
• Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• Fix signal filtering settings. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 5, context: html, text, full: html, text
• Rename Huh7.5 object as period in name bothered database. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 1, context: html, text, full: html, text
• Creating the notes file. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeAnalysisHg19/wgEncodeAwgDnaseUniform.release1.notes - lines changed 287, context: html, text, full: html, text
• Needed to add metadata object for composite. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 6, context: html, text, full: html, text
• Fix composite metadata object. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 7, context: html, text, full: html, text
• Make common.mk consistent with policy of not stripping binaries by default (Mark D. recommendation, on advisement from Hiram). This takes care of all those directories that haven't had strip removed or commented out of makefiles (e.g. tools)
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
• Enhancement to mdbPrint -composite option for readability of .ra file. It will now print the composite object first (previously relied strictly on alpha sorting)
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 17, context: html, text, full: html, text
• Readability fix -- move composite object to start of file. Required tweak to mdbPrint. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 10, context: html, text, full: html, text
• Switch STRIP to true in the interests of minimalism (thanks Angie)
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
• Getting ready for QA. #9850 ENCODE Uniform DNase I HS track
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 3, context: html, text, full: html, text
• More renames to make ENCODE tools happy. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt - lines changed 184, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/awgUniform.txt - lines changed 184, context: html, text, full: html, text
• Notes files for QA. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgDnaseUniform.release1.notes - lines changed 287, context: html, text, full: html, text
• Major pass on track description. #9850 - ENCODE Uniform DNase1 HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 46, context: html, text, full: html, text
• Fix misspelling
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html - lines changed 2, context: html, text, full: html, text
• Fix problem introduced by #9328. #9944 hgFileUi track description appears twice
  • src/hg/hgFileUi/hgFileUi.c - lines changed 2, context: html, text, full: html, text
• Rename to make ENCODE tools happy. #9850 Uniform DNaseI HS
  • src/hg/makeDb/doc/encodeAnalysisHg19/wgEncodeAwgDnaseUniform.release1.notes - lines changed 287, context: html, text, full: html, text
• Fix merge conflict
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
• Sort cluster lists by metadata terms for more reliable ordering. Needed for #9954 ENCODE Regulation: DNase Clusters V2
  • src/hg/hgc/peakClusters.c - lines changed 1, context: html, text, full: html, text
• Add hgc handler. #9954 ENCODE Regulation: DNase Clusters V2
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• Organize make doc and trackDb. #9954 ENCODE Regulation: DNase Clusters V2
  • src/hg/makeDb/doc/encodeRegHg19.txt - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release4.ra - lines changed 366, context: html, text, full: html, text
• Merge branch 'reg'
• Tools and trackDb updates. #7526: ENCODE regulation track update (in progress). #9954: DNase Clusters V2 (displayed on genome-test)
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release4.ra - lines changed 1, context: html, text, full: html, text
• Add missing metadata. #9850 Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 1, context: html, text, full: html, text
• Magic number update. #9850 Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 1, context: html, text, full: html, text
• Add missing dccAccessions (mostly these are the treatment experiments) and fix an incorrect treatment. #9850 Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra - lines changed 13, context: html, text, full: html, text
• Trim unneeded experiment accession from supplementary table. #9554 ENCODE Regulation: DNase Clusters V2
  • src/hg/lib/clusterInputAwgDnase.as - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/clusterInputAwgDnase.c - lines changed 139, context: html, text, full: html, text
  • src/hg/lib/clusterInputAwgDnase.h - lines changed 64, context: html, text, full: html, text
  • src/hg/lib/clusterInputAwgDnase.sql - lines changed 14, context: html, text, full: html, text
• Track description for updated track. #9954 ENCODE Regulation: DNase Clusters V2
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html - lines changed 28, context: html, text, full: html, text
• .gitignore
  • .gitignore - lines changed 1, context: html, text, full: html, text
• Add Methods section to track description. Other refinements. #9954: ENCODE Regulation: DNase Clusters V2
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html - lines changed 30, context: html, text, full: html, text
• Prune overlong track labels found by QA. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 2, context: html, text, full: html, text
• Trim trackDb to remove redundacies and to make filters consistent (subtrack vs. composite). Response to QA. #9850 ENCODE Uniform DNaseI HS
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 127, context: html, text, full: html, text
• Limit override of displaySubtracks setting to large composites having a matrix (so large tracks w/o matrix can default show all subtracks)
  • src/hg/lib/hui.c - lines changed 3, context: html, text, full: html, text
• Reverting track type. NarrowPeak visibilities don't seem to work properly at composite level (only shows 3 vis options).
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra - lines changed 132, context: html, text, full: html, text