File Changes for kate

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

• .gitignore
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    .gitignore
• src/hg/hgFileUi/hgFileUi.c
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    Fix problem introduced by #9328. #9944 hgFileUi track description appears twice
• src/hg/hgc/hgc.c
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    Add hgc handler. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/hgc/peakClusters.c
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    Sort cluster lists by metadata terms for more reliable ordering. Needed for #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/lib/clusterInputAwgDnase.as
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    Trim unneeded experiment accession from supplementary table. #9554 ENCODE Regulation: DNase Clusters V2
• src/hg/lib/clusterInputAwgDnase.c
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    Trim unneeded experiment accession from supplementary table. #9554 ENCODE Regulation: DNase Clusters V2
• src/hg/lib/clusterInputAwgDnase.h
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    Trim unneeded experiment accession from supplementary table. #9554 ENCODE Regulation: DNase Clusters V2
• src/hg/lib/clusterInputAwgDnase.sql
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    Trim unneeded experiment accession from supplementary table. #9554 ENCODE Regulation: DNase Clusters V2
• src/hg/lib/hui.c
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    Limit override of displaySubtracks setting to large composites having a matrix (so large tracks w/o matrix can default show all subtracks)
• src/hg/makeDb/doc/encodeAnalysisHg19/awg.txt
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Rename Huh7.5 object as period in name bothered database. #9850 - ENCODE Uniform DNase1 HS
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    Creating the notes file. #9850 - ENCODE Uniform DNase1 HS
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    Needed to add metadata object for composite. #9850 - ENCODE Uniform DNase1 HS
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    Getting ready for QA. #9850 ENCODE Uniform DNase I HS track
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    More renames to make ENCODE tools happy. #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/doc/encodeAnalysisHg19/wgEncodeAwgDnaseUniform.release1.notes
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    Creating the notes file. #9850 - ENCODE Uniform DNase1 HS
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    Rename to make ENCODE tools happy. #9850 Uniform DNaseI HS
• src/hg/makeDb/doc/encodeAwgHg19/.awg.txt.swp
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/doc/encodeAwgHg19/awg.txt
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/doc/encodeDccHg19/awgUniform.txt
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    More renames to make ENCODE tools happy. #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgDnaseUniform.release1.notes
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    Notes files for QA. #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/doc/encodeRegHg19.txt
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    Add make docs for ENCODE Regulation tracks (some pulled from hg18.txt)
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    Use AWG Dnase from new Uniform track as basis of Clustered DNase
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    Organize make doc and trackDb. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/doc/encodeRegMm9.txt
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    Add make docs for ENCODE Regulation tracks (some pulled from hg18.txt)
• src/hg/makeDb/doc/hg19.txt
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    Starting V2 of ENCODE Regulation (#7526)
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    Added histones and TFBS, retrieving from EBI
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    Cluster DNase and load track
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    Start TFBS
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    Finish formatting of RNA signal. Add to trackDb in Txn track
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    1. Add 10th cell type to Txn (HMEC). 2. Fix corrupt HepG2 Txn 3. Create track for Uniform DNase. #7526: ENCODE Regulation (V2)
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    Experiment with small RNA and FAIRE as potential tracks for ENCODE Regulation V2
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    Fixing merge conflict
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    Cluster TFBS from 2012 freeze
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    Move ENCODE Reg to its own make doc
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    Fix merge
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    Tools and trackDb updates. #7526: ENCODE regulation track update (in progress). #9954: DNase Clusters V2 (displayed on genome-test)
• src/hg/makeDb/doc/mm9.txt
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    Start Mouse Integrated Regulatory track
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    Back out mm9 changes for now
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    Backing out for now
• src/hg/makeDb/mdbUpdate/mdbPrint.c
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    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/trackDb/human/hg19/metaDb/alpha/makefile
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    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
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgDnaseUniform.ra
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Rename Huh7.5 object as period in name bothered database. #9850 - ENCODE Uniform DNase1 HS
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    Needed to add metadata object for composite. #9850 - ENCODE Uniform DNase1 HS
  • lines changed 7, context: html, text, full: html, text
    Fix composite metadata object. #9850 - ENCODE Uniform DNase1 HS
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    Readability fix -- move composite object to start of file. Required tweak to mdbPrint. #9850 - ENCODE Uniform DNase1 HS
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    Add missing metadata. #9850 Uniform DNaseI HS
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    Magic number update. #9850 Uniform DNaseI HS
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    Add missing dccAccessions (mostly these are the treatment experiments) and fix an incorrect treatment. #9850 Uniform DNaseI HS
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    Cluster DNase and load track
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    Merge branch 'master' into reg
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    1. Add 10th cell type to Txn (HMEC). 2. Fix corrupt HepG2 Txn 3. Create track for Uniform DNase. #7526: ENCODE Regulation (V2)
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    Fixing merge conflict
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    Fix merge
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Corrections to pubs section of track description. #9850 - ENCODE Uniform DNase1 HS
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    Fix merge conflict
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    Organize make doc and trackDb. #9954 ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnase.ra
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    1. Add 10th cell type to Txn (HMEC). 2. Fix corrupt HepG2 Txn 3. Create track for Uniform DNase. #7526: ENCODE Regulation (V2)
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    Tune configuration
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniPk.html
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Corrections to pubs section of track description. #9850 - ENCODE Uniform DNase1 HS
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    Major pass on track description. #9850 - ENCODE Uniform DNase1 HS
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    Fix misspelling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
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    Fix signal filtering settings. #9850 - ENCODE Uniform DNase1 HS
  • lines changed 1, context: html, text, full: html, text
    Rename Huh7.5 object as period in name bothered database. #9850 - ENCODE Uniform DNase1 HS
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    Prune overlong track labels found by QA. #9850 ENCODE Uniform DNaseI HS
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    Trim trackDb to remove redundacies and to make filters consistent (subtrack vs. composite). Response to QA. #9850 ENCODE Uniform DNaseI HS
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    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/wgEncodeReg.release4.ra
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    Organize make doc and trackDb. #9954 ENCODE Regulation: DNase Clusters V2
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    Tools and trackDb updates. #7526: ENCODE regulation track update (in progress). #9954: DNase Clusters V2 (displayed on genome-test)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.release2.html
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    Track description for updated track. #9954 ENCODE Regulation: DNase Clusters V2
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    Add Methods section to track description. Other refinements. #9954: ENCODE Regulation: DNase Clusters V2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegV2.ra
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    Finish formatting of RNA signal. Add to trackDb in Txn track
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    Add HeLa and HepG2 to Txn
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    1. Add 10th cell type to Txn (HMEC). 2. Fix corrupt HepG2 Txn 3. Create track for Uniform DNase. #7526: ENCODE Regulation (V2)
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    Add experimental short RNA and Transfac/Jaspar motif tracks to look at in context of integrated regulatory track update
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    Use AWG Dnase from new Uniform track as basis of Clustered DNase
• src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/makefile
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    Cluster TFBS from 2012 freeze
• src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/wgEncodeRegTfbsDedupeHelp.c
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    Cluster TFBS from 2012 freeze
• src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
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    Tools updates for next iteration of Integrated Regulatory track
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
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    Tools updates for next iteration of Integrated Regulatory track
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
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    Cluster DNase and load track
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    Tools updates for next iteration of Integrated Regulatory track
• src/inc/common.mk
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    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)
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    Switch STRIP to true in the interests of minimalism (thanks Angie)