All File Changes

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

• .gitignore
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    .gitignore
• src/hg/hgBlat/hgBlat.c
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    fixing blat documentation to match our use of stepSize=5 with hgBlat/gfServer which we have been doing since hgPcr came out.
• src/hg/hgFileUi/hgFileUi.c
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    Fix problem introduced by #9328. #9944 hgFileUi track description appears twice
• src/hg/hgGene/hgGene.c
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    fix bug in first fix in #9668 where hgGene crashed near the bottom of the page which is why no one caught it. Also, added a little code to save position in cart after getting it from a gene name.
• src/hg/hgGene/synonym.c
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    fix bug in first fix in #9668 where hgGene crashed near the bottom of the page which is why no one caught it. Also, added a little code to save position in cart after getting it from a gene name.
• src/hg/hgc/hgc.c
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    redmine 9269: Change track exonJunctionPrimers to of type bedDetail 14 to minimize impact to hgc.c based on Hiram's feedback from CR #9927
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    fix linkout URL to DECIPHER #8840
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    Add hgc handler. #9954 ENCODE Regulation: DNase Clusters V2
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    Make hgc's doDgv SQL query more specific -- latest data has thousandsof nameless items, which were all appearing in hgc when clicking on one.
    
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    remove Stanford SOURCE link from refGene and few other places #9962
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• 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/htdocs/FAQ/FAQreleases.html
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    Added petMar2 (redmine #9153)
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    Updating release information for bosTau7 to 4.6.1 MLQ# 9936
• src/hg/htdocs/goldenPath/credits.html
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    Added petMar2 (redmine #9153)
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    Updated the lamprey credits section
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    Fixed a broken link in the lamprey section
• src/hg/htdocs/images/phylo/mm10_60way.gif
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    added s to Glire and Euarchontoglire in mm10_60way image
• 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/hdb.c
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    do a little clean-up on error if extFile is missing or wrong size. In response to code review #9929. Thanks Angie!
• 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/lib/pgSnp.c
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    Fixing VCF-to-pgSnp translation for sketchy VCF from Complete Genomics that has AN(=0) and no AC.
• src/hg/lib/trackHub.c
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    increase limit of trackDb.txt to 64Mb. #9937We should probably look into whether we need to have a fixed limit at all
    
• 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
  • lines changed 3, context: html, text, full: html, text
    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
  • lines changed 287, context: html, text, full: html, text
    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)
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• src/hg/makeDb/doc/mm10.txt
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• 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/doc/musFur1.txt
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    Adding new makedoc, for new assembly.
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    Updating makedoc, for new assembly.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
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    ongoing work on UCSC genes for hg19 #9783
• 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/schema/all.joiner
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    adding identifier mm10Patch1ExtFileId for mm10 patch1
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    Added mm10 tablesIgnored section and added altSeqLiftOverPslP1 and altSeqPatchesP1 to it (redmine #8909)
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    add Mm10Patch1 to the chainDest list
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    Changed 'cpgIslandExt' back to 'cpgIsland%' per Brooke's code review (redmine #9919)
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    see redmine #9811 notes 3-4
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
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    removed extra '$'
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    commented out a line
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    Added mm10snp137 to databasesIgnored. Moved the hg19.gwasCatalog/snp version reminder comment down (it moves with hg19.gwasCatalog.name).
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/chainNet.html
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    Changing references using getTrackReferences to point to NCBI Pubmed, QA of GCR Patch10 RM#9066
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseGene.html
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    Updated journal links; dropped link to PubMed abstract; updated links to FlyBase
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseNoncoding.html
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    Updated journal links; dropped link to PubMed abstract; updated links to FlyBase
• src/hg/makeDb/trackDb/human/altSeqComposite.html
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    Changing references using getTrackReferences to point to NCBI Pubmed, QA of GCR Patch10 RM#9066
• src/hg/makeDb/trackDb/human/coriellDelDup.html
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    changes per data provider
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    dropped a comma per Luvina
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    small changes per coriell
• src/hg/makeDb/trackDb/human/decipher.html
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    Uodated journal link; made some other minor corrections (redmine #8840)
• src/hg/makeDb/trackDb/human/dgv.html
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    removing / on first /em to allow italics on references to show up for dgv.html RM#9401
• src/hg/makeDb/trackDb/human/hg19/chainSelf.html
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    Changing references using getTrackReferences to point to NCBI Pubmed, QA of GCR Patch10 RM#9066
• 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
  • lines changed 4, context: html, text, full: html, text
    Rename Huh7.5 object as period in name bothered database. #9850 - ENCODE Uniform DNase1 HS
  • lines changed 6, context: html, text, full: html, text
    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
  • lines changed 10, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    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/metaDb/beta/makefile
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    Staging Encode AWG DNase Uniform track (RM#9850) (Release 1) on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgDnaseUniform.ra
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    Staging Encode AWG DNase Uniform track (RM#9850) (Release 1) on beta
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    Made adjustments for chain/net tracks to appear properly (redmine #9153)
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    Staging GRC hg19 Patch10 on beta, RM #9066
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    redmine 9269: Change track exonJunctionPrimers to of type bedDetail 14 to minimize impact to hgc.c based on Hiram's feedback from CR #9927
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    Adding GRC 9 back to alpha, should have only removed it from beta, RM#9066
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    Adding GRC Patch 10 for RR release, removing patch 9, RM#9066
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    updated gwas info with snp137, redmine #9811
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• 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)
  • lines changed 14, context: html, text, full: html, text
    Fixing merge conflict
  • lines changed 8, context: html, text, full: html, text
    Fix merge
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    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • lines changed 1, context: html, text, full: html, text
    Corrections to pubs section of track description. #9850 - ENCODE Uniform DNase1 HS
  • lines changed 3, context: html, text, full: html, text
    Fix merge conflict
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    Organize make doc and trackDb. #9954 ENCODE Regulation: DNase Clusters V2
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    Staging Encode AWG DNase Uniform track (RM#9850) (Release 1) on beta
• 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
  • lines changed 59, context: html, text, full: html, text
    Some renames for clarity/consistency (and to make ENCODE tools happy). #9850 - ENCODE Uniform DNase1 HS
  • lines changed 11, context: html, text, full: html, text
    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
  • 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
  • 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
  • lines changed 5, context: html, text, full: html, text
    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
  • lines changed 2, context: html, text, full: html, text
    Prune overlong track labels found by QA. #9850 ENCODE Uniform DNaseI HS
  • lines changed 127, 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
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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/makeDb/trackDb/human/hg19Patch10/trackDb.ra
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    adding hg19Patch10 to the build
• src/hg/makeDb/trackDb/human/omimAvSnp.html
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    the omim track nows gets SNP's out of snp137 instead of snp132 #7311
• src/hg/makeDb/trackDb/human/trackDb.ra
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    changes per data provider
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    Fixed journal URL - updated from early version to final version - per Brooke's code review (redmine #9919)
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Made adjustments for chain/net tracks to appear properly (redmine #9153)
• src/hg/makeDb/trackDb/makefile
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    adding hg19Patch10 to the build so it can have a trackDb file
• src/hg/makeDb/trackDb/medaka/oryLat1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/medaka/oryLat2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Removed release tag from petMar1 entry
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 22, context: html, text, full: html, text
    changed names from Glire to Glires and same for Euarchontoglires
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    redmine 9269: Change track exonJunctionPrimers to of type bedDetail 14 to minimize impact to hgc.c based on Hiram's feedback from CR #9927
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Made adjustments for chain/net tracks to appear properly (redmine #9153)
• src/hg/makeDb/trackDb/opossum/monDom1/description.html
  • lines changed 2, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/opossum/monDom2/description.html
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    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/opossum/monDom4/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/qPcrPrimers.html
  • lines changed 91, context: html, text, full: html, text
    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
  • lines changed 7, context: html, text, full: html, text
    Changed format of quotes in text to be html-friendly.
  • lines changed 62, context: html, text, full: html, text
    Whitespace changes. Also fixed a few more instances of non-html-friendly quotes.
• src/hg/makeDb/trackDb/qpcrPrimers.html
  • lines changed 91, context: html, text, full: html, text
    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• src/hg/makeDb/trackDb/rat/rn1/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/rat/rn2/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/rat/rn3/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/rat/rn4/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 1, context: html, text, full: html, text
    Added '%20' into photo links per Brooke's code review (redmine #9919); also fixed a broken link in monDom1
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    changed names from Glire to Glires and same for Euarchontoglires
  • lines changed 2, context: html, text, full: html, text
    Removed 'glire' and 'euarchontoglire' lines
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Uncommented the include statement for the chainNetPetMar1.ra file
• src/hg/makeDb/trackDb/trackDb.ra
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    redmine 9269: Change track exonJunctionPrimers to of type bedDetail 14 to minimize impact to hgc.c based on Hiram's feedback from CR #9927
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    redmine #9269 rename track, redmine title, and html file name from exonJunctionPrimers to qPcrPrimers.
• src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/makefile
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    Cluster TFBS from 2012 freeze
• src/hg/oneShot/wgEncodeRegTfbsDedupeHelp/wgEncodeRegTfbsDedupeHelp.c
  • lines changed 71, context: html, text, full: html, text
    Cluster TFBS from 2012 freeze
• src/hg/pslDiff/pslDiff.c
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    add an option to pslDiff to check for same locus #7568
• src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
  • lines changed 21, context: html, text, full: html, text
    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
  • lines changed 9, context: html, text, full: html, text
    Cluster DNase and load track
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    Tools updates for next iteration of Integrated Regulatory track
• src/hg/utils/automation/buildOmimTracks.csh
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    remove old versions of these scripts #5172
• src/hg/utils/automation/checkOmim.sh
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    remove old versions of these scripts #5172
• src/hg/utils/omim/buildOmimTracks.csh
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    the omim track nows gets SNP's out of snp137 instead of snp132 #7311
• 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)
• src/lib/cheapcgi.c
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    calling exit(1) after receiving SIGTERM allows atexit cleanup when apache kills timed-out cgi
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    Changing setMaxAlloc default to 100G, and making an undocumented maxGigs command line option to address bedGraphToBigWigh memory issue in redmine #9935
• src/utils/qa/weeklybld/buildEnv.csh
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    v278 preview2

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• files changed: 186