All File Changes

v268_preview2 to v268_base (2012-05-29 to 2012-06-05) v268

• python/lib/ucscGb/qa/encode/tableCheck.py
  • lines changed 1, context: html, text, full: html, text
    chnged timeout to 60 seconds
• python/lib/ucscGb/qa/tables/genePredQa.py
  • lines changed 4, context: html, text, full: html, text
    Replaced function recordPassOrError with two functions, recordPass and recordError. Also removed the word ERROR from the tableDescriptions and underscore check messages. Redmine #7939.
  • lines changed 1, context: html, text, full: html, text
    Fixed comments on validation methods.
• python/lib/ucscGb/qa/tables/pointerQa.py
  • lines changed 1, context: html, text, full: html, text
    Fixed comments on validation methods.
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 16, context: html, text, full: html, text
    Replaced function recordPassOrError with two functions, recordPass and recordError. Also removed the word ERROR from the tableDescriptions and underscore check messages. Redmine #7939.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo.
• python/lib/ucscGb/qa/tables/pslQa.py
  • lines changed 4, context: html, text, full: html, text
    Replaced function recordPassOrError with two functions, recordPass and recordError. Also removed the word ERROR from the tableDescriptions and underscore check messages. Redmine #7939.
  • lines changed 1, context: html, text, full: html, text
    Fixed comments on validation methods.
• python/lib/ucscGb/qa/tables/tableQa.py
  • lines changed 18, context: html, text, full: html, text
    Replaced function recordPassOrError with two functions, recordPass and recordError. Also removed the word ERROR from the tableDescriptions and underscore check messages. Redmine #7939.
  • lines changed 8, context: html, text, full: html, text
    Pulled check for being a table with an allowed underscore into a separate function. Redmine #7939.
  • lines changed 1, context: html, text, full: html, text
    Fixed comments on validation methods.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    adding in gff validation and acceptance
• src/hg/hgLogin/hgLogin.c
  • lines changed 10, context: html, text, full: html, text
    After signup return to returnto URL
  • lines changed 9, context: html, text, full: html, text
    Make confirmation mail vague.
  • lines changed 77, context: html, text, full: html, text
    Return to 'returnto' URL after signup successful.
  • lines changed 10, context: html, text, full: html, text
    Send forgotten username list using only one mail.
  • lines changed 24, context: html, text, full: html, text
    create getReturnToURL() function for used by returnToURL.
  • lines changed 2, context: html, text, full: html, text
    Avoid printing MD5 value out on screen.
  • lines changed 10, context: html, text, full: html, text
    Add 'Your account has been activated.' message to login screen after account is activated.
  • lines changed 3, context: html, text, full: html, text
    iFinished new hgSession welcome and account info UI change.
  • lines changed 13, context: html, text, full: html, text
    Use genome-www@soe.ucsc.edu as sender of all out going mails.
  • lines changed 11, context: html, text, full: html, text
    Always return to hgSession when Cancel button is clicked.
  • lines changed 58, context: html, text, full: html, text
    Validate email address format.
  • lines changed 8, context: html, text, full: html, text
    Check email address format in forgot password panel.
• src/hg/hgSession/hgSession.c
  • lines changed 4, context: html, text, full: html, text
    After signup return to returnto URL
  • lines changed 21, context: html, text, full: html, text
    iFinished new hgSession welcome and account info UI change.
  • lines changed 21, context: html, text, full: html, text
    Add spce to login links in hgSession.
  • lines changed 1, context: html, text, full: html, text
    Corrected typo error \li to /li
• src/hg/hgTables/hgTables.c
  • lines changed 26, context: html, text, full: html, text
    special case out of memory aborts to give a better error message (#5147)
• src/hg/hgTables/joining.c
  • lines changed 25, context: html, text, full: html, text
    fix for #4009, so hgTables identifiers are used in filtering even if no fields from the primary table are selected for output
• src/hg/hgTables/vcf.c
  • lines changed 18, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    Bug #8048: Fix suggested by Tim: add a class to ldUi's inversion checkboxes,and detect that class when marking changes in subCfg.js. Also found an slSort
    that was missing & for its first arg, resulting in weird sorting of subtracks
    for inversion checkbox display.
    
  • lines changed 3, context: html, text, full: html, text
    use hgFixed.trackVersion.version (if available) for 'Data Version' (#8032)
• src/hg/hgTracks/hgTracks.c
  • lines changed 27, context: html, text, full: html, text
    code cleanup (delete some dead code)
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    highlight element of linkedFeatures holds a Color so it should be unsigned
• src/hg/hgTracks/imageV2.h
  • lines changed 3, context: html, text, full: html, text
    code cleanup (delete some dead code)
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 45, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): UI seems to work on IEand Chrome now too, not just FireFox. Lessons learned: 1. event bubbling
    behavior is unique to each browser; 2. If there's a jquery way to do it,
    use jquery.
    
• src/hg/hgc/hgc.c
  • lines changed 10, context: html, text, full: html, text
    use hgFixed.trackVersion.version (if available) for 'Data Version' (#8032)
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 11, context: html, text, full: html, text
    Put the basic draft of the quality metrics content up and updated the data summary page with a paragraph on the metrics page. Redmine# 7780
  • lines changed 11, context: html, text, full: html, text
    Edit for conciseness and consistency. Make URL's relative
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 25, context: html, text, full: html, text
    Initial checkin of the ENCODE Quality Metrics Page. Ingore this checkin for code review as there will be many more checkins before release. Redmine# 7780
  • lines changed 158, context: html, text, full: html, text
    Put the basic draft of the quality metrics content up and updated the data summary page with a paragraph on the metrics page. Redmine# 7780
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    Added a missing newline to the MAF description section. Thanks, Dent.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    corrected Open Helix link
  • lines changed 30, context: html, text, full: html, text
    Added a small section about Track Hubs
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 168, context: html, text, full: html, text
    Added new sample query page (redmine #7751)
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 34, context: html, text, full: html, text
    Cleaned up some style, moving to css. Further organized js.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 80, context: html, text, full: html, text
    Cleaned up some style, moving to css. Further organized js.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 88, context: html, text, full: html, text
    Cleaned up some style, moving to css. Further organized js.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 43, context: html, text, full: html, text
    Cleaned up some style, moving to css. Further organized js.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbTestBlurbs.html
  • lines changed 10, context: html, text, full: html, text
    Cleaned up some style, moving to css. Further organized js.
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 1, context: html, text, full: html, text
    Added missing bracket on </P> tag
• src/hg/htdocs/images/homeIconSprite.png
  • lines changed 0, context: html, text, full: html, text
    Renamed this file using camelCase.
• src/hg/htdocs/images/home_icon_sprite_white.png
  • lines changed 0, context: html, text, full: html, text
    Removed files that had been renamed.
• src/hg/htdocs/images/internal_bg1.jpg
  • lines changed 0, context: html, text, full: html, text
    Jabico produced background image.
• src/hg/htdocs/inc/global-nav-bar.inc
  • lines changed 4, context: html, text, full: html, text
    remove extra hgTracks link
  • lines changed 88, context: html, text, full: html, text
    Removed files that had been renamed.
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 88, context: html, text, full: html, text
    Renamed this file using camelCase.
• src/hg/htdocs/style/nice_menu.css
  • lines changed 1, context: html, text, full: html, text
    Small edit due to file name change.
  • lines changed 9, context: html, text, full: html, text
    Changed style to make navigation items left aligned, instead of center. Added some left margin so the home icon is not all the way against the left of the page.
  • lines changed 4, context: html, text, full: html, text
    Made menu height shorter by 4px. Changed toppadding to list items so they are vertically centered. Added a small margin to bottom of menu, so text on page would not be so close.
  • lines changed 1, context: html, text, full: html, text
    Since the blue bar was shortened by a couple pixels, the drop down menus, when they appeared, were too low/not aligned with the botton of the blue bar. Fixed that.
• src/hg/htdocs/training.html
  • lines changed 1, context: html, text, full: html, text
    corrected Open Helix link
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v268
• src/hg/inc/wikiLink.h
  • lines changed 3, context: html, text, full: html, text
    After signup return to returnto URL
  • lines changed 3, context: html, text, full: html, text
    iFinished new hgSession welcome and account info UI change.
• src/hg/js/hgVarAnnogrator.js
  • lines changed 38, context: html, text, full: html, text
    Larry refactored hgCustom's loading image and message to ajax.js,so use that in hgVarAnnogrator.js instead of copied hgCustom code.
    
  • lines changed 53, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): UI seems to work on IEand Chrome now too, not just FireFox. Lessons learned: 1. event bubbling
    behavior is unique to each browser; 2. If there's a jquery way to do it,
    use jquery.
    
  • lines changed 1, context: html, text, full: html, text
    Typo fix.
• src/hg/js/jquery.plugins.js
  • lines changed 1, context: html, text, full: html, text
    Turned on superfish arrow markup. I.e. little arrows will now appear to the right of menu text signifying that it is a dropdown menu. Will be getting rid of the + signs on the left of the menu items.
• src/hg/js/subCfg.js
  • lines changed 5, context: html, text, full: html, text
    Bug #8048: Fix suggested by Tim: add a class to ldUi's inversion checkboxes,and detect that class when marking changes in subCfg.js. Also found an slSort
    that was missing & for its first arg, resulting in weird sorting of subtracks
    for inversion checkbox display.
    
• src/hg/lib/bbiChroms.as
  • lines changed 1, context: html, text, full: html, text
    Tweaking column name to be consistent with prior BAM usage & code.
• src/hg/lib/bbiChroms.sql
  • lines changed 2, context: html, text, full: html, text
    Tweaking column name to be consistent with prior BAM usage & code.
• src/hg/lib/fileUi.c
  • lines changed 1, context: html, text, full: html, text
    open RESTRICTED link in a new window and use relative link (#7842)
• src/hg/lib/hdb.c
  • lines changed 44, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/lib/ncbiIncidentDb.as
  • lines changed 9, context: html, text, full: html, text
    replaced by grcIncidentDb.as
• src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
  • lines changed 36, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/lib/wikiLink.c
  • lines changed 26, context: html, text, full: html, text
    After signup return to returnto URL
  • lines changed 19, context: html, text, full: html, text
    iFinished new hgSession welcome and account info UI change.
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 27, context: html, text, full: html, text
    joinerCheck clean and in the pushQ
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 12, context: html, text, full: html, text
    add quality table creation procedure
  • lines changed 33, context: html, text, full: html, text
    adding search rules for assembly and Ensembl Gene Scaffold tracks
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release3.notes
  • lines changed 434, context: html, text, full: html, text
    Updated factor ordering and naming in html. Also updated html methods section regarding cells using specific protocols. Redmine #7510.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release5.notes
  • lines changed 10, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 28, context: html, text, full: html, text
    joinerCheck clean and in the pushQ
• src/hg/makeDb/doc/hg18.txt
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 37, context: html, text, full: html, text
    add exoniphy for ucsc gene build (#7045)
  • lines changed 243, context: html, text, full: html, text
    load of maf frames data for 60-way alignment
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 61, context: html, text, full: html, text
    some progress on mm10 UCSC genes (#7045)
  • lines changed 12, context: html, text, full: html, text
    incremental UCSC genes progress
  • lines changed 36, context: html, text, full: html, text
    w00t! made it all the way through... though bypassed some things.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 27, context: html, text, full: html, text
    genbank.mrna.xeno.load is way too much for obscure assemblies, especially scaffold assemblies
  • lines changed 1, context: html, text, full: html, text
    and need to explicitly turn off genbank.mrna.xeno.load when not wanted
  • lines changed 13, context: html, text, full: html, text
    reversing some of Hiram's over-enthusiastic abandoning of xeno mrna
• src/hg/makeDb/trackDb/chicken/galGal4/gap.html
  • lines changed 59, context: html, text, full: html, text
    correct contents to match reality
  • lines changed 22, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/chicken/galGal4/gold.html
  • lines changed 9, context: html, text, full: html, text
    correct contents to match reality
  • lines changed 26, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/cow/bosTau7/gap.html
  • lines changed 41, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/cow/bosTau7/gold.html
  • lines changed 36, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Added appropriate override sections so mm9/mm10 would be 'named' Chain/Net tracks in appropriate assemblies (redmine #6044)
  • lines changed 6, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Search prefix is either JH or GL.
  • lines changed 1, context: html, text, full: html, text
    Change '\.1' to '\.[0-9]
  • lines changed 2, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added appropriate override sections so mm9/mm10 would be 'named' Chain/Net tracks in appropriate assemblies (redmine #6044)
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 13, context: html, text, full: html, text
    Added typeOfTerm for type promoter to fix error in cvValidate. Term is only used in hg18.
  • lines changed 26, context: html, text, full: html, text
    Fixing blood vessel cells in cv
  • lines changed 3, context: html, text, full: html, text
    updating description for ENSEMBL views. At the request of CSHL
  • lines changed 18, context: html, text, full: html, text
    Adding epithelium changes to CV
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 34, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/ensemblGeneScaffold.html
  • lines changed 34, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/est.html
  • lines changed 77, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 47, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 536, context: html, text, full: html, text
    making patch for UwAffy Exon after moving out the file in an earlier commit from trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.patch.ra
  • lines changed 530, context: html, text, full: html, text
    making patch for UwAffy Exon after moving out the file in an earlier commit from trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.ra
  • lines changed 532, context: html, text, full: html, text
    loading in patch for affy Rna Seq
  • lines changed 1, context: html, text, full: html, text
    making patch for UwAffy Exon after moving out the file in an earlier commit from trackDb.wgEncode.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2192, context: html, text, full: html, text
    adding in new ExonsDeNovo view
  • lines changed 163, context: html, text, full: html, text
    added in the last of the Nhek cells exon denovos
  • lines changed 82, context: html, text, full: html, text
    more stragglers to load exons denovo
  • lines changed 101, context: html, text, full: html, text
    removed useless items
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    revoked a contig view that was a dupe of another one, but the names changed earlier on, so there was no collision detected.
  • lines changed 423, context: html, text, full: html, text
    removed useless items
  • lines changed 643, context: html, text, full: html, text
    mass rename of all unrelease raw signals
  • lines changed 203, context: html, text, full: html, text
    renaming for corrections to expId1090 and 1740
  • lines changed 21, context: html, text, full: html, text
    correcting the replicates in the metadata number
  • lines changed 341, context: html, text, full: html, text
    Trying to remove all cases of PlusRawSiganl and MinsuRawSignal
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 49, context: html, text, full: html, text
    added in missing metaData
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 369, context: html, text, full: html, text
    Changing from raw signals to signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 106, context: html, text, full: html, text
    updateing labExpIds for UwDgf
  • lines changed 10, context: html, text, full: html, text
    filled in hand labExpIds, and other metaData fixes
  • lines changed 2, context: html, text, full: html, text
    filling in the last hole
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 823, context: html, text, full: html, text
    filled in hand labExpIds, and other metaData fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 874, context: html, text, full: html, text
    filling in missing labExpIds
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    filled in hand labExpIds, and other metaData fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 544, context: html, text, full: html, text
    updating labExpIds for uwtfbs
  • lines changed 43, context: html, text, full: html, text
    filled in hand labExpIds, and other metaData fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 22896, context: html, text, full: html, text
    Staging CSH Long RNA-seq (release2), redmine# 5698
  • lines changed 2373, context: html, text, full: html, text
    incorporating changes Matt made to the metadata to hgwbeta for CSHL Long, redmine# 5698, note# 86.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
  • lines changed 99, context: html, text, full: html, text
    preparing for release of Release 2 of the Txn Factor ChIP track, redmine #7462
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
  • lines changed 99, context: html, text, full: html, text
    preparing for release of Release 2 of the Txn Factor ChIP track, redmine #7462
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls): adding trackDb entryand code support for database table that has per-chromosome fileNames
    because 1000 Genomes provides enormous per-chromosome files.
    This is very similar to code support for per-chromosome BAM.
    To-do: refactor out bam-specific code and trackDbCustom.c's
    tdbBigFileName to use bbiNameFromSettingOrTable(Chrom).
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    actually realized the release tags were part of gencode. Changed to public for GENCODE super track release, redmine# 7633
  • lines changed 2, context: html, text, full: html, text
    Adding a patch to change label from Signal to Raw Signal
  • lines changed 2, context: html, text, full: html, text
    Staging CSH Long RNA-seq (release2), redmine# 5698
  • lines changed 2, context: html, text, full: html, text
    starting a release5 FINAL for UwHistone
  • lines changed 1, context: html, text, full: html, text
    moving over to .patch.ra instead for uw histone
  • lines changed 2, context: html, text, full: html, text
    adding track to corrent tag errors, and also promote cell time from tier 2.5 to tier 2.
  • lines changed 3, context: html, text, full: html, text
    preparing for release of Release 2 of the Txn Factor ChIP track, redmine #7462
  • lines changed 2, context: html, text, full: html, text
    corrected mispelling
  • lines changed 2, context: html, text, full: html, text
    releasing release 2 of the Txn Factor ChIP track, redmine #7462
  • lines changed 3, context: html, text, full: html, text
    adding in patch stub for affy rna chip
  • lines changed 2, context: html, text, full: html, text
    loading in patch for affy Rna Seq
  • lines changed 1, context: html, text, full: html, text
    adding alpha for methyl rrbs
  • lines changed 2, context: html, text, full: html, text
    fixing raw signal labels (#383), fixing tags that start with a numeral, e.g. 1K562 to t1K562 (#6813)
  • lines changed 2, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813, and HepG2 label was fixed to be labeled correctly as a Tier2, P in Prostate was made lowercase, space at the end of the shortLabels was removed
  • lines changed 1, context: html, text, full: html, text
    I left in the .patch.ra instead of copying the .patch.ra over the .ra and leaving in the include for the .ra instead
• src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.ra
  • lines changed 17, context: html, text, full: html, text
    Replace numeric tags. Redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.patch.ra
  • lines changed 249, context: html, text, full: html, text
    adding in patch stub for affy rna chip
  • lines changed 27, context: html, text, full: html, text
    loading in patch for affy Rna Seq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 29, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813, and HepG2 label was fixed to be labeled correctly as a Tier2, P in Prostate was made lowercase, space at the end of the shortLabels was removed
  • lines changed 28, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra
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    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
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    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 5, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 3, context: html, text, full: html, text
    fixing the html for vanessa
  • lines changed 29, context: html, text, full: html, text
    correcting html errors
  • lines changed 3, context: html, text, full: html, text
    Fixing release notes for Vanessa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 387, context: html, text, full: html, text
    correct some defaults and removed origAssembly lines
  • lines changed 12, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 12, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 12, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
  • lines changed 733, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra
  • lines changed 132, context: html, text, full: html, text
    Removing the origAssembly
  • lines changed 4, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.html
  • lines changed 32, context: html, text, full: html, text
    filling in missing labExpIds
  • lines changed 3, context: html, text, full: html, text
    fixing trackDb and html for mass rename
  • lines changed 5, context: html, text, full: html, text
    Adding the Carrie changes to the methods section for this trackDB
  • lines changed 6, context: html, text, full: html, text
    Fixing merge conflict
  • lines changed 9, context: html, text, full: html, text
    Trying to remove all cases of PlusRawSiganl and MinsuRawSignal
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 7, context: html, text, full: html, text
    revoked a contig view that was a dupe of another one, but the names changed earlier on, so there was no collision detected.
  • lines changed 549, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
  • lines changed 560, context: html, text, full: html, text
    fixing trackDb and html for mass rename
  • lines changed 1, context: html, text, full: html, text
    Adding the Carrie changes to the methods section for this trackDB
  • lines changed 807, context: html, text, full: html, text
    Changing Plus Raw Signal to Plus Signal
  • lines changed 24, context: html, text, full: html, text
    forgot to add trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
  • lines changed 1, context: html, text, full: html, text
    correcting the indent for Duke Afft Exon release 3
  • lines changed 154, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813, and promote cells to tier2 and better alphabetizing, redmine #3584
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 1, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Changing dense to pack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.ra
  • lines changed 2, context: html, text, full: html, text
    Changing dense to pack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release2.ra
  • lines changed 6, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 6, context: html, text, full: html, text
    Removing numberic tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 2, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 2, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 1, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 2, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 181, context: html, text, full: html, text
    promoting the cell lines from 2.5 to 2 in these tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 2, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 5, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.ra
  • lines changed 5, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 5, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 31, context: html, text, full: html, text
    promoting the cell lines from 2.5 to 2 in these tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 5, context: html, text, full: html, text
    promoting the cell lines from 2.5 to 2 in these tracks
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
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    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra
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    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
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    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 0, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 2, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
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    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.patch.ra
  • lines changed 1847, context: html, text, full: html, text
    adding track to corrent tag errors, and also promote cell time from tier 2.5 to tier 2.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 9, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 2, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
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    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
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    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
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    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra
  • lines changed 1, context: html, text, full: html, text
    adding html line to wgEncodeRegTfbsClusteredV2 stanza because with V2, it no longer has the same name as the html file and therefore needs the html line in the trackDb entry, redmine #7462
  • lines changed 1, context: html, text, full: html, text
    making a new release2.html so i can add release notes section for TFBS Clustered, redmine #7462
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release3.ra
  • lines changed 1, context: html, text, full: html, text
    adding html line to TFBS Clustered V2 so that the description will be displayed (already made the change in release2.ra), redmine #7462
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.release2.html
  • lines changed 64, context: html, text, full: html, text
    making a new release2.html so i can add release notes section for TFBS Clustered, redmine #7462
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
  • lines changed 12, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra
  • lines changed 4229, context: html, text, full: html, text
    starting release 4, this commit already has the cell 2.5 -> 2 promotion done.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
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    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 1, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 1, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 1, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
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    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 4, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 3, context: html, text, full: html, text
    Updated factor ordering and naming in html. Also updated html methods section regarding cells using specific protocols. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 5, context: html, text, full: html, text
    Updated factor ordering and naming in html. Also updated html methods section regarding cells using specific protocols. Redmine #7510.
  • lines changed 4, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 4, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 4, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 2, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 2, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 2, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
  • lines changed 3, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.patch.html
  • lines changed 140, context: html, text, full: html, text
    Adding a patch to change label from Signal to Raw Signal
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.patch.ra
  • lines changed 128, context: html, text, full: html, text
    Adding a patch to change label from Signal to Raw Signal
  • lines changed 13, context: html, text, full: html, text
    fixing raw signal labels (#383), fixing tags that start with a numeral, e.g. 1K562 to t1K562 (#6813)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
  • lines changed 19, context: html, text, full: html, text
    I left in the .patch.ra instead of copying the .patch.ra over the .ra and leaving in the include for the .ra instead
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 6, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
  • lines changed 6, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 6, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 6, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 3, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 3, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 3, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 2, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 2, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 2, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indent on publc uncBsuProt
  • lines changed 8, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 0, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
  • lines changed 12, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 13, context: html, text, full: html, text
    Matt's fix to tags starting with numbers, redmine #6813
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 0, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra
  • lines changed 6, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
  • lines changed 3, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 6299, context: html, text, full: html, text
    moving over to .patch.ra instead for uw histone
  • lines changed 54, context: html, text, full: html, text
    fixing matrix and defaults
  • lines changed 12, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 12, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 12, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.ra
  • lines changed 6299, context: html, text, full: html, text
    starting a release5 FINAL for UwHistone
  • lines changed 6299, context: html, text, full: html, text
    moving over to .patch.ra instead for uw histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 0, context: html, text, full: html, text
    correcting indents on the trackDb.ra files
  • lines changed 0, context: html, text, full: html, text
    Revert "correcting indents on the trackDb.ra files"need to check why 50 lines disappeared.
    This reverts commit 3a48c28ef2cd3aa394f43881f9f4caa68ad8e96f.
    
  • lines changed 0, context: html, text, full: html, text
    indents for reals this time, the extra deleteions were due to white space collapsing from two newlines to one, and 6 lines of comments i manually eliminated to fix a trackDb problem
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
  • lines changed 1, context: html, text, full: html, text
    fixing indents in public tracks
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/intronEst.html
  • lines changed 78, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/mgcFullMrna.html
  • lines changed 43, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
  • lines changed 27, context: html, text, full: html, text
    removed human datasets specific content, changed genome to mm9 from hg19 etc, copied alignement definition from human SydhRnaSeq description
  • lines changed 1, context: html, text, full: html, text
    remove custom tag content from the copyover from human alighment definition, see note 29 redmine #829, Philip replied that there is no custom tag in this track
  • lines changed 1, context: html, text, full: html, text
    clean up desp
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    remove RNAExtract column from sort order
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 5, context: html, text, full: html, text
    Fixed tag to be alphanumeric.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 59, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/ncbiIncidentDb.html
  • lines changed 26, context: html, text, full: html, text
    replaced by grcIncidentDb.html redmine 7978
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 79, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/rat/rn5/gap.html
  • lines changed 54, context: html, text, full: html, text
    correct contents to better match reality
  • lines changed 23, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/rat/rn5/gold.html
  • lines changed 5, context: html, text, full: html, text
    correct contents to better match reality
  • lines changed 33, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/refGene.html
  • lines changed 53, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/refGene.new.html
  • lines changed 62, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 83, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/tenrec/echTel1/gap.html
  • lines changed 16, context: html, text, full: html, text
    override global gap.html
  • lines changed 16, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    override global gap.html
• src/hg/makeDb/trackDb/tenrec/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/tenrec/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    add search rule for gold table and therefore assembly track
  • lines changed 6, context: html, text, full: html, text
    search rule for ensemblGeneScaffold almost works
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
  • lines changed 51, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    removing ncbiIncidentDb track definition, replaced by grcIncidentDb redmine 7978
• src/hg/makeDb/trackDb/turtle/chrPic1/gap.html
  • lines changed 59, context: html, text, full: html, text
    corrected contents to match reality
  • lines changed 21, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/turtle/chrPic1/gold.html
  • lines changed 4, context: html, text, full: html, text
    corrected contents to match reality
  • lines changed 24, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes appropriate to adding chain/net tracks for the new assemblies: bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/windowmaskerSdust.html
  • lines changed 21, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 66, context: html, text, full: html, text
    Fixed html formatting. Made various corrections. Part of QA of new assembly releases bosTau7 (redmine #6044), chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269).
• src/hg/pslCDnaFilter/cDnaAligns.c
  • lines changed 2, context: html, text, full: html, text
    added check for inconsistent qSizes in a PSL
• src/hg/pslCDnaFilter/tests/expected/inconsistentQSizeTest.err
  • lines changed 1, context: html, text, full: html, text
    added check for inconsistent qSizes in a PSL
• src/hg/pslCDnaFilter/tests/input/inconsistentQSize.psl
  • lines changed 2, context: html, text, full: html, text
    added check for inconsistent qSizes in a PSL
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    added check for inconsistent qSizes in a PSL
• src/hg/utils/automation/HgDb.pm
  • lines changed 49, context: html, text, full: html, text
    refactor conf file loading code into loadConfFile so we can use it elsewhere
• src/hg/utils/automation/loadCosmic.pl
  • lines changed 14, context: html, text, full: html, text
    add row to trackVersion
• src/inc/annoFormatter.h
  • lines changed 8, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
  • lines changed 15, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/inc/annoOption.h
  • lines changed 22, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/inc/annoStreamer.h
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/inc/options.h
  • lines changed 2, context: html, text, full: html, text
    options.h depends on common.h because it uses boolean.
• src/lib/annoFormatTab.c
  • lines changed 34, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/annoFormatter.c
  • lines changed 99, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/lib/annoGratorQuery.c
  • lines changed 12, context: html, text, full: html, text
    Refactoring for #6152: instead of having each formatter do its owncollection of rows, annoGratorQueryExecute should collect the rows
    and pass them to each formatter.
    
• src/lib/annoOption.c
  • lines changed 97, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/lib/annoStreamVcf.c
  • lines changed 8, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/annoStreamer.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added getHeader methodto annoStreamer so formatters can include primary source's header in
    output -- header is a crucial part of some formats e.g. VCF.
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Refactoring for #6152: there's nothing formatter-specific about annoFormatterOption,so move it out into independent annoOption.
    
• src/utils/qa/qaGbTracks
  • lines changed 1, context: html, text, full: html, text
    Added a missing parenthesis.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v268 final build
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 3, context: html, text, full: html, text
    One final touchup also recommended by Hiram.
  • lines changed 2, context: html, text, full: html, text
    Hiram noticed that autoincrement was missing from the userDb, among others. Hopefully this correction is the last one for redmine 8036.
  • lines changed 17, context: html, text, full: html, text
    Little by little. Can't use 'REPLACE' option on tables without unique keys. So the 5 tables without unique keys (even though it seems like they should get unique keys) are being reverted to the drop/create/insert logic of old.

• lines changed: 68434
• files changed: 396