All File Changes

v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293

• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/makk
  • lines changed 3, context: html, text, full: html, text
    Adding script to copy into production.
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c
  • lines changed 62, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/edwFixCshlSpikeins.c
  • lines changed 77, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/edwFixGbb2.c
  • lines changed 12, context: html, text, full: html, text
    Simplified to avoid a bug.
  • lines changed 49, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/edwFixRenamed.c
  • lines changed 101, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/edwFixReplaced.c
  • lines changed 284, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRevoked/edwFixRevoked.c
  • lines changed 90, context: html, text, full: html, text
    Somehow this stray got lost in directory move.
• src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/edwFixTechRep1.c
  • lines changed 72, context: html, text, full: html, text
    Patch to pull paired_end and technical_replicate out of edwFile and into the appropriate columns of edwValidFile now applied.
  • lines changed 72, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/makefile
  • lines changed 4, context: html, text, full: html, text
    Patch to pull paired_end and technical_replicate out of edwFile and into the appropriate columns of edwValidFile now applied.
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c
  • lines changed 26, context: html, text, full: html, text
    Moving edwMakeTempFastqSample to library where it can be shared.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c
  • lines changed 120, context: html, text, full: html, text
    Starting to work on program to check read pairing for fastqs. It is maybe 1/3 baked now.
  • lines changed 70, context: html, text, full: html, text
    Further work, maybe 2/3rds baked now.
  • lines changed 168, context: html, text, full: html, text
    Program to add pairedEnd qa seems to work.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to work on program to check read pairing for fastqs. It is maybe 1/3 baked now.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makk
  • lines changed 3, context: html, text, full: html, text
    Script to copy exe to production added.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 2, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makk
  • lines changed 3, context: html, text, full: html, text
    Adding script to copy into production.
• src/hg/encode3/encodeDataWarehouse/fix/README
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/edwFixAddFastq.c
  • lines changed 47, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makk
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/edwFixBasesInSample.c
  • lines changed 62, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/edwFixBzip.c
  • lines changed 73, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/edwFixCshlSpikeins.c
  • lines changed 77, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/edwFixGbb2.c
  • lines changed 49, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/edwFixGtfBigBed.c
  • lines changed 134, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/edwFixQualsAtPos.c
  • lines changed 73, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makk
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/edwFixRenamed.c
  • lines changed 101, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c
  • lines changed 284, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/edwFixRevoked.c
  • lines changed 90, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/edwFixTechRep1.c
  • lines changed 72, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Moving edwMakeTempFastqSample to library where it can be shared.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 4, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 74, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 37, context: html, text, full: html, text
    Adding to tables that get records deleted when a file needs revalidation. Moving edwMakeTempfFastqSample here where it can be shared.
  • lines changed 1, context: html, text, full: html, text
    INcreasing buffer size for sql query in edwFileAllIntactBetween.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 4, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 15, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 21, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 178, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 3, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 17, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Adding technicalReplicate and pairedEnd to vf view.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 3, context: html, text, full: html, text
    Fixing a dependency that broke parallel make (thanks Jonathan for finding!) and using ${MAKE} instead of make so that parallel make won't warn about 'jobserver unavailable'.
  • lines changed 1, context: html, text, full: html, text
    A change that will hopefully make the build utils work again.
  • lines changed 5, context: html, text, full: html, text
    allow encodeDataWarehouse to participate in the daily build
  • lines changed 1, context: html, text, full: html, text
    Adding a missing dependency (cgi depends on edwLib) in hopes that it prevents sporadic errors from ld reading nonsense.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/makefile
  • lines changed 3, context: html, text, full: html, text
    Program to build a table based on ENCODED experiments seems to work.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 99, context: html, text, full: html, text
    Program to build a table based on ENCODED experiments seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/README
  • lines changed 3, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c
  • lines changed 136, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makefile
  • lines changed 3, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makk
  • lines changed 4, context: html, text, full: html, text
    Script to copy exe to production added.
• src/hg/genePredToMafFrames/orgGenes.c
  • lines changed 1, context: html, text, full: html, text
    remove erroneous subtraction of 1 from end coordinate. Fixs problemwith maf blocks of size 1 not being annotated.
    
• src/hg/hgTables/gffOut.c
  • lines changed 32, context: html, text, full: html, text
    fixes #12274. Fixes a new problem in hgTables caused by a recent bugfix. This makes it super specific so that even the exonCount, exonStarts, and exonEnds match.
  • lines changed 1, context: html, text, full: html, text
    oops, removing comment
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 25, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/hg/hgTracks/factorSource.c
  • lines changed 3, context: html, text, full: html, text
    Enable motif display in dense mode. refs #9092
  • lines changed 60, context: html, text, full: html, text
    Add mapping table to factorSource track (and peakCluster track details) that links factor (HGNC gene ID) to canonical motif in motif table and PWM. refs #9092
  • lines changed 4, context: html, text, full: html, text
    Undo scoring tweak for qvalue scores. Better to fix data. refs #9092
  • lines changed 6, context: html, text, full: html, text
    Revert to no motif display in dense mode for now. Change Motif section label as per QA to clarify it matches strand. refs #9092
• src/hg/hgTracks/pubsTracks.c
  • lines changed 4, context: html, text, full: html, text
    fixing bug that appeared when two pubs traks were activated
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fixed typo in comment
  • lines changed 3, context: html, text, full: html, text
    fixing simple typos in comments
• src/hg/hgVai/hgVai.c
  • lines changed 47, context: html, text, full: html, text
    Added a couple ENCODE Regulation summary tracks to hgVai. refs #11461
  • lines changed 3, context: html, text, full: html, text
    Finally added hgTrackUi links for tracks offered by hgVai. Thanks for the prod, Jonathan! refs #11461
  • lines changed 47, context: html, text, full: html, text
    Revert "Added a couple ENCODE Regulation summary tracks to hgVai. refs #11461"This reverts commit c65b04d176ad125c1eddd777fb8befd481bdba2c.
    I decided that hgVai's support for regulatory tracks is not sufficient to roll
    out to the RR because annoFormatVep isn't yet smart enough to add regulatory
    consequence SO term (regulatory_region_variant) when one or more of these overlap.
    Also, there really should be some filtering - I suspect the false positive rate
    will be too high otherwise because the Tfbs cover 1/8th of the genome. The next
    release to the RR is not until Jan. 21, more than a month from now. I'll bring
    this back after the v293 build is tagged.
    refs #11461
    
• src/hg/hgc/peakClusters.c
  • lines changed 20, context: html, text, full: html, text
    Add mapping table to factorSource track (and peakCluster track details) that links factor (HGNC gene ID) to canonical motif in motif table and PWM. refs #9092
  • lines changed 2, context: html, text, full: html, text
    Undo scoring tweak for qvalue scores. Better to fix data. refs #9092
• src/hg/hgc/regMotif.c
  • lines changed 1, context: html, text, full: html, text
    Revert to no motif display in dense mode for now. Change Motif section label as per QA to clarify it matches strand. refs #9092
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 3, context: html, text, full: html, text
    Adding new links to new ENCODE File Formats page, (and correcting a ENCODE FAQ question so link works from reset cart) refs #12203
• src/hg/htdocs/ENCODE/fileFormats.html
  • lines changed 289, context: html, text, full: html, text
    Adding new ENCODE file formats page, per Mike Pazin request, refs #12203
  • lines changed 18, context: html, text, full: html, text
    Changing we --> the consortium, other corrections, and removing some white space, refs #12203
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Adding new links to new ENCODE File Formats page, (and correcting a ENCODE FAQ question so link works from reset cart) refs #12203
• src/hg/htdocs/cite.html
  • lines changed 9, context: html, text, full: html, text
    Updated GB DB citation to Karolchik et al.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    Adding hyperlink and hyphen per code review. refs #12250
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 8, context: html, text, full: html, text
    Updated 2013 Karolchik + Raney citations.
• src/hg/htdocs/images/mapAustralia.jpg
  • lines changed 0, context: html, text, full: html, text
    Added a small map to each section. Alphabetized continents. Added disclaimer at top to emphasize fact that these are mirrors not maintained or supported by UCSC. Map files are included in this commit, refs #12175
• src/hg/htdocs/images/mapEuro.jpg
  • lines changed 0, context: html, text, full: html, text
    Added a small map to each section. Alphabetized continents. Added disclaimer at top to emphasize fact that these are mirrors not maintained or supported by UCSC. Map files are included in this commit, refs #12175
• src/hg/htdocs/images/mapNAmer.jpg
  • lines changed 0, context: html, text, full: html, text
    Added a small map to each section. Alphabetized continents. Added disclaimer at top to emphasize fact that these are mirrors not maintained or supported by UCSC. Map files are included in this commit, refs #12175
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    Adding hyperlink and hyphen per code review. refs #12250
• src/hg/htdocs/mirror.html
  • lines changed 147, context: html, text, full: html, text
    Organized mirror page by geographical location, plus fixed some other links, refs #12175
  • lines changed 102, context: html, text, full: html, text
    Added a small map to each section. Alphabetized continents. Added disclaimer at top to emphasize fact that these are mirrors not maintained or supported by UCSC. Map files are included in this commit, refs #12175
• src/hg/htdocs/style/nice_menu.css
  • lines changed 1, context: html, text, full: html, text
    Fix for disappearing menu text (white on white) described in redmine #11745
  • lines changed 5, context: html, text, full: html, text
    Fix 'dark-blue on pretty-blue' problem in some IE10 browsers. Redmine 11745.
• src/hg/inc/jsHelper.h
  • lines changed 59, context: html, text, full: html, text
    Adding a bunch of functions to help work with output of jsParse.
  • lines changed 124, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 6, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v293
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    Fixed edge case bug in history that Max found. Redmine 12253.
• src/hg/lib/jsHelper.c
  • lines changed 270, context: html, text, full: html, text
    Adding a bunch of functions to help work with output of jsParse.
  • lines changed 682, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 14, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/hg/lib/pgSnp.c
  • lines changed 37, context: html, text, full: html, text
    Support for UWash Exome Variants to decifer 'TAC' allele counts. Redmine #9329.
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    don't crash if given file names with ':' in them. Fixes #12267
• src/hg/makeDb/doc/go.txt
  • lines changed 10, context: html, text, full: html, text
    update GO database
• src/hg/makeDb/doc/hg19.txt
  • lines changed 143, context: html, text, full: html, text
    Added EVS Variants (release alpha) for consideration. Redmine #9329.
  • lines changed 16, context: html, text, full: html, text
    pubsBingBlat track doc
• src/hg/makeDb/doc/mm10.txt
  • lines changed 9, context: html, text, full: html, text
    Reloading jaxQtl after sorting bed file. refs #7040
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    switch to new hg19 ccds version
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 8, context: html, text, full: html, text
    don't create lock files when using initialLoad to load a database. Thedatabase will still me locked. #10357
    
• src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c
  • lines changed 4, context: html, text, full: html, text
    explain how to load sorted bed files refs #7040
• src/hg/makeDb/schema/all.joiner
  • lines changed 15, context: html, text, full: html, text
    joiner file for pubsBing
  • lines changed 6, context: html, text, full: html, text
    Adding ucsf brain methyl tables to tables ignored. refs #2540
• src/hg/makeDb/trackDb/apis/all_est.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/apis/all_mrna.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/apis/chainDm1.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/apis/intronEst.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/apis/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/apis/xenoMrna.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/blastDm1FB.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on apiMel track description pages
• src/hg/makeDb/trackDb/blastDm2FB.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/blastHg16KG.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/blastHg18KG.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/blatFr1.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/cat/felCat3/description.html
  • lines changed 4, context: html, text, full: html, text
    Correcting links on cat (felCat3) track description pages
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 8, context: html, text, full: html, text
    Correcting links on cat (felCat3) track description pages
• src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
  • lines changed 5, context: html, text, full: html, text
    Correcting links on cat (felCat3) track description pages
• src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html
  • lines changed 2, context: html, text, full: html, text
    Correcting links on cat (felCat3) track description pages
• src/hg/makeDb/trackDb/chainDm2.html
  • lines changed 4, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/chainDm3.html
  • lines changed 1, context: html, text, full: html, text
    Changing links for both droAna assemblies
  • lines changed 3, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/chimp/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/axtNetHg16.html
  • lines changed 3, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/ctgPos.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/gold.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/humanDels.html
  • lines changed 5, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on various chimp (panTro1) track description pages
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some links on dog track description pages
• src/hg/makeDb/trackDb/dog/canFam3/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some links on dog track description pages
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
  • lines changed 4, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/drosophila/droAna1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/drosophila/droAna2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/drosophila/droAna2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/drosophila/droAna2/gold.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/drosophila/mrna.html
  • lines changed 1, context: html, text, full: html, text
    Changing links for both droAna assemblies
  • lines changed 2, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/drosophila/refGene.html
  • lines changed 3, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/drosophila/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/drosophila/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    Changing links for both droAna assemblies
  • lines changed 2, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/drosophila/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing links for both droAna assemblies
  • lines changed 1, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some links on gibbon track description pages
• src/hg/makeDb/trackDb/gibbon/nomLeu2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some links on gibbon track description pages
• src/hg/makeDb/trackDb/gibbon/nomLeu2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some links on gibbon track description pages
• src/hg/makeDb/trackDb/horse/equCab1/description.html
  • lines changed 2, context: html, text, full: html, text
    Correcting links on horse (equCab1) track description pages
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Added EVS Variants (release alpha) for consideration. Redmine #9329.
  • lines changed 4, context: html, text, full: html, text
    Removed stanza for non-existent snpArray track, refs #12227
  • lines changed 10, context: html, text, full: html, text
    adding preliminary gene interactions track to pub group
  • lines changed 1, context: html, text, full: html, text
    fixing typo
  • lines changed 68, context: html, text, full: html, text
    adding bing and pubs2 test tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Add mapping table to factorSource track (and peakCluster track details) that links factor (HGNC gene ID) to canonical motif in motif table and PWM. refs #9092
  • lines changed 18, context: html, text, full: html, text
    Revert to no motif display in dense mode for now. Change Motif section label as per QA to clarify it matches strand. refs #9092
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    adding bing and pubs2 test tracks
• src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html
  • lines changed 52, context: html, text, full: html, text
    Adding pubmed links to references for UCSF Brain Methylation track, refs #2540
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 6, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 5, context: html, text, full: html, text
    Correcting links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 8, context: html, text, full: html, text
    Correcting links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/nscanGene.html
  • lines changed 6, context: html, text, full: html, text
    Correcting links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html
  • lines changed 5, context: html, text, full: html, text
    Correcting links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/microsat.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on cat (felCat3) track description pages
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on naked mole rat track description pages
• src/hg/makeDb/trackDb/moleRat/hetGla2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on naked mole rat track description pages
• src/hg/makeDb/trackDb/moleRat/hetGla2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on naked mole rat track description pages
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changing release tags for mm10 MGI QTL track, refs #7040
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    jaxQtl names have .[123] suffix add to search rule refs #7040
• src/hg/makeDb/trackDb/netDm2.html
  • lines changed 5, context: html, text, full: html, text
    Changing links for both droAna assemblies
• src/hg/makeDb/trackDb/netDm3.html
  • lines changed 1, context: html, text, full: html, text
    Changing links for both droAna assemblies
  • lines changed 2, context: html, text, full: html, text
    Fixing more links on droAna track description pages
• src/hg/makeDb/trackDb/nscanGene.html
  • lines changed 6, context: html, text, full: html, text
    Fixing some links on turkey track description pages
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/pubsBingBlat.html
  • lines changed 63, context: html, text, full: html, text
    help page for pubsBing track
  • lines changed 14, context: html, text, full: html, text
    changing pubsBingBlat text slightly
• src/hg/makeDb/trackDb/rnaCluster.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some saiBol1 track description page links
• src/hg/makeDb/trackDb/saiBol/saiBol1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some saiBol1 track description page links
• src/hg/makeDb/trackDb/saiBol/saiBol1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some saiBol1 track description page links
• src/hg/makeDb/trackDb/sgpGene.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on horse (equCab1) track description pages
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/shrew/sorAra1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/shrew/sorAra1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/sibTxGraph.html
  • lines changed 4, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/simpleRepeat.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/squirrel/speTri2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/squirrel/speTri2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
• src/hg/makeDb/trackDb/squirt/all_est.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/all_mrna.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/ci2/description.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/gap.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/intronEst.html
  • lines changed 3, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/refGene.html
  • lines changed 3, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/xenoMrna.html
  • lines changed 3, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/squirt/xenoRefGene.html
  • lines changed 2, context: html, text, full: html, text
    Correcting links on squirt track description pages
• src/hg/makeDb/trackDb/tRNAs.html
  • lines changed 31, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Add mapping table to factorSource track (and peakCluster track details) that links factor (HGNC gene ID) to canonical motif in motif table and PWM. refs #9092
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    tiny longLabel change
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 2, context: html, text, full: html, text
    Fixing some links on turkey track description pages
• src/hg/makeDb/trackDb/twinscan.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/blastCe4SG.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/blastCe6SG.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/caeJap1/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/caeJap1/description.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/caeRem3/description.html
  • lines changed 4, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 2, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/caeRem3/gap.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/caeRem3/gold.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/cb1/blastzCe1.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/cb1/ce1Chain.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/cb3/description.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 2, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/cb3/gap.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/cb3/gold.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce10/description.html
  • lines changed 3, context: html, text, full: html, text
    Correcting more links on worm track description pages
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce10/gap.html
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/ce10/gold.html
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 1, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce2/blastzSelf.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
  • lines changed 6, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
  • lines changed 4, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/description.html
  • lines changed 1, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce2/netCb1.html
  • lines changed 6, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/picTar.html
  • lines changed 4, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/sangerGenefinder.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce2/wabaCbr.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce4/description.html
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
  • lines changed 1, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce4/gap.html
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/ce4/gold.html
  • lines changed 1, context: html, text, full: html, text
    Correcting more links on worm track description pages
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 4, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
  • lines changed 7, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCaePb2.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCb3.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCe4.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainCe6.html
  • lines changed 4, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
  • lines changed 5, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/chainSelf.html
  • lines changed 4, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/est.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/htmlPages
  • lines changed 187, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 187, context: html, text, full: html, text
    Removed temp file I accidentally added
• src/hg/makeDb/trackDb/worm/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/mrna.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCaeJap1.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCaePb1.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCaePb2.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCaeRem2.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCaeRem3.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCb3.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCe4.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netCe6.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/netPriPac1.html
  • lines changed 3, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/worm/nucleosome.html
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/nucleosomeControlCoverage.html
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/nucleosomeDensity.html
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/nucleosomeStringency.html
  • lines changed 2, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/refGene.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
  • lines changed 1, context: html, text, full: html, text
    Correcting even more links I missed on worm track description pages
• src/hg/makeDb/trackDb/worm/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    correcting links on track description pages for a number of worm species
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing some links on anoCar2 track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 6, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 3, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
  • lines changed 4, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makeDb/trackDb/zebrafish/danRer7/gold.html
  • lines changed 3, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makeDb/trackDb/zebrafish/mgcFullMrna.html
  • lines changed 2, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makeDb/trackDb/zebrafish/mgcGenes.html
  • lines changed 1, context: html, text, full: html, text
    Correcting links on zebrafish track description pages
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    allow encodeDataWarehouse to participate in the daily build
• src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/filt.out
  • lines changed 5, context: html, text, full: html, text
    add a test for repsAsMatch pslCDnaFilter flag
• src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/keep.psl
  • lines changed 11, context: html, text, full: html, text
    add a test for repsAsMatch pslCDnaFilter flag
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    add a test for repsAsMatch pslCDnaFilter flag
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 212, context: html, text, full: html, text
    v74 update refs #12288
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 7, context: html, text, full: html, text
    now creating bigBed and ixx index files for assembly hub use refs #12288
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 89, context: html, text, full: html, text
    changes to makeTableList to cache field names. In preparation for browser box
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 62, context: html, text, full: html, text
    make changes to the login procedures because decipher changed them.
• src/hg/utils/otto/decipher/login.perl
  • lines changed 14, context: html, text, full: html, text
    make changes to the login procedures because decipher changed them.
• src/hg/utils/otto/decipher/validateDecipher.sh
  • lines changed 8, context: html, text, full: html, text
    make changes to the login procedures because decipher changed them.
• src/inc/jsonParse.h
  • lines changed 132, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 1, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/inc/linefile.h
  • lines changed 4, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
• src/lib/annoGratorQuery.c
  • lines changed 21, context: html, text, full: html, text
    In annoGratorQueryExecute, if we're searching a specific region andthe primary source's first item comes from some later chromosome,
    that simply means that the primary source has no items on the
    specified chrom. So instead of passing it to the grators, just
    quit. Also when searching a specific region, if there are no rows
    from the primary source, add a comment to the output(s).
    fixes #12278
    
• src/lib/hmac.c
  • lines changed 2, context: html, text, full: html, text
    Per CR #12255 feedback:Add one more character and initialized all elements to zero
    when declare the hmacStr array:
    
    -char hmacStr[40];
    +char hmacStr[41]="";
    
    -char hmacStr[32];
    +char hmacStr[33]="";
    
  • lines changed 4, context: html, text, full: html, text
    Use cloneStringZ(hmacStr, sizeof(hmacStr)) to null terminate the hmacStr character array safely.
• src/lib/jsonParse.c
  • lines changed 692, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 10, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/lib/linefile.c
  • lines changed 10, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Splitting jsonParse out of jsHelper.
• src/lib/net.c
  • lines changed 16, context: html, text, full: html, text
    net.c dealing with FTP subtleties regarding url-encoding and the leading slash in the path requested
• src/lib/sqlList.c
  • lines changed 44, context: html, text, full: html, text
    these functions should be using dyCannibalize to avoid an extra clone and free that are unneeded. Probably this is very old code from before dyCannibalize was written.
• src/product/README.requirements
  • lines changed 6, context: html, text, full: html, text
    Making some small wording changes based on Code Review, refs #12247
  • lines changed 1, context: html, text, full: html, text
    Adding line about Apache web server under software requirements, refs #12247, #11941
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
  • lines changed 30, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
  • lines changed 1, context: html, text, full: html, text
    Actually using seed.
  • lines changed 103, context: html, text, full: html, text
    Simplifying initial step down to make it give consistent result across read pairs.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v293 final build

• lines changed: 7843
• files changed: 348