CVS changes by file

branch to review (2010-05-18 to 2010-05-25) v232

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.101 lines changed: 2, context: html, text, full: html, text
    fix multiz of therAggr1
  • 1.100 lines changed: 13, context: html, text, full: html, text
    add therAggr1
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.30 lines changed: 1, context: html, text, full: html, text
    fix path for trackDb.ra
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.12 lines changed: 1, context: html, text, full: html, text
    fix path for trackDb.ra
• src/hg/bedSort/makefile
  • 1.9 lines changed: 8, context: html, text, full: html, text
    adding bedSort
• src/hg/encode/DAFs/2.0/renMm9Tfbs.daf
  • 1.1 lines changed: 38, context: html, text, full: html, text
    Add new Daf for Ren Lab submissions
• src/hg/encode/DAFs/2.0/renSample.ddf
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Add new Sample DDF for Ren Lab submissions
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.240 lines changed: 118, context: html, text, full: html, text
    Added tissue types for cell types
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.225 lines changed: 26, context: html, text, full: html, text
    add checking for sex of cell type for BAM's
• src/hg/encode/validateFiles/validateFiles.c
  • 1.42 lines changed: 2, context: html, text, full: html, text
    allow N's in both reference and query if nMatch is on.
• src/hg/hgApi/hgApi.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    change to returning a list
  • 1.1 lines changed: 97, context: html, text, full: html, text
    support a JSON based API to the browser
• src/hg/hgApi/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    support a JSON based API to the browser
• src/hg/hgGenome/import.c
  • 1.21 lines changed: 14, context: html, text, full: html, text
    fixing for Views, and for case of allTracks with null track
• src/hg/hgGetAnn/tests/expected/chrRangePslKeepBin.psl
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Use blatFugu instead of mrna; code now uses all_mrna but that has no bin column in hg15.
• src/hg/hgTables/bigBed.c
  • 1.11 lines changed: 5, context: html, text, full: html, text
    only print out the item count on bigBed's after version 2 when the value is valid
  • 1.10 lines changed: 2, context: html, text, full: html, text
    add primary table and database to schema output
• src/hg/hgTables/correlate.c
  • 1.80 lines changed: 0, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTables/hgTables.c
  • 1.198 lines changed: 3, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
  • 1.197 lines changed: 6, context: html, text, full: html, text
    Fixing crash on regulation group from container track.
• src/hg/hgTables/hgTables.h
  • 1.146 lines changed: 5, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
• src/hg/hgTables/identifiers.c
  • 1.31 lines changed: 1, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTables/mainPage.c
  • 1.153 lines changed: 1, context: html, text, full: html, text
    Add text describing GREAT usage
  • 1.152 lines changed: 2, context: html, text, full: html, text
    Cause Galaxy and GREAT checkboxes to preserve state across filtering, intersecting, etc.
  • 1.151 lines changed: 1, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
• src/hg/hgTables/schema.c
  • 1.65 lines changed: 1, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTables/usage.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Add text describing GREAT usage
• src/hg/hgTracks/bedGraph.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
• src/hg/hgTracks/cds.c
  • 1.107 lines changed: 1, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
• src/hg/hgTracks/container.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/hgTracks.c
  • 1.1648 lines changed: 45, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/hgTracks.h
  • 1.211 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/imageV2.c
  • 1.32 lines changed: 6, context: html, text, full: html, text
    fixup URLs that may have blanks in them, do not quote the whole thing
  • 1.31 lines changed: 11, context: html, text, full: html, text
    Second attempt to allow 'target=' in URL.
  • 1.30 lines changed: 3, context: html, text, full: html, text
    Fix for Harum's sending a target=blank with his link.
• src/hg/hgTracks/simpleTracks.c
  • 1.141 lines changed: 6, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
  • 1.140 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/wigTrack.c
  • 1.112 lines changed: 5, context: html, text, full: html, text
    Making log transform not crash on negative data values.
  • 1.111 lines changed: 48, context: html, text, full: html, text
    Making it so that whiskers mode only sets each pixel once, so it works better in transparent mode.
  • 1.110 lines changed: 16, context: html, text, full: html, text
    Making variable x to hold x1+xOff.
• src/hg/hgc/hgc.c
  • 1.1634 lines changed: 50, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
  • 1.1633 lines changed: 1, context: html, text, full: html, text
    In printTrackHtml, we still need hTableForTrack so that we can find a split table given an unsplit table name (to find out update time).
  • 1.1632 lines changed: 2, context: html, text, full: html, text
    Fixing typo of hTableForTrack when I meant hGetTableForTrack. Fixes problem in mrna/est details display on hg19
  • 1.1631 lines changed: 3, context: html, text, full: html, text
    htcCdnaAliInWindow: hFindSplitTable needs tdb->table, not track name, in order to work for mrna/est.
  • 1.1630 lines changed: 4, context: html, text, full: html, text
    initial code for text2Genome details
  • 1.1629 lines changed: 14, context: html, text, full: html, text
    Making hgc output closing HTML tags that were missing in many cases. Still look to be missing in a few more though. Making a call to printAlignmentsSimple use track rather than table name to keep it like everywhere else.
  • 1.1628 lines changed: 4, context: html, text, full: html, text
    Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention.
  • 1.1627 lines changed: 348, context: html, text, full: html, text
    Making big hgc track dispatch use table instead of track.
  • 1.1626 lines changed: 2, context: html, text, full: html, text
    bolded statement about track needing to be in non-hide mode in order to see it in this grid.
• src/hg/hgc/hgc.h
  • 1.55 lines changed: 4, context: html, text, full: html, text
    initial code for text2Genome details
• src/hg/hgc/makefile
  • 1.68 lines changed: 1, context: html, text, full: html, text
    initial code for text2Genome details
• src/hg/hgc/mgcClick.c
  • 1.34 lines changed: 1, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/peakClusters.c
  • 1.6 lines changed: 37, context: html, text, full: html, text
    Writing out table of cell types and single letter abbreviations on factorSource details page. Removing some debugging.
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention.
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding end to some peakClusters web pages.
• src/hg/hgc/retroClick.c
  • 1.16 lines changed: 13, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/t2g.c
  • 1.5 lines changed: 29, context: html, text, full: html, text
    better position header information
  • 1.4 lines changed: 3, context: html, text, full: html, text
    using style to set font size for abstract
  • 1.3 lines changed: 13, context: html, text, full: html, text
    rearrange heading information in t2g printout
  • 1.2 lines changed: 45, context: html, text, full: html, text
    Adding version information printout
  • 1.1 lines changed: 112, context: html, text, full: html, text
    initial code for text2Genome details
• src/hg/hgc/transMapClick.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/virusClick.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgsqlSwapTables/hgsqlSwapTables.c
  • 1.1 lines changed: 79, context: html, text, full: html, text
    a utility to swap tables with renames while checking for existance
• src/hg/hgsqlSwapTables/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a utility to swap tables with renames while checking for existance
• src/hg/inc/hdb.h
  • 1.171 lines changed: 3, context: html, text, full: html, text
    Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash.
  • 1.170 lines changed: 3, context: html, text, full: html, text
    Adding hGetTrackForTable()
• src/hg/inc/hgFind.h
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global.
• src/hg/inc/hui.h
  • 1.153 lines changed: 4, context: html, text, full: html, text
    Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag.
• src/hg/inc/jksql.h
  • 1.88 lines changed: 3, context: html, text, full: html, text
    add sqlRenameTable
• src/hg/inc/trackDb.h
  • 1.60 lines changed: 5, context: html, text, full: html, text
    Exposing trackDbSettingsFromString and using it in place of raFromString.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Bittner_Multi_cancer.ra
  • 1.2 lines changed: 83, context: html, text, full: html, text
    Added url entries for SU2C datasets which had PubMed IDs known. Turned visibility off on all but 12 Bittner_Multi_cancer clinical values per Jing.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.su2c_processed.ra
  • 1.3 lines changed: 38, context: html, text, full: html, text
    Added url entries for SU2C datasets which had PubMed IDs known. Turned visibility off on all but 12 Bittner_Multi_cancer clinical values per Jing.
• src/hg/js/hui.js
  • 1.56 lines changed: 10, context: html, text, full: html, text
    If one filter box is not selected, then other filterboxes exclude nothing
  • 1.55 lines changed: 1, context: html, text, full: html, text
    Make sure to block new 'exclude' options logic from filterBy boxes that are not filtering subtracks
  • 1.54 lines changed: 66, context: html, text, full: html, text
    Support for excluding inappropriate choices from filterComposite boxes, by graying text.
• src/hg/js/ui.dropdownchecklist.js
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Extra pixels for width so that Safari and Chrom don't add scrollbar
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Added 'Click to select...' title
  • 1.5 lines changed: 59, context: html, text, full: html, text
    Support for excluding inappropriate choices from filterComposite boxes, by graying text.
  • 1.4 lines changed: 500, context: html, text, full: html, text
    Undos wiped out file. Now its back
• src/hg/js/utils.js
  • 1.30 lines changed: 10, context: html, text, full: html, text
    Added support for aryRemoveVals() to subtrack 1 array from another
• src/hg/lib/cart.c
  • 1.120 lines changed: 3, context: html, text, full: html, text
    Making cartWebStart included jquery.js and utils.js. The function that does this already gaurds against multiple inclusion, so this should work.
• src/hg/lib/hdb.c
  • 1.433 lines changed: 18, context: html, text, full: html, text
    hFindTableInfoWithConn: changed split table logic so that we test mrna/all_mrna and est/all_est before checking whether a chrom has been passed in and split table exists. For mrna and est, now we don't want to know if split tables still exist; it confuses other parts of the code.
  • 1.432 lines changed: 9, context: html, text, full: html, text
    makeDbTableToTrackHash should also use tableName from database (hel->name) and add all_mrna/all_est table if an older trackDb doesn't have that setting.
  • 1.431 lines changed: 4, context: html, text, full: html, text
    Making makeTrackSettingsHash use tableName from database rather than track from settings as key, for slightly better backwards compatibility.
  • 1.430 lines changed: 6, context: html, text, full: html, text
    Making findTdbForTable use hTrackForTable before it searches for track. Fixes missing all_mrna table in table browser correlate page.
  • 1.429 lines changed: 65, context: html, text, full: html, text
    Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash.
  • 1.428 lines changed: 49, context: html, text, full: html, text
    Adding hGetTrackForTable()
• src/hg/lib/hgFind.c
  • 1.230 lines changed: 6, context: html, text, full: html, text
    addPslResultToHgp: don't trim initial all_ from table name, we need it now.
  • 1.229 lines changed: 23, context: html, text, full: html, text
    Further work adapting hgFind to separate track and table names.
  • 1.228 lines changed: 3, context: html, text, full: html, text
    Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global.
• src/hg/lib/hui.c
  • 1.294 lines changed: 2, context: html, text, full: html, text
    Back to Filter Composite titles above filter box.
  • 1.293 lines changed: 1, context: html, text, full: html, text
    Changed 'Filter by' to 'Filter items by:' in preparation for distinguishing filterBy from filterComposite
  • 1.292 lines changed: 146, context: html, text, full: html, text
    Fixed the matrix CB initialization problem seen while QAing v231. Also simplified and cleaned up some code by using fully populated membersForAll struct
  • 1.291 lines changed: 3, context: html, text, full: html, text
    Simplifying wording around transparent overlay in user interface.
  • 1.290 lines changed: 18, context: html, text, full: html, text
    Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag.
  • 1.289 lines changed: 6, context: html, text, full: html, text
    Removed offending assert
• src/hg/lib/jksql.c
  • 1.140 lines changed: 8, context: html, text, full: html, text
    add sqlRenameTable
• src/hg/lib/t2gArticle.sql
  • 1.1 lines changed: 15, context: html, text, full: html, text
    initial format of text2Genome data tables
• src/hg/lib/t2gSequence.sql
  • 1.1 lines changed: 8, context: html, text, full: html, text
    initial format of text2Genome data tables
• src/hg/lib/trackDbCustom.c
  • 1.90 lines changed: 2, context: html, text, full: html, text
    Exposing trackDbSettingsFromString and using it in place of raFromString.
  • 1.89 lines changed: 1, context: html, text, full: html, text
    Fixing reference to nonexistant function in comment.
• src/hg/lib/web.c
  • 1.173 lines changed: 3, context: html, text, full: html, text
    Fixed indentation a little
• src/hg/makeDb/doc/calJac3.txt
  • 1.13 lines changed: 180, context: html, text, full: html, text
    13-Way multiz gene frames
  • 1.12 lines changed: 1, context: html, text, full: html, text
    forgot to update makedoc with the final version of the find command I used to change the date for calJac3
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.15 lines changed: 126, context: html, text, full: html, text
    13-Way multiz reading frames
• src/hg/makeDb/doc/hg19.txt
  • 1.113 lines changed: 1, context: html, text, full: html, text
    add a missing mkdir ss
• src/hg/makeDb/mdbUpdate/tests/expected/chipSeqTest1.ra
  • 1.1 lines changed: 191, context: html, text, full: html, text
    First unit test
• src/hg/makeDb/mdbUpdate/tests/input/chipSeqTest1.ra
  • 1.1 lines changed: 191, context: html, text, full: html, text
    First unit test
• src/hg/makeDb/mdbUpdate/tests/makefile
  • 1.1 lines changed: 21, context: html, text, full: html, text
    First unit test
• src/hg/makeDb/schema/all.joiner
  • 1.804 lines changed: 4, context: html, text, full: html, text
    correct db spec for t2g tables and minCheck coverage
  • 1.803 lines changed: 10, context: html, text, full: html, text
    adding text2Genome definitions
  • 1.802 lines changed: 2, context: html, text, full: html, text
    Added mm9 to ucscRetroInfo rule and removed minCheck as not applicable.
• src/hg/makeDb/trackDb/apis/trackDb.ra
  • 1.18 lines changed: 7, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
  • 1.5 lines changed: 2, context: html, text, full: html, text
    13-Way multiz reading frames
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • 1.10 lines changed: 3, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/chimp/bacEndPairs.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/drosophila/dp2/trackDb.ra
  • 1.15 lines changed: 6, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/dp3/trackDb.ra
  • 1.19 lines changed: 4, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droAna1/trackDb.ra
  • 1.18 lines changed: 4, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droAna2/trackDb.ra
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droMoj1/trackDb.ra
  • 1.17 lines changed: 4, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droMoj2/trackDb.ra
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droVir1/trackDb.ra
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droVir2/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/drosophila/droYak2/description.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.83 lines changed: 3, context: html, text, full: html, text
    Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks.
• src/hg/makeDb/trackDb/gap.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding t2g html page, fix error in gap.html and reset labels for t2g
• src/hg/makeDb/trackDb/human/chimpParalogy.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/cnpIafrate.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/cnpSebat.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/encodeStanfordNRSF.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepOrigins.html
  • 1.17 lines changed: 4, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/encode_UVA_DNARep.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg12/syntenyMouse.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg13/humMusL.html
  • 1.6 lines changed: 5, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg13/syntenyMouse.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg13/syntenyRat.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg15/syntenyMouse.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg15/syntenyRat.html
  • 1.9 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/allb100i96.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/cnp.html
  • 1.14 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/fosmidDiscordant.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/hetChimp.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/rhb100i96.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/syntenyMm3.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/syntenyMm4.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg16/syntenyRn3.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/cnp.html
  • 1.9 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/encodeRegulomeDnaseArray.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/ensRatMusHom.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/exoniphyGene.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/hars.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/syntenyMm4.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/syntenyMm5.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg17/syntenyRn3.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/cnp.html
  • 1.19 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/divMKAR.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/eioJcviNAS.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/encodeRegulomeDnaseArray.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/fantomCageGraphTop.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/hars.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/laminB1Super.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.14 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/sangamoDnaseHs.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/snpArray.html
  • 1.18 lines changed: 6, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
  • 1.17 lines changed: 12, context: html, text, full: html, text
    Updated HumanCytoSNP-12 v2.1 section.
• src/hg/makeDb/trackDb/human/hg18/snpArrayBeta.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/snpArrayWith1M.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.489 lines changed: 3, context: html, text, full: html, text
    set visibility modes for UCSF Brain DNA methylation
  • 1.488 lines changed: 168, context: html, text, full: html, text
    add Ting's ucsfBrainMethyl track
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.983 lines changed: 21, context: html, text, full: html, text
    add release alpha to jim's encode regulation supertrack
  • 1.982 lines changed: 1, context: html, text, full: html, text
    Minor sort order change to HAIB TFBS
  • 1.981 lines changed: 58, context: html, text, full: html, text
    removed release tags for wgEncodeDukeAffyExonArray
  • 1.980 lines changed: 1, context: html, text, full: html, text
    Removing tags and pointing to new settings for release of this track
  • 1.979 lines changed: 26, context: html, text, full: html, text
    fixed release tags for mapability track
  • 1.978 lines changed: 8, context: html, text, full: html, text
    change Tags to Alignments in GIS RNA-seq, put space in SplitAligns
  • 1.977 lines changed: 6, context: html, text, full: html, text
    changed release tags
  • 1.976 lines changed: 61, context: html, text, full: html, text
    Removed subtracks not yet on the RR for Mapability.
  • 1.975 lines changed: 11, context: html, text, full: html, text
    Tweaking settings for regulatory track.
• src/hg/makeDb/trackDb/human/hg18/ucsfBrainMethyl.html
  • 1.1 lines changed: 84, context: html, text, full: html, text
    description page for Ting's ucsfBrainMethyl track
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSignal.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSites.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uppsalaChipSuper.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uwNucOcc.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uwNucOccA375.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uwNucOccDennis.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/uwNucOccMec.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.html
  • 1.5 lines changed: 7, context: html, text, full: html, text
    updated the description page to be consistant with other encode pages
  • 1.4 lines changed: 7, context: html, text, full: html, text
    changed links to relative links, changed the html formatting, and changed the sentence structure
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.12 lines changed: 6, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.11 lines changed: 3, context: html, text, full: html, text
    change more tags to alignments
  • 1.10 lines changed: 2, context: html, text, full: html, text
    change SplitAligns to Split Alignments
  • 1.9 lines changed: 9, context: html, text, full: html, text
    add contact
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.19 lines changed: 6, context: html, text, full: html, text
    change Tags view back to Alignments, move the Release Notes section
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra
  • 1.4 lines changed: 33, context: html, text, full: html, text
    make all tier1 cell lines on by default
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change Tags view back to Alignments, move the Release Notes section
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
  • 1.2 lines changed: 194, context: html, text, full: html, text
    Removing tags and pointing to new settings for release of this track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • 1.2 lines changed: 465, context: html, text, full: html, text
    SYDH TFBS:Updated MetaData to include 4 new submissions
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • 1.10 lines changed: 31, context: html, text, full: html, text
    SYDH TFBS: Added 4 new submissions to track. (1203,1204,1206,1207).
  • 1.9 lines changed: 44, context: html, text, full: html, text
    SYDH TFBS: Started to add new submssuin id (1203 adn 1204). Still need to clean up
• src/hg/makeDb/trackDb/human/stanfordNRSF.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/lancelet/braFlo1/gold.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • 1.3 lines changed: 12, context: html, text, full: html, text
    adding better examples to description page for calJac3
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra
  • 1.5 lines changed: 7, context: html, text, full: html, text
    adding overrides so default position looks nice
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.9 lines changed: 7, context: html, text, full: html, text
    adding overrides so default position looks nice
  • 1.8 lines changed: 2, context: html, text, full: html, text
    13-Way multiz reading frames
• src/hg/makeDb/trackDb/mouse/mm3/syntenyHuman.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm3/syntenyRat.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm4/syntenyHg16.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm4/syntenyRn3.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm5/ensRatMusHg17.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm8/broadChromatinChIPSeq.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhHistone.ra
  • 1.3 lines changed: 29, context: html, text, full: html, text
    moved this down to metaDb
  • 1.2 lines changed: 67, context: html, text, full: html, text
    Added new submissions
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.ra
  • 1.2 lines changed: 551, context: html, text, full: html, text
    this is down in metaDb now
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • 1.1 lines changed: 29, context: html, text, full: html, text
    moved from above
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • 1.1 lines changed: 572, context: html, text, full: html, text
    moved from above
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/wgEncodeSydhTfbs.ra
  • 1.2 lines changed: 572, context: html, text, full: html, text
    moved into alpha
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • 1.4 lines changed: 42, context: html, text, full: html, text
    SYDH: I have changed the short and long labels on all Snyder mm9 tracks to refelct that only Stanford and Yale are working on generating data. According the Stephen Landt the new name is Stan/Yale.
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Fixed the Signal Tracks failing to scale problem. Added ViewSig on the end of the subtrack names
  • 1.2 lines changed: 102, context: html, text, full: html, text
    Color changes for MEL cells, and new CH12 tracks added for Histone
• src/hg/makeDb/trackDb/mouse/recombRateMouse.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • 1.29 lines changed: 1, context: html, text, full: html, text
    moving chain/net shortLabel override for calJac3 up one level
• src/hg/makeDb/trackDb/orangutan/ponAbe2/gold.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/parsPValues.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • 1.9 lines changed: 5, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/platypus/ornAna1/gold.html
  • 1.2 lines changed: 3, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rat/recombRateRat.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rat/rn1/ensRatMusHom.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rat/rn3/ensRatMusHom.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rat/rn3/syntenyHg15.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rgdRatQtl.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rhesus/rheMac2/ctgPos.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/rhesus/rheMac2/gold.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/stickleback/gasAcu1/description.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/syntenyHuman.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/syntenyMouse.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/syntenyRat.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/t2g.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    fixing error
  • 1.2 lines changed: 56, context: html, text, full: html, text
    initial text description for text2Genome
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Adding t2g html page, fix error in gap.html and reset labels for t2g
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.27 lines changed: 1, context: html, text, full: html, text
    add bedGraph to dividers
  • 1.26 lines changed: 2, context: html, text, full: html, text
    initial experiment for text2Genome
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Adding showSubtrackColorOnUi
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Fixing typo in comment
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.94 lines changed: 1, context: html, text, full: html, text
    moving chain/net shortLabel override for calJac3 up one level
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.633 lines changed: 3, context: html, text, full: html, text
    Adding t2g html page, fix error in gap.html and reset labels for t2g
  • 1.632 lines changed: 12, context: html, text, full: html, text
    initial experiment for text2Genome
• src/hg/makeDb/trackDb/urchin/strPur1/description.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/worm/25mersRepeats.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/zebrafish/danRer1/ctgPos2.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/makeDb/trackDb/zebrafish/danRer2/ctgPos2.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts).
• src/hg/mouseStuff/mafFetch/mafFetch.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    typo fix in usage help
• src/hg/ratStuff/mafSplit/mafSplit.c
  • 1.7 lines changed: 30, context: html, text, full: html, text
    adding option to mafSplit to allow it to simply split by chrom/scaffold keeping the target name
• src/hg/utils/automation/Encode.pm
  • 1.65 lines changed: 1, context: html, text, full: html, text
    change download directory
• src/hg/utils/automation/HgAutomate.pm
  • 1.29 lines changed: 3, context: html, text, full: html, text
    htdocs-download is actually htdocs-hgdownload
  • 1.28 lines changed: 1, context: html, text, full: html, text
    change download directory
• src/hg/utils/automation/HgDb.pm
  • 1.9 lines changed: 7, context: html, text, full: html, text
    added quote function, forwared from DBI
• src/hg/utils/automation/makeDownloads.pl
  • 1.27 lines changed: 2, context: html, text, full: html, text
    adding 2bit sequence file to bigZips
• src/hg/utils/gff3ToGenePred/tests/expected/bogusQuotesTest.out
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/hg/utils/gff3ToGenePred/tests/input/bogusQuotes.gff3
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/hg/utils/gff3ToGenePred/tests/makefile
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/inc/gff3.h
  • 1.3 lines changed: 7, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/lib/gff3.c
  • 1.5 lines changed: 109, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/lib/tests/input/specialCasesTest.gff3
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values.
• src/makefile
  • 1.72 lines changed: 1, context: html, text, full: html, text
    adding bedSort
• src/test/buildTableDescriptions.pl
  • 1.45 lines changed: 2, context: html, text, full: html, text
    changing of the guard
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.27 lines changed: 2, context: html, text, full: html, text
    add information about how to sort the input file with sort
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.24 lines changed: 3, context: html, text, full: html, text
    add unix sort command example
• src/utils/cvsTools/cvsFiles
  • 1.5 lines changed: 6, context: html, text, full: html, text
    allow specifying directories
• src/utils/faSplit/faSplit.c
  • 1.37 lines changed: 4, context: html, text, full: html, text
    nobody wants duplicate smaller than extra overhang
  • 1.36 lines changed: 1, context: html, text, full: html, text
    fixing help
• src/utils/qa/backupCentral.csh
  • 1.15 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/browserUsage.csh
  • 1.6 lines changed: 3, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/checkGbdbDiffs.csh
  • 1.8 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/checkMetaAday.csh
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/checkWigFiles.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/databaseAday.csh
  • 1.13 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/full_joinerCheck.csh
  • 1.4 lines changed: 42, context: html, text, full: html, text
    removing old script that won't survive change to git
• src/utils/qa/gc-stats.pl
  • 1.2 lines changed: 7, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/getChainLines.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/getGbdbBeta.csh
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/getJoinerKeyErrors.pl
  • 1.5 lines changed: 4, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/getMatrixLines.csh
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/hgFindSpecGlobal.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/makeUniProtFile.csh
  • 1.8 lines changed: 3, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/qaEnsGenes.csh
  • 1.24 lines changed: 1, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/syncAday.csh
  • 1.11 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/trackDbGlobal.csh
  • 1.32 lines changed: 1, context: html, text, full: html, text
    added newline after archived in output to improve the look of forwarded messages in T-bird clients
  • 1.31 lines changed: 2, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.27 lines changed: 6, context: html, text, full: html, text
    fixing oops
  • 1.26 lines changed: 6, context: html, text, full: html, text
    changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.115 lines changed: 1, context: html, text, full: html, text
    v232 preview
  • 1.114 lines changed: 2, context: html, text, full: html, text
    v232 preview
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • 1.11 lines changed: 2, context: html, text, full: html, text
    removing ann
• src/utils/wigSetSpanOrStep/expectedFixed.wig
  • 1.1 lines changed: 106, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/expectedVar.wig
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/inFixed.wig
  • 1.1 lines changed: 106, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/inVar.wig
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/makefile
  • 1.1 lines changed: 24, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
  • 1.1 lines changed: 112, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....

• lines changed: 7481
• files changed: 235