CVS changes by file

branch to review (2010-02-16 to 2010-02-23) v226

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.14 lines changed: 12, context: html, text, full: html, text
    add multiz for IMG cistern spring, joseph coats, and monarch geyser
  • 1.13 lines changed: 11, context: html, text, full: html, text
    add Private in Tax_ID for all private metagenomes
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.98 lines changed: 8, context: html, text, full: html, text
    add multiz for Synechococcus
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.27 lines changed: 1, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.26 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.25 lines changed: 108, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.41 lines changed: 1, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.18 lines changed: 12, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.11 lines changed: 1, context: html, text, full: html, text
    fix tracksDb dir in multiz creation
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.11 lines changed: 16, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.53 lines changed: 4, context: html, text, full: html, text
    remove GOLD ID line if value does not exist
  • 1.52 lines changed: 9, context: html, text, full: html, text
    Use publication instead of isolation for metagenomes
  • 1.51 lines changed: 58, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.24 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.23 lines changed: 79, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/make-metagenome-info
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fix problem when org name has slashes
  • 1.1 lines changed: 760, context: html, text, full: html, text
    create script to get metagenome info and sequences, initially from JGI IMG/M
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Add execute bit so Apache correctly handles SSI (server-side include) adjustment of hgTrackUi relative path
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.98 lines changed: 4, context: html, text, full: html, text
    removing automatic -allowReloads that got added due to some misunderstanding long ago
• src/hg/hgTables/pal.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    take out cartSaveSession which ends up swallowing our output
• src/hg/hgTracks/hgTracks.c
  • 1.1631 lines changed: 2, context: html, text, full: html, text
    give the suggest input a name to make a robot happy
  • 1.1630 lines changed: 7, context: html, text, full: html, text
    Larry pointed out tool tips that were wrong.
  • 1.1629 lines changed: 36, context: html, text, full: html, text
    Dinks to the navigation links, by request
• src/hg/hgc/bamClick.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Make the link to hgTrackUi for all custom tracks (except those that exit hgCustom() early).
• src/hg/hgc/bigBedClick.c
  • 1.9 lines changed: 26, context: html, text, full: html, text
    Instead of dumping out the full BED+ record when there are more than 6 BED fields (we don't subject our users to that on plain BED track details pages), display non-BED fields if there are any.
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Added printCustomUrl -- user noticed its absence.
• src/hg/hgc/hgc.c
  • 1.1600 lines changed: 127, context: html, text, full: html, text
    Added section to process rgdGene2 track.
  • 1.1599 lines changed: 1, context: html, text, full: html, text
    fix link to ENSEMBL
  • 1.1598 lines changed: 2, context: html, text, full: html, text
    take out some periods (per Ann)
  • 1.1597 lines changed: 5, context: html, text, full: html, text
    added details page for PAR tracks
  • 1.1596 lines changed: 2, context: html, text, full: html, text
    Make the link to hgTrackUi for all custom tracks (except those that exit hgCustom() early).
• src/hg/hgc/hgc.h
  • 1.50 lines changed: 3, context: html, text, full: html, text
    Make the link to hgTrackUi for all custom tracks (except those that exit hgCustom() early).
• src/hg/hgc/makefile
  • 1.65 lines changed: 1, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/hgc/parClick.c
  • 1.2 lines changed: 6, context: html, text, full: html, text
    fixed bug when clicking on one par when both are displayed
  • 1.1 lines changed: 150, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/hgc/parClick.h
  • 1.1 lines changed: 8, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/inc/hgRelate.h
  • 1.17 lines changed: 10, context: html, text, full: html, text
    allow defaulting to TMPDIR directory
• src/hg/instinct/hgMicroscope/microscope/README
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Removed old README from visigene
• src/hg/instinct/hgMicroscope/microscope/configPage.c
  • 1.2 lines changed: 37, context: html, text, full: html, text
    Removed configPage stuff
• src/hg/instinct/hgMicroscope/microscope/configPage.h
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Removed configPage stuff
• src/hg/instinct/hgMicroscope/microscope/dot_clear.gif
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Cleaning up files
• src/hg/instinct/hgMicroscope/microscope/hgMicroscope.c
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Removed config page stuff
• src/hg/instinct/hgMicroscope/microscope/makefile
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Cleaning up files
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Removed configPage stuff
• src/hg/instinct/hgMicroscope/microscope/testVisiSearch.c
  • 1.2 lines changed: 67, context: html, text, full: html, text
    Removed visiSearch
• src/hg/instinct/hgMicroscope/microscopeLoad/test/test.tab
  • 1.4 lines changed: 8, context: html, text, full: html, text
    New data
  • 1.3 lines changed: 3, context: html, text, full: html, text
    New test images
• src/hg/instinct/hgMicroscope/microscopeLoad/test/testcaptions.txt
  • 1.4 lines changed: 9, context: html, text, full: html, text
    New data
  • 1.3 lines changed: 3, context: html, text, full: html, text
    new test images
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.39 lines changed: 1, context: html, text, full: html, text
    add adjustBenjaminiHochberg
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.65 lines changed: 133, context: html, text, full: html, text
    add adjustBenjaminiHochberg
• src/hg/instinct/lib/tests/benjaminiHochberg.R
  • 1.1 lines changed: 2, context: html, text, full: html, text
    tests framework for benjamini-hochberg code
• src/hg/instinct/lib/tests/benjaminiHochberg.c
  • 1.1 lines changed: 41, context: html, text, full: html, text
    tests framework for benjamini-hochberg code
• src/hg/instinct/lib/tests/expected/benjaminiHochberg.out
  • 1.1 lines changed: 15, context: html, text, full: html, text
    tests framework for benjamini-hochberg code
• src/hg/instinct/lib/tests/input/p.txt
  • 1.1 lines changed: 15, context: html, text, full: html, text
    input p-value
• src/hg/instinct/lib/tests/makefile
  • 1.1 lines changed: 43, context: html, text, full: html, text
    tests framework for benjamini-hochberg code
• src/hg/js/hgTracks.js
  • 1.55 lines changed: 4, context: html, text, full: html, text
    Fixed tiny bug that prevented hgTracks cfg page to work.
• src/hg/lib/hgConfig.c
  • 1.23 lines changed: 12, context: html, text, full: html, text
    check that all config files starting with dot are only readable by the owner
• src/hg/lib/hgRelate.c
  • 1.26 lines changed: 21, context: html, text, full: html, text
    allow defaulting to TMPDIR directory
• src/hg/lib/hui.c
  • 1.262 lines changed: 2, context: html, text, full: html, text
    fiddle with the wiggle dialog a little to get the YLineOff drop down in the right place
  • 1.261 lines changed: 1, context: html, text, full: html, text
    Fixed obscure bug that was evident during composite reset to defaults
• src/hg/lib/jaxQTL.sql
  • 1.4 lines changed: 20, context: html, text, full: html, text
    Removed to avoid clash with jaxQtl.sql (QA's preferred name). hgc still uses jaxQTL.[ch].
• src/hg/makeDb/doc/calJac3.txt
  • 1.4 lines changed: 265, context: html, text, full: html, text
    trying to lastz papHam1 ogoGar1 micMur1 and tarSyr1 with difficulty
• src/hg/makeDb/doc/danRer6.txt
  • 1.17 lines changed: 332, context: html, text, full: html, text
    multiz6way, annotated mafs, annotated and upstream downloads, frames
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.12 lines changed: 39, context: html, text, full: html, text
    Backlog of notes from freeze work
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • 1.12 lines changed: 305, context: html, text, full: html, text
    Backlog of notes from freeze work
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.6 lines changed: 453, context: html, text, full: html, text
    Backlog of notes from freeze work
• src/hg/makeDb/doc/encodeDccHg18/uwChIPseq.release1.notes.txt
  • 1.5 lines changed: 24, context: html, text, full: html, text
    Added 23 tagAligns which are the missing inputs
  • 1.4 lines changed: 113, context: html, text, full: html, text
    Updated files list for Jan 2010 freeze
• src/hg/makeDb/doc/encodeDccHg18/uwDnaseSeq.release3.notes.txt
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Minor clarification
  • 1.1 lines changed: 773, context: html, text, full: html, text
    Files list for release 3
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.7 lines changed: 396, context: html, text, full: html, text
    Backlog of notes from freeze work
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.15 lines changed: 592, context: html, text, full: html, text
    Backlog of notes from freeze work
• src/hg/makeDb/doc/gorGor2.txt
  • 1.3 lines changed: 53, context: html, text, full: html, text
    done with genbank run
  • 1.2 lines changed: 100, context: html, text, full: html, text
    adding other gaps and ready for kluster scratch/data rsync
  • 1.1 lines changed: 110, context: html, text, full: html, text
    initial assembly build and done with repeatMasker and simpleRepeats
• src/hg/makeDb/doc/hg18.txt
  • 1.399 lines changed: 30, context: html, text, full: html, text
    Added a Signal track for the Burge RNA-seq data. Updated trackDb entry for this track to include views.
  • 1.398 lines changed: 6, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/doc/hg19.txt
  • 1.85 lines changed: 6, context: html, text, full: html, text
    Changed value in genomicSuperDups table for segmental duplications track.
  • 1.84 lines changed: 38, context: html, text, full: html, text
    Added a Signal track for the Burge RNA-seq data. Updated trackDb entry for this track to include views.
  • 1.83 lines changed: 8, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/doc/mm9.txt
  • 1.126 lines changed: 3, context: html, text, full: html, text
    Added note for next time about NIAGene track.
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.121 lines changed: 2, context: html, text, full: html, text
    added some examples to look at
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.112 lines changed: 1, context: html, text, full: html, text
    Added gorGor2 - Gorilla Gorilla
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.364 lines changed: 19, context: html, text, full: html, text
    adding gorilla gorGor2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.116 lines changed: 1, context: html, text, full: html, text
    Added gorGor2 - Gorilla Gorilla
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.76 lines changed: 2, context: html, text, full: html, text
    adding names for gorilla species
• src/hg/makeDb/hgPar/hgPar.c
  • 1.2 lines changed: 104, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 105, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/makefile
  • 1.1 lines changed: 23, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.as
  • 1.1 lines changed: 11, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.c
  • 1.1 lines changed: 138, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.h
  • 1.1 lines changed: 63, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/tests/expected/par.bed
  • 1.1 lines changed: 4, context: html, text, full: html, text
    used BED format for PAR
• src/hg/makeDb/hgPar/tests/input/test.parspec
  • 1.3 lines changed: 0, context: html, text, full: html, text
    removed stray space
  • 1.2 lines changed: 2, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 2, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/tests/makefile
  • 1.2 lines changed: 3, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgRgdParsePathwayObo/hgRgdParsePathwayObo.c
  • 1.1 lines changed: 125, context: html, text, full: html, text
    Created hgRgdParsePathwayObo.c
• src/hg/makeDb/hgRgdParsePathwayObo/makefile
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Created makefile.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.63 lines changed: 9, context: html, text, full: html, text
    do some release tag checking
  • 1.62 lines changed: 21, context: html, text, full: html, text
    fix the code to check that subGroups have the predefined attributes from the composite. This got broken in Jim's trackDb overhaul.
• src/hg/makeDb/makefile
  • 1.44 lines changed: 1, context: html, text, full: html, text
    Removing stray character that made make barf.
  • 1.43 lines changed: 2, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.14 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.chainNet.ra
  • 1.3 lines changed: 9, context: html, text, full: html, text
    moved all danRer4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.589 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.455 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/human/hg18/burgeRnaSeqGemMapperAlign.html
  • 1.5 lines changed: 29, context: html, text, full: html, text
    Added more method details and information about track configuration.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Added missing </A> tags, found by hgTablesTest on the description page.
• src/hg/makeDb/trackDb/human/hg18/trackDb.cancer2.ra
  • 1.4 lines changed: 16, context: html, text, full: html, text
    UPdated track names
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.469 lines changed: 3, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.879 lines changed: 2, context: html, text, full: html, text
    Back to the release 3 version of UW DNaseI HS
  • 1.878 lines changed: 2, context: html, text, full: html, text
    Removed duplicated subTrack lines from mapability track entry.
  • 1.877 lines changed: 661, context: html, text, full: html, text
    extract RikenCage to include files
  • 1.876 lines changed: 8, context: html, text, full: html, text
    Changed the names of 4 HAIB Chip tracks because they should have been versioned
  • 1.875 lines changed: 2, context: html, text, full: html, text
    Reverted UW DNaseI HS to release 2 temprarily for a minor texting change on the RR
  • 1.874 lines changed: 3, context: html, text, full: html, text
    Neglected to make replaced tables release beta
  • 1.873 lines changed: 16, context: html, text, full: html, text
    Getting ready for UW DNase release 3
  • 1.872 lines changed: 1, context: html, text, full: html, text
    Removed duplicate subTrack line.
  • 1.871 lines changed: 225, context: html, text, full: html, text
    Added release alpha/beta versions for the Mapability track. The beta version uses an older description html that omits description for the new CRG subtracks.
  • 1.870 lines changed: 1, context: html, text, full: html, text
    Final touchup before unbouncing to pushQ A
  • 1.869 lines changed: 39, context: html, text, full: html, text
    splitting Orchid and Chai tracks into two separate entities
  • 1.868 lines changed: 5, context: html, text, full: html, text
    keep using wgEncodeSangerGencode
  • 1.867 lines changed: 123, context: html, text, full: html, text
    Fixed the filterBy settings for UW Chip
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
  • 1.2 lines changed: 133, context: html, text, full: html, text
    add insertLength variables for those tracks who didn't specify it
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra
  • 1.2 lines changed: 7, context: html, text, full: html, text
    take out insertLength which isn't in release1
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapabilityOld.html
  • 1.1 lines changed: 109, context: html, text, full: html, text
    Older version of Mapability track description before CRG data added. This is for the release beta version.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • 1.1 lines changed: 699, context: html, text, full: html, text
    extract RikenCage track to its own include
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.beta.ra
  • 1.1 lines changed: 699, context: html, text, full: html, text
    extract RikenCage track to its own include
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.15 lines changed: 4, context: html, text, full: html, text
    fix a typo and long line
  • 1.14 lines changed: 87, context: html, text, full: html, text
    replaced with human/wgEncodeGencode.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    fixed typo
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
  • 1.6 lines changed: 24, context: html, text, full: html, text
    Final touchup before unbouncing to pushQ A
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.13 lines changed: 5, context: html, text, full: html, text
    Back to the release 3 version
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fixed typos in newly added Release Notes section
  • 1.11 lines changed: 5, context: html, text, full: html, text
    Setting this back to a release 3 version.
  • 1.10 lines changed: 11, context: html, text, full: html, text
    Getting ready for UW DNase release 3
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
  • 1.5 lines changed: 30, context: html, text, full: html, text
    Added more method details and information about track configuration.
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Added missing </A> tags, found by hgTablesTest on the description page.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.99 lines changed: 34, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/human/par.html
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.36 lines changed: 7, context: html, text, full: html, text
    moved all danRer4 chains and nets to composite and dropped individual tracks
  • 1.35 lines changed: 4, context: html, text, full: html, text
    Changed strPur2 nets and chains to composites.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.520 lines changed: 32, context: html, text, full: html, text
    For Burge RNA-seq track, made all subtracks on by default and changed the upper view limit to be 1000.
  • 1.519 lines changed: 1, context: html, text, full: html, text
    Corrected setting for jaxQtlMapped (mm8 table name changed a long time ago).
  • 1.518 lines changed: 7, context: html, text, full: html, text
    Changed strPur2 nets and chains to composites.
  • 1.517 lines changed: 167, context: html, text, full: html, text
    Added subtracks and views for the Burge RNA-seq track.
  • 1.516 lines changed: 112, context: html, text, full: html, text
    Adding single subtracks to test views for Burge RNA-seq data track.
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • 1.2 lines changed: 72, context: html, text, full: html, text
    cleaned up discussion and references, ready to go
• src/hg/makeDb/trackDb/marmoset/calJac3/gap.html
  • 1.2 lines changed: 41, context: html, text, full: html, text
    cleaned up gap types to cover all included in this assembly
• src/hg/makeDb/trackDb/marmoset/calJac3/gold.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Correct text
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Adding an 8-way conservation
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.9 lines changed: 9, context: html, text, full: html, text
    moved all danRer4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/jaxQTL.html
  • 1.6 lines changed: 15, context: html, text, full: html, text
    Removing since we no longer have any hgwdev databases with jaxQTL tables (just jaxQtl now), and MarkD found CVS error on Mac's default-case-insensitive filesystem.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.67 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.68 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/mouse/mm9/mapability.html
  • 1.3 lines changed: 25, context: html, text, full: html, text
    Updated description based on that provided by the data providers.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.85 lines changed: 1, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.209 lines changed: 6, context: html, text, full: html, text
    Removed vestigial searchSpec.
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.54 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Changed monDom4 chain and net shortLabels to match chainNet shortLabel.
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.81 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • 1.12 lines changed: 7, context: html, text, full: html, text
    Changed monDom4 chain and net shortLabels to match chainNet shortLabel.
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    edited name of Broad Istitute and added link to Broad Institute
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.3 lines changed: 8, context: html, text, full: html, text
    some better defaults on initial track visibilities
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra
  • 1.5 lines changed: 2, context: html, text, full: html, text
    some better defaults on initial track visibilities
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • 1.14 lines changed: 8, context: html, text, full: html, text
    moved all danRer4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.82 lines changed: 49, context: html, text, full: html, text
    Changed strPur2 nets and chains to composites.
  • 1.81 lines changed: 1, context: html, text, full: html, text
    Removed an old comment.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.619 lines changed: 16, context: html, text, full: html, text
    added PAR tracks
  • 1.618 lines changed: 24, context: html, text, full: html, text
    Changed strPur2 nets and chains to composites.
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.35 lines changed: 1, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.77 lines changed: 6, context: html, text, full: html, text
    Changed Vega Genes so that the genes and pseudogenes subtracks have different colours.
  • 1.76 lines changed: 5, context: html, text, full: html, text
    Changed the colour for vegaGenes release beta to the same as for release alpha.
  • 1.75 lines changed: 4, context: html, text, full: html, text
    add release alpha and beta to subTracks
  • 1.74 lines changed: 0, context: html, text, full: html, text
    Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter.
• src/hg/makefile
  • 1.155 lines changed: 1, context: html, text, full: html, text
    add hgSuggest
• src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Fixing so it doesn't get misdirected by critically placed comments.
• src/hg/pslCDnaFilter/cDnaAligns.c
  • 1.20 lines changed: 24, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/cDnaAligns.h
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • 1.22 lines changed: 7, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/drop.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/filt.out
  • 1.1 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/keep.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/weird.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/drop.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/filt.out
  • 1.1 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/keep.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/weird.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/drop.psl
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/filt.out
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/keep.psl
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/weird.psl
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/input/ignoreIntrons.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/makefile
  • 1.14 lines changed: 11, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/usage.txt
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.32 lines changed: 11, context: html, text, full: html, text
    adding an elapsed time calculation when successful completion
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.28 lines changed: 23, context: html, text, full: html, text
    Added new required setting assemblyShortLabel, an abbreviated form of the sequencing center's ID for the assembly (which is often more familiar to users), e.g. NCBI36 for hg18.
• src/hg/utils/automation/n50.pl
  • 1.3 lines changed: 13, context: html, text, full: html, text
    working even if contig names are identical and ignoring extra columns on input
• src/lib/htmshell.c
  • 1.67 lines changed: 5, context: html, text, full: html, text
    fixing the cut-paste problem with the warnbox on non-warning plain text messages
  • 1.66 lines changed: 5, context: html, text, full: html, text
    undoing 1.65, returning to same contents as 1.64
• src/utils/qa/makefile
  • 1.118 lines changed: 1, context: html, text, full: html, text
    print a manual of all csh files usage statements
• src/utils/qa/printMan.csh
  • 1.1 lines changed: 57, context: html, text, full: html, text
    print a manual of all csh files usage statements
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.101 lines changed: 2, context: html, text, full: html, text
    v226 preview

• lines changed: 10216
• files changed: 146