CVS changes by file

branch to review (2010-05-25 to 2010-06-01) v233

• src/hg/archaeStuff/chooseorg/chooseorg.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Renaming aliTrack to aliTable to help clarify track/table confusion.
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Renaming aliTrack to aliTable to help clarify track/table confusion.
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Changed DAF to accept Signals of type:wig instead of type:BigWig
  • 1.3 lines changed: 17, context: html, text, full: html, text
    Updated DAF to reflect new bigWig Raw signal format and fix Tfsb->Tfbs format
• src/hg/encode/DAFs/2.0/renMm9Tfbs.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Validate atleast 1000 on fastqs. I am not 'quick' works on fastq.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Minor touch-ups
• src/hg/encode/DAFs/2.0/renSample.ddf
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Minor touch-ups
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Make sure therre are tabls and dummy up one experiment
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • 1.1 lines changed: 41, context: html, text, full: html, text
    A new DAF for the Stanford mm9 Histone Modification Experiments
• src/hg/encode/DAFs/2.0/sunyGeneST.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    The new dafs for the SUNY lab
• src/hg/encode/DAFs/2.0/sunyRipChip.ddf
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Fixed the .ddf to drop accession and labVersion at Labs request
• src/hg/encode/DAFs/2.0/sunyTiling.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    The new dafs for the SUNY lab
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • 1.14 lines changed: 9, context: html, text, full: html, text
    added flag to skip md5 sums for faster run time
  • 1.13 lines changed: 21, context: html, text, full: html, text
    change md5 sum calcs to better handle HUGH files, updated paths for htdocs-hgdownload
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.248 lines changed: 18, context: html, text, full: html, text
    Added U2OS to the Tier 3 human cell types
  • 1.247 lines changed: 1, context: html, text, full: html, text
    Try that one more time. Removed Input from ripAntibodies and put None in ripProteins.
  • 1.246 lines changed: 15, context: html, text, full: html, text
    Removed the Input in ripAntibodies and was able to do this better
  • 1.245 lines changed: 9, context: html, text, full: html, text
    I entered an Input type for the ripAntibodies, so that we could validate over the weekend. This should be removed and done the same way that Antibodies is.
  • 1.244 lines changed: 28, context: html, text, full: html, text
    added more ripAntibodies
  • 1.243 lines changed: 9, context: html, text, full: html, text
    Moved CELF1 from ripAntibodies table to ripTargetProtien
  • 1.242 lines changed: 18, context: html, text, full: html, text
    Registered New Cell Line: Raji with provided protocol from SYDH (Farnham).
  • 1.241 lines changed: 20, context: html, text, full: html, text
    A lot of 'organism Human' lines were missing from cells
• src/hg/encode/encodeValidate/config/expVars.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed bug where BAM validator was breaking the cell CV term validator
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.32 lines changed: 5, context: html, text, full: html, text
    Added origAssembly to help distinguish hg18 to hg19 datasets.
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.17 lines changed: 15, context: html, text, full: html, text
    Get release date from pushQ
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.229 lines changed: 1, context: html, text, full: html, text
    made all warnings fatal
  • 1.228 lines changed: 5, context: html, text, full: html, text
    fixed bug where BAM validator was breaking the cell CV term validator
  • 1.227 lines changed: 12, context: html, text, full: html, text
    At Venkat's urging, added useful comment to trackDb entry with subId
  • 1.226 lines changed: 21, context: html, text, full: html, text
    Added origAssembly metadata term. Moved metadata lines from trackDb.ra and fileDb.ra to mdb.txt
• src/hg/encode/encodeValidate/makefile
  • 1.19 lines changed: 2, context: html, text, full: html, text
    fixed bug where BAM validator was breaking the cell CV term validator
• src/hg/encode/hgEncodeSubmit/README.UCSC
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Update for newer usage
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.34 lines changed: 3, context: html, text, full: html, text
    Oops. Lost them all.
  • 1.33 lines changed: 35, context: html, text, full: html, text
    Improvements needed for passing list of terms: support control terms mixed with Antibodies
  • 1.32 lines changed: 78, context: html, text, full: html, text
    Extended to allow requesting a comma separated list of terms or tags
• src/hg/encode/utils/tagAlignToSAM/tagAlignToSAM.py
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added one more comment
  • 1.4 lines changed: 10, context: html, text, full: html, text
    Added some comments to point to where people can add code to change the MAPQ policy
  • 1.3 lines changed: 9, context: html, text, full: html, text
    After some debate, we now always report MAPQ=255
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed bug identified by Tim Durham @ Broad
• src/hg/encode/validateFiles/validateFiles.c
  • 1.43 lines changed: 190, context: html, text, full: html, text
    move BAM specific code inside ifdef
• src/hg/hgApi/hgApi.c
  • 1.3 lines changed: 43, context: html, text, full: html, text
    add metaDb command
• src/hg/hgCustom/hgCustom.c
  • 1.142 lines changed: 2, context: html, text, full: html, text
    made bedGraph not ALL CAPS to match usual usage
• src/hg/hgGetAnn/tests/makefile
  • 1.4 lines changed: 1, 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/great.c
  • 1.3 lines changed: 17, context: html, text, full: html, text
    stdout stream is not assignable on some operating systems
• src/hg/hgTracks/bamTrack.c
  • 1.32 lines changed: 59, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/hgTracks.c
  • 1.1649 lines changed: 3, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/hgTracks.h
  • 1.212 lines changed: 2, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/searchTracks.c
  • 1.8 lines changed: 41, context: html, text, full: html, text
    trivial changes: metadata is one word
  • 1.7 lines changed: 90, context: html, text, full: html, text
    refactor code to allow variable number of metadata selects
  • 1.6 lines changed: 107, context: html, text, full: html, text
    include metadata in description search; make last metadata select variable (with a javascript callback)
  • 1.5 lines changed: 213, context: html, text, full: html, text
    use new metaDb table (if it exists); make description search "google style" (independent of word order); code cleanup
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fix build problem (mapName -> track)
  • 1.3 lines changed: 89, context: html, text, full: html, text
    get cell types/antibodies from cv.ra; this is temporary code (will convert to using metaDb in the near future)
• src/hg/hgTracks/simpleTracks.c
  • 1.145 lines changed: 14, context: html, text, full: html, text
    Added logic to set a DECIPHER entry's color to gray when its mean_ratio = 0.
  • 1.144 lines changed: 46, context: html, text, full: html, text
    Added function to set color for DECIPHER entries.
  • 1.143 lines changed: 2, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
  • 1.142 lines changed: 4, context: html, text, full: html, text
    Fix for memory overrun when many classes are being selected via filterBySet()
• src/hg/hgTracks/wigTrack.c
  • 1.113 lines changed: 44, context: html, text, full: html, text
    Making log transform work with whiskers.
• src/hg/hgc/hgc.c
  • 1.1636 lines changed: 21, context: html, text, full: html, text
    Changed a compound query of DECIPHER track into two queries to improve performance.
  • 1.1635 lines changed: 2, context: html, text, full: html, text
    Updated OMIM URL.
• src/hg/hgc/t2g.c
  • 1.7 lines changed: 6, context: html, text, full: html, text
    update to abstract display to keep in more condensed
  • 1.6 lines changed: 55, context: html, text, full: html, text
    new version now with seqIds in t2g.sql
• src/hg/inc/hui.h
  • 1.154 lines changed: 1, context: html, text, full: html, text
    fix makeDownloadslink use the current database rather than defaulting to hg18
• src/hg/instinct/flatfileToBED15/flatfileToBED15.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Removed some unecessary printlines
  • 1.5 lines changed: 85, context: html, text, full: html, text
    Added writing microarrayGroups file
• src/hg/instinct/hgBamBam/drawingCode.c
  • 1.7 lines changed: 10, context: html, text, full: html, text
    minor update
  • 1.6 lines changed: 18, context: html, text, full: html, text
    fixed up
  • 1.5 lines changed: 31, context: html, text, full: html, text
    minor tweakpdate
  • 1.4 lines changed: 347, context: html, text, full: html, text
    big update
  • 1.3 lines changed: 3, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 140, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 389, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/css/hgHeatmapStyle.css
  • 1.7 lines changed: 12, context: html, text, full: html, text
    update
  • 1.6 lines changed: 7, context: html, text, full: html, text
    minor updtae
  • 1.5 lines changed: 13, context: html, text, full: html, text
    minor update
  • 1.4 lines changed: 18, context: html, text, full: html, text
    added sharing
  • 1.3 lines changed: 85, context: html, text, full: html, text
    big update
  • 1.2 lines changed: 13, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 315, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/css/jquery-ui-1.7.1.css
  • 1.1 lines changed: 404, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/css/uploadWidget.css
  • 1.1 lines changed: 385, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/img/XPButtonUploadText_61x22.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/index.html
  • 1.1 lines changed: 6, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/js/hgBamBam.js
  • 1.9 lines changed: 14, context: html, text, full: html, text
    updated
  • 1.8 lines changed: 12, context: html, text, full: html, text
    minor updtae
  • 1.7 lines changed: 52, context: html, text, full: html, text
    minor update
  • 1.6 lines changed: 110, context: html, text, full: html, text
    added sharing
  • 1.5 lines changed: 18, context: html, text, full: html, text
    initial commit
  • 1.4 lines changed: 136, context: html, text, full: html, text
    big update
  • 1.3 lines changed: 124, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 202, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/js/jquery-1.3.2.js
  • 1.1 lines changed: 4376, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/js/jquery-ui-1.7.1.min.js
  • 1.1 lines changed: 298, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/js/jquery.parsequery.js
  • 1.1 lines changed: 20, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/frontend/view.html
  • 1.9 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.8 lines changed: 16, context: html, text, full: html, text
    update
  • 1.7 lines changed: 4, context: html, text, full: html, text
    minor updtae
  • 1.6 lines changed: 4, context: html, text, full: html, text
    minor update
  • 1.5 lines changed: 18, context: html, text, full: html, text
    added sharing
  • 1.4 lines changed: 2, context: html, text, full: html, text
    minor tweakpdate
  • 1.3 lines changed: 34, context: html, text, full: html, text
    big update
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 99, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/hgAnnotations.c
  • 1.5 lines changed: 13, context: html, text, full: html, text
    fixed up
  • 1.4 lines changed: 9, context: html, text, full: html, text
    minor tweakpdate
  • 1.3 lines changed: 512, context: html, text, full: html, text
    big update
  • 1.2 lines changed: 224, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 713, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/hgBamBam.c
  • 1.8 lines changed: 5, context: html, text, full: html, text
    updated
  • 1.7 lines changed: 21, context: html, text, full: html, text
    minor update
  • 1.6 lines changed: 12, context: html, text, full: html, text
    minor updtae
  • 1.5 lines changed: 35, context: html, text, full: html, text
    added sharing
  • 1.4 lines changed: 105, context: html, text, full: html, text
    big update
  • 1.3 lines changed: 75, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 92, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 222, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/hgBamBam.h
  • 1.6 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 2, context: html, text, full: html, text
    minor update
  • 1.4 lines changed: 6, context: html, text, full: html, text
    added sharing
  • 1.3 lines changed: 25, context: html, text, full: html, text
    big update
  • 1.2 lines changed: 20, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 89, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/makefile
  • 1.1 lines changed: 27, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgBamBam/trashDirMD5.c
  • 1.1 lines changed: 71, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.89 lines changed: 4, context: html, text, full: html, text
    Added microscope toggle support, removed local_url support
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.53 lines changed: 1, context: html, text, full: html, text
    Added microscope toggle support, removed local_url support
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.39 lines changed: 51, context: html, text, full: html, text
    Added microscope flag, removed local_url flags
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.88 lines changed: 10, context: html, text, full: html, text
    Added microscope button toggling
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Added microscope toggle support, removed local_url support
• src/hg/instinct/inc/raDb.h
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Added microscope toggle, removed local_url support
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.71 lines changed: 3, context: html, text, full: html, text
    Added microscope toggle support, removed local_url support
• src/hg/instinct/lib/raDb.c
  • 1.2 lines changed: 79, context: html, text, full: html, text
    Added microscope toggle support
• src/hg/instinct/raToDb/raDb.as
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Added microscope toggle support
• src/hg/instinct/raToDb/raDb.sql
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Added microscope toggle support
• src/hg/instinct/raToDb/raToDb.c
  • 1.12 lines changed: 8, context: html, text, full: html, text
    Added Microscope toggle support
• src/hg/js/hui.js
  • 1.57 lines changed: 4, context: html, text, full: html, text
    Empty selection is invalid fro filterBy. Force it to 'All' when this case happens.
• src/hg/js/ui.dropdownchecklist.js
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Fixed bug wherre instance was referenced when it was null
  • 1.8 lines changed: 19, context: html, text, full: html, text
    Empty selection is invalid fro filterBy. Force it to 'All' when this case happens.
• src/hg/lib/customFactory.c
  • 1.126 lines changed: 1, context: html, text, full: html, text
    cannot use char which is 1 byte to represent EOF, must use int
  • 1.125 lines changed: 1, context: html, text, full: html, text
    cannot use char which is 1 byte to represent EOF, must use int
• src/hg/lib/hgFind.c
  • 1.231 lines changed: 2, context: html, text, full: html, text
    avoid segv on bad table in search
• src/hg/lib/hui.c
  • 1.296 lines changed: 3, context: html, text, full: html, text
    Fix for '(null)' showing up in sortColumn header
  • 1.295 lines changed: 6, context: html, text, full: html, text
    fix makeDownloadslink use the current database rather than defaulting to hg18
• src/hg/lib/snp125Ui.c
  • 1.33 lines changed: 3, context: html, text, full: html, text
    Added new func code cds-indel, moved coding-synonymy-unknown from synonymous category (oops) to non-synon category. Thanks Mary!
• src/hg/lib/snpSeq.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Corrected table description (thanks Mary!).
• src/hg/lib/t2g.sql
  • 1.1 lines changed: 19, context: html, text, full: html, text
    new version now with seqIds in t2g.sql
• src/hg/lib/t2gArticle.sql
  • 1.2 lines changed: 3, context: html, text, full: html, text
    new version now with seqIds in t2g.sql
• src/hg/lib/t2gSequence.sql
  • 1.2 lines changed: 3, context: html, text, full: html, text
    new version now with seqIds in t2g.sql
• src/hg/lib/wigAsciiToBinary.c
  • 1.34 lines changed: 3, context: html, text, full: html, text
    Making wigEncode default the span to the stepSize in fixedStep wigs.
• src/hg/lib/wikiTrack.c
  • 1.29 lines changed: 3, context: html, text, full: html, text
    show wiki track even if not logged in
  • 1.28 lines changed: 1, context: html, text, full: html, text
    fixup target blank for itemUrl om hgc wiki item click URL
• src/hg/liftUp/makefile
  • 1.11 lines changed: 6, context: html, text, full: html, text
    allow DESTDIR to be used
• src/hg/makeDb/doc/calJac3.txt
  • 1.14 lines changed: 363, context: html, text, full: html, text
    htdocs-hgdownload change
• src/hg/makeDb/doc/danRer6.txt
  • 1.19 lines changed: 366, context: html, text, full: html, text
    multiz6way, annotated, mafSummary, phylotree, phastCons
• src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt
  • 1.13 lines changed: 1, context: html, text, full: html, text
    fixing release2 total download file count
  • 1.12 lines changed: 39, context: html, text, full: html, text
    moved 8 tables from new to untouched; moved the associated 8 .wib files from new to untouched; adjusted counts
  • 1.11 lines changed: 7, context: html, text, full: html, text
    removed 2 deprecated tables because they were not part of release1; two were mis-named release2 tables and one was a release2 experimental table. Tim removed all three from dev. Also added a note to two of the deprecated tables that were part on beta & rr as part of release1 but never had a trackDb entry so didn't display in the track
  • 1.10 lines changed: 3, context: html, text, full: html, text
    removed two tables that I had listed as deprecated accidently. These tables were listed in the trackDb for release1 but never existed in the database. Since they never existed, they cannot be deprecated
  • 1.9 lines changed: 14, context: html, text, full: html, text
    added 11 tables to the Deprecated list
  • 1.8 lines changed: 2, context: html, text, full: html, text
    added two missing tables to New tables list
  • 1.7 lines changed: 45, context: html, text, full: html, text
    Rearranged some files due to Katrina's careful QA work
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeCaltechRnaSeq.release2.notes.txt
  • 1.1 lines changed: 516, context: html, text, full: html, text
    notes!
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • 1.2 lines changed: 30, context: html, text, full: html, text
    more load procedures
  • 1.1 lines changed: 25, context: html, text, full: html, text
    very preliminary
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.16 lines changed: 384, context: html, text, full: html, text
    htdocs-hgdownload change
• src/hg/makeDb/doc/hg18.txt
  • 1.421 lines changed: 35, context: html, text, full: html, text
    Built DECIPHER track.
• src/hg/makeDb/doc/hg19.txt
  • 1.115 lines changed: 130, context: html, text, full: html, text
    Made snp131-masked genome sequences.
  • 1.114 lines changed: 73, context: html, text, full: html, text
    Rebuilt snp131 and snp131CodingDbSnp with corrected function codes from dbSNP.
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.19 lines changed: 877, context: html, text, full: html, text
    all v58 build sequences done
  • 1.18 lines changed: 71, context: html, text, full: html, text
    bosTau4 and gasAcu1 problems taken care of for v58 update
  • 1.17 lines changed: 116, context: html, text, full: html, text
    v58 done for hg19,mm9,rn4
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.121 lines changed: 1, context: html, text, full: html, text
    Adding felCat4 - Cat - Felis catus
  • 1.120 lines changed: 1, context: html, text, full: html, text
    removed felCatV17e
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.371 lines changed: 16, context: html, text, full: html, text
    remove felCatV17e
  • 1.370 lines changed: 18, context: html, text, full: html, text
    adding felCat4
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.114 lines changed: 1, context: html, text, full: html, text
    removed felCatV17e
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.125 lines changed: 1, context: html, text, full: html, text
    Adding felCat4 - Cat - Felis catus
  • 1.124 lines changed: 1, context: html, text, full: html, text
    removed felCatV17e
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.93 lines changed: 1, context: html, text, full: html, text
    turning genbank updates on for calJac3
• src/hg/makeDb/hgLoadWiggle/test_data/testBedGraph.wig
  • 1.1 lines changed: 64, context: html, text, full: html, text
    adding test sets
• src/hg/makeDb/hgLoadWiggle/test_data/testFixed.wig
  • 1.1 lines changed: 106, context: html, text, full: html, text
    adding test sets
• src/hg/makeDb/hgLoadWiggle/test_data/testVar.wig
  • 1.1 lines changed: 77, context: html, text, full: html, text
    adding test sets
• src/hg/makeDb/schema/all.joiner
  • 1.807 lines changed: 6, context: html, text, full: html, text
    Added the section of decipherId.
  • 1.806 lines changed: 19, context: html, text, full: html, text
    Added snp131 & exceptions.
  • 1.805 lines changed: 19, context: html, text, full: html, text
    Adding some missing entries found by Antonio.
• src/hg/makeDb/trackDb/README
  • 1.108 lines changed: 3, context: html, text, full: html, text
    Adding info on showSubtrackColorOnUi
  • 1.107 lines changed: 14, context: html, text, full: html, text
    Adding docs on new tags.
• src/hg/makeDb/trackDb/cat/felCat4/ctgPos2.html
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Initial descriptions for felCat4.
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    minor html correction
  • 1.1 lines changed: 130, context: html, text, full: html, text
    Initial descriptions for felCat4.
• src/hg/makeDb/trackDb/cat/felCat4/gap.html
  • 1.1 lines changed: 33, context: html, text, full: html, text
    Initial descriptions for felCat4.
• src/hg/makeDb/trackDb/cat/felCat4/gold.html
  • 1.1 lines changed: 35, context: html, text, full: html, text
    Initial descriptions for felCat4.
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Initial descriptions for felCat4.
• src/hg/makeDb/trackDb/human/decipher.html
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Added color scheme description and reference.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • 1.2 lines changed: 18, context: html, text, full: html, text
    Removed an object that didn't belong
  • 1.1 lines changed: 327, context: html, text, full: html, text
    Forgot to load Yale PolyA into the mdb earlier
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.490 lines changed: 61, context: html, text, full: html, text
    Cleaning up the conservation track default settings a little. Commenting out some '_v2' versions of the conservation wiggles that have been up along side the normal one for months now.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.1000 lines changed: 6, context: html, text, full: html, text
    Removed dateSubmitted from all metadata for Mapability track to remove Restricted Until date on the config page as this does not apply for this track.
  • 1.999 lines changed: 1, context: html, text, full: html, text
    add parent for public mapability track
  • 1.998 lines changed: 25, context: html, text, full: html, text
    Renaming wgEncodeRegMarkEnhancer subtracks to have the expected prefix rather than 'jkEnh'
  • 1.997 lines changed: 1, context: html, text, full: html, text
    change wgEncodeGisPet.alpha.ra to wgEncodeGisPet.ra
  • 1.996 lines changed: 5, context: html, text, full: html, text
    Changed the colour of CRG Mapability subtracks.
  • 1.995 lines changed: 6, context: html, text, full: html, text
    Changed colour of CRG Mapability subtracks.
  • 1.994 lines changed: 1, context: html, text, full: html, text
    added win to dimensions in mapability track
  • 1.993 lines changed: 4785, context: html, text, full: html, text
    Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra
  • 1.992 lines changed: 1623, context: html, text, full: html, text
    Split Broad Histone out of trackdDb.wgEnocde.ra
  • 1.991 lines changed: 2185, context: html, text, full: html, text
    Split Open Chromatin out of trackdDb.wgEnocde.ra
  • 1.990 lines changed: 2377, context: html, text, full: html, text
    Split Yale TFBS out of trackdDb.wgEnocde.ra
  • 1.989 lines changed: 3639, context: html, text, full: html, text
    Split HAIB TFBS out of trackDb.wgEnocde.ra
  • 1.988 lines changed: 2, context: html, text, full: html, text
    make calTech include files follow spec
  • 1.987 lines changed: 6, context: html, text, full: html, text
    added release alpha to new calTech tracks in Jims enhancer track
  • 1.986 lines changed: 320, context: html, text, full: html, text
    removed release alpha,beta lines to release Yale TFBS; also removed two ghost sub-block entries for tables that don't exist in the Yale TFBS track
  • 1.985 lines changed: 1510, context: html, text, full: html, text
    removed release public trackDb entry of Yale TFBS (release 2) in prep for release 3 of that track
  • 1.984 lines changed: 76, context: html, text, full: html, text
    Removing stray 'ES' from label of non-ES cells in wgEncodeReg track.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
  • 1.1 lines changed: 1626, context: html, text, full: html, text
    Split Broad Histone out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
  • 1.10 lines changed: 1537, context: html, text, full: html, text
    moved to official names
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra
  • 1.5 lines changed: 1534, context: html, text, full: html, text
    moved to official names
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
  • 1.2 lines changed: 144, context: html, text, full: html, text
    changed release tags
  • 1.1 lines changed: 1537, context: html, text, full: html, text
    move to official names
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Uncommented dimensions line to fix (null) label on rr
  • 1.2 lines changed: 144, context: html, text, full: html, text
    take out beta
  • 1.1 lines changed: 1534, context: html, text, full: html, text
    move to official names
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.ra
  • 1.1 lines changed: 2188, context: html, text, full: html, text
    Split Open Chromatin out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDnaMethylSuper.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Add Melissa's supertrack descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeExonArraySuper.html
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Add Melissa's supertrack descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra
  • 1.15 lines changed: 1048, context: html, text, full: html, text
    moved to wgEncodeGisPet.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.14 lines changed: 15, context: html, text, full: html, text
    minor grammar updates and display things
  • 1.13 lines changed: 22, context: html, text, full: html, text
    grammar fixes and jolly updates
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
  • 1.2 lines changed: 80, context: html, text, full: html, text
    releasing public
  • 1.1 lines changed: 1048, context: html, text, full: html, text
    move this from wgEncodeGisPet.alpha.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • 1.1 lines changed: 3188, context: html, text, full: html, text
    Split HAIB TFBS out of trackDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
  • 1.1 lines changed: 457, context: html, text, full: html, text
    Split HAIB TFBS out of trackDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.21 lines changed: 1, context: html, text, full: html, text
    fixed a typo
  • 1.20 lines changed: 11, context: html, text, full: html, text
    fixed grammar issues for CRG Alignability subtrack decscription
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRnaSeqSuper.html
  • 1.1 lines changed: 98, context: html, text, full: html, text
    Add Melissa's supertrack descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeTfBindingSuper.html
  • 1.1 lines changed: 65, context: html, text, full: html, text
    Add Melissa's supertrack descriptions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
  • 1.1 lines changed: 2613, context: html, text, full: html, text
    Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra
  • 1.1 lines changed: 241, context: html, text, full: html, text
    Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • 1.1 lines changed: 1938, context: html, text, full: html, text
    Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 2381, context: html, text, full: html, text
    Split Yale TFBS out of trackdDb.wgEnocde.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • 1.2 lines changed: 141, context: html, text, full: html, text
    Updated metaDb using newly generated,by pipeline, mdb.txt for submission 1210.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • 1.2 lines changed: 133, context: html, text, full: html, text
    SYDH Histone: Added meta data from submission 1205
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • 1.3 lines changed: 197, context: html, text, full: html, text
    Added metaData from submission 1208, 1209
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Changed colour of CRG Mapability subtracks.
  • 1.17 lines changed: 6, context: html, text, full: html, text
    Changed colour of CRG Mapability subtracks.
  • 1.16 lines changed: 28, context: html, text, full: html, text
    SYDH TFBS: Add Cell Line Raji subtracks (submissions: 1208 and 1209)
  • 1.15 lines changed: 137, context: html, text, full: html, text
    first cut at v4 Gencode genes
  • 1.14 lines changed: 1, context: html, text, full: html, text
    fix downloads link for Mapability track
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add canPack to Mapability track
  • 1.12 lines changed: 41, context: html, text, full: html, text
    HAIB TFBS: Added subtracks from submission 1210.
  • 1.11 lines changed: 27, context: html, text, full: html, text
    SYDH Histone: Added subtracks from submission 1205
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • 1.1 lines changed: 246, context: html, text, full: html, text
    first cut at v4 description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed a typo
  • 1.3 lines changed: 11, context: html, text, full: html, text
    fixed grammar issues for CRG Alignability subtrack decscription
  • 1.2 lines changed: 7, context: html, text, full: html, text
    changed the mail to to be the name instead
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding dimensions to tracks that were getting a (null) label in hgTrackUi on the sortOrder. According to Brian, this problem is occurring in the v232 CGIs on composits with sortOrders that include things that are not views and that are not included in the dimensions.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.536 lines changed: 6, context: html, text, full: html, text
    Added search term for DECIPHER.
  • 1.535 lines changed: 3, context: html, text, full: html, text
    Updated OMIM URL.
• src/hg/makeDb/trackDb/human/wgEncodeGencode.html
  • 1.8 lines changed: 254, context: html, text, full: html, text
    move down into hg19
• src/hg/makeDb/trackDb/makefile
  • 1.289 lines changed: 1, context: html, text, full: html, text
    Added felCat4 to DBS.
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.12 lines changed: 5, context: html, text, full: html, text
    add search on bacEnds table
  • 1.11 lines changed: 7, context: html, text, full: html, text
    adding bac end track
  • 1.10 lines changed: 9, context: html, text, full: html, text
    adding ctgPos2 to trackDb. Copied it exactly from susScr2
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Stan/Yale Histone: Shortened Subtrack Long labels to comply with 80 character rule. Modifications -> Mods.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
  • 1.1 lines changed: 150, context: html, text, full: html, text
    Updated Description page with preliminary information provided by Stephen Landt
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • 1.2 lines changed: 92, context: html, text, full: html, text
    Updated Description page with preliminary information provided by Stephen Landt
• src/hg/makeDb/trackDb/snp131.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    minor change: fixing name of reference file for SNP track
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Added new functional annotattion codes cds-indel, coding-synonymy-unknown; added 1000Genomes as validation type. Thanks Mary!
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Adding transformFunc to wig and bigWig types.
• src/hg/makeDb/trackDb/trackDb.nt.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adding dimensions to tracks that were getting a (null) label in hgTrackUi on the sortOrder. According to Brian, this problem is occurring in the v232 CGIs on composits with sortOrders that include things that are not views and that are not included in the dimensions.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.638 lines changed: 31, context: html, text, full: html, text
    Removing temporary fix to all_mrna and all_est tracks now that v232 cgis are out on the RR.
  • 1.637 lines changed: 25, context: html, text, full: html, text
    fixed search problems with ucscRetroAli
  • 1.636 lines changed: 1, context: html, text, full: html, text
    changed the temporary all_mrna track that angie added to visibility dense.
  • 1.635 lines changed: 10, context: html, text, full: html, text
    add search for retrogene track
  • 1.634 lines changed: 31, context: html, text, full: html, text
    Adding back all_mrna and all_est with release public for backwards compatibility with CGIs currently on RR.
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
  • 1.12 lines changed: 35, context: html, text, full: html, text
    added multiz6way and phastCons
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.6 lines changed: 18, context: html, text, full: html, text
    Improving indentation. Improving an error message, and the test that triggers it.
• src/hg/tcga/pBamBam/asBamBam.c
  • 1.12 lines changed: 8, context: html, text, full: html, text
    added new mutation caller
  • 1.11 lines changed: 323, context: html, text, full: html, text
    added new mutation caller
• src/hg/tcga/pBamBam/makefile
  • 1.8 lines changed: 3, context: html, text, full: html, text
    added new mutation caller
• src/hg/tcga/pBamBam/pBamBamSNP.c
  • 1.2 lines changed: 47, context: html, text, full: html, text
    added new mutation caller
• src/hg/utils/automation/Encode.pm
  • 1.67 lines changed: 1, context: html, text, full: html, text
    make a variable bamTypes
  • 1.66 lines changed: 1, context: html, text, full: html, text
    Added mdb.txt file for metadata lines
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.24 lines changed: 168, context: html, text, full: html, text
    adding version 58 to the listings
• src/hg/utils/automation/makefile
  • 1.15 lines changed: 1, context: html, text, full: html, text
    need to mkdir scripts
• src/inc/bwgInternal.h
  • 1.10 lines changed: 71, context: html, text, full: html, text
    Moving some stuff from bwgCreate to bwgInternal.h where it can be shared a bit more. Tweaking things so first zoom level is a better size, which speeds up 100k views.
• src/inc/common.h
  • 1.173 lines changed: 10, context: html, text, full: html, text
    Adding some const to string function parameters to better work with C standard library code as callbacks.
  • 1.172 lines changed: 3, context: html, text, full: html, text
    add slNameIntersection
• src/inc/common.mk
  • 1.80 lines changed: 1, context: html, text, full: html, text
    SCRIPTS is now HOME/bin/scripts not /cluster/bin/scripts
• src/inc/correlate.h
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Adding correlateNextMulti
• src/lib/bbiRead.c
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Reducing amount of zoom oversampling, which speeds up 100k views a fair bit.
• src/lib/bwgCreate.c
  • 1.25 lines changed: 76, context: html, text, full: html, text
    Moving some stuff from bwgCreate to bwgInternal.h where it can be shared a bit more. Tweaking things so first zoom level is a better size, which speeds up 100k views.
  • 1.24 lines changed: 5, context: html, text, full: html, text
    Making it so wigToBigWig will default span to step size.
• src/lib/common.c
  • 1.150 lines changed: 18, context: html, text, full: html, text
    Adding some const to string function parameters to better work with C standard library code as callbacks.
  • 1.149 lines changed: 16, context: html, text, full: html, text
    add slNameIntersection
• src/lib/correlate.c
  • 1.3 lines changed: 16, context: html, text, full: html, text
    Adding correlateNextMulti
• src/makefile
  • 1.75 lines changed: 3, context: html, text, full: html, text
    added needed include
  • 1.74 lines changed: 2, context: html, text, full: html, text
    may as well mkdir on scripts and destdir bindir as we start up
  • 1.73 lines changed: 2, context: html, text, full: html, text
    adding liftUp to the userApps build
• src/test/buildTableDescriptions.pl
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Warn, don't die, when there are duplicate .as files, so tableDescriptions tables are still updated.
• src/utils/correlate/correlate.c
  • 1.1 lines changed: 58, context: html, text, full: html, text
    Seems to work.
• src/utils/correlate/expected
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Seems to work.
• src/utils/correlate/makefile
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Seems to work.
• src/utils/correlate/test.tab
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Seems to work.
• src/utils/plotDataMatrix/enh.tab
  • 1.1 lines changed: 28, context: html, text, full: html, text
    Matrix plotter seems to work.
• src/utils/plotDataMatrix/enhCol.tab
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Matrix plotter seems to work.
• src/utils/plotDataMatrix/enhRow.tab
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Matrix plotter seems to work.
• src/utils/plotDataMatrix/makefile
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Matrix plotter seems to work.
• src/utils/plotDataMatrix/plotDataMatrix.c
  • 1.1 lines changed: 240, context: html, text, full: html, text
    Matrix plotter seems to work.
• src/utils/qa/qaEncodeTracks.csh
  • 1.13 lines changed: 8, context: html, text, full: html, text
    needed to trap the case of missing entry in trackDb file
• src/utils/qa/syncAday.csh
  • 1.12 lines changed: 2, context: html, text, full: html, text
    sendiing output to stdout instead of to kuhn to make it easier to send to more than one person via cronjob
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.117 lines changed: 2, context: html, text, full: html, text
    v233 preview
• src/utils/qa/weeklybld/buildUtils.csh
  • 1.19 lines changed: 8, context: html, text, full: html, text
    override new default SCRIPTS location
  • 1.18 lines changed: 6, context: html, text, full: html, text
    pains with utils build
• src/utils/qa/weeklybld/doNewBranch.csh
  • 1.36 lines changed: 1, context: html, text, full: html, text
    fixing URL now at genecats
• src/utils/wigCorrelate/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Still half baked, but it compiles at least.
• src/utils/wigCorrelate/wigCorrelate.c
  • 1.3 lines changed: 20, context: html, text, full: html, text
    Adding clampMax option.
  • 1.2 lines changed: 63, context: html, text, full: html, text
    Cleaned up a bit and tested more. Fixed a bug that made it hang after about 25 pairwise correlations.
  • 1.1 lines changed: 389, context: html, text, full: html, text
    Still half baked, but it compiles at least.
• src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Improving usage message.
• src/utils/wigTestMaker/timeNotes
  • 1.2 lines changed: 110, context: html, text, full: html, text
    SOme more timing measurements.
  • 1.1 lines changed: 168, context: html, text, full: html, text
    Putting timing notes under CVS.
• src/utils/wigToBigWig/testFixed.wig
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Taking out span since it now defaults in one fixedStep line of test.

• lines changed: 59795
• files changed: 177