All File Changes

v256_preview2 to v256_base (2011-08-23 to 2011-08-29) v256

• java/src/edu/ucsc/genome/qa/cgiCheck/HGGeneCheck.java
  • lines changed 2, context: html, text, full: html, text
    Added rgdGenes2 to HGGeneCheck tracks and made QADBLibrary.getGenes() work when there is no proteinID present in the known genes table.
• java/src/edu/ucsc/genome/qa/lib/QADBLibrary.java
  • lines changed 10, context: html, text, full: html, text
    Added rgdGenes2 to HGGeneCheck tracks and made QADBLibrary.getGenes() work when there is no proteinID present in the known genes table.
• python/lib/ucscgenomics/compositetrack/CompositeTrack.py
  • lines changed 264, context: html, text, full: html, text
    added composite track, used by mkGeoPkg and mkChangeNotes
• python/lib/ucscgenomics/compositetrack/__init__.py
  • lines changed 0, context: html, text, full: html, text
    added composite track, used by mkGeoPkg and mkChangeNotes
• python/lib/ucscgenomics/rafile/RaFile.py
  • lines changed 23, context: html, text, full: html, text
    added minor fix for rafile
• python/lib/ucscgenomics/textstyle/TextStyle.py
  • lines changed 40, context: html, text, full: html, text
    added composite track, used by mkGeoPkg and mkChangeNotes
• python/lib/ucscgenomics/textstyle/__init__.py
  • lines changed 0, context: html, text, full: html, text
    added composite track, used by mkGeoPkg and mkChangeNotes
• python/programs/mkGeoPkg/README
  • lines changed 9, context: html, text, full: html, text
    added minor fix for rafile
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 9, context: html, text, full: html, text
    changed come numeric processing behavior, fixed a typo
• src/hg/hgGateway/hgGateway.c
  • lines changed 13, context: html, text, full: html, text
    remove visibe image width input (see redmine #2633)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    some changes from code review with Hiram #5049
  • lines changed 1, context: html, text, full: html, text
    add jquery.cookie.js so Greg can add the stuff to remember the tabs
  • lines changed 8, context: html, text, full: html, text
    take out the code that tried to guess the correct tab to be highlighted. Greg added Javascript code to remember the last tab, which works better #4912
• src/hg/hgTables/vcf.c
  • lines changed 1, context: html, text, full: html, text
    Fixing use of uninitialized variable that was caught only when compilingwith -O, which I had omitted from my $COPT for debugging.
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    Removing position variable from hgTracks' hotlinks where possible.Now that the image and position input are updated by javascript, the position info in the static hotlinks HTML gets stale. We can just use the cart position for internal links (hgTables, hgConvert) but the stale HTML is still an issue for hotlinks that have separate variables for chrom, start and end: DNA, Ensembl, NCBI.
  • lines changed 2, context: html, text, full: html, text
    Fix from code review to use sessionId in dirty page reload. Note that Larry and I have seen that the new 'location' isn't even used, but changing the location does trigger the cache load to be abandoned and the isDirty code in hgTracks.js to be called sooner.
  • lines changed 17, context: html, text, full: html, text
    add id's to external links so we can fix-up the coordinates when doing in-place update
  • lines changed 1, context: html, text, full: html, text
    add id's to DNA link so we can fix-up the coordinates when doing in-place update
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    If items are only one pixel in full, the map item is so small that it isn't written. This is a bug in dragScrioll and is now fixed.
• src/hg/hgc/rnaFoldClick.c
  • lines changed 30, context: html, text, full: html, text
    Add organism name for EvoFold V2.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    Removed opacity from HGStyle waitMask, and put it into utils.js. This will satisfy Kate and will keep ie special casing in one place.
• src/hg/inc/pbCommon.h
  • lines changed 18, context: html, text, full: html, text
    Adding a central place for #defines common to the proteome browser code
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v256
• src/hg/js/hgHubConnect.js
  • lines changed 8, context: html, text, full: html, text
    added line to tabs initialization that will set a browser cookie to remember what tab was selected last so that when user returns to page, they are on that tab again. This cookie can be overwritten elsewhere when needed.
  • lines changed 1, context: html, text, full: html, text
    Added extra comment noting file dependency.
• src/hg/js/hgTracks.js
  • lines changed 6, context: html, text, full: html, text
    Limiting panning by wingSize is not needed at this time. Correction made for portal coords being half open.
  • lines changed 3, context: html, text, full: html, text
    Katrina says 'No need to change size (and loose commas) when panning.'
  • lines changed 4, context: html, text, full: html, text
    A more complete solution to half open portal coords while dragScrolling.
  • lines changed 41, context: html, text, full: html, text
    add experimental (and dead) code to do dynamic addition of tracks
  • lines changed 35, context: html, text, full: html, text
    fixup coordinates in external links when position is changed
  • lines changed 9, context: html, text, full: html, text
    fixup DNA link coordinates when changing position
• src/hg/js/jquery.imgareaselect.js
  • lines changed 5, context: html, text, full: html, text
    Against larry's advice, I did finish implementing the crosshair solution that QA requested.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    remove jquery.autocomplete.js from JQUERY_FILES as it is no longer used
  • lines changed 2, context: html, text, full: html, text
    added jquery.cookie.js to make file; is to be used for hgHubConnect
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    Removed opacity from HGStyle waitMask, and put it into utils.js. This will satisfy Kate and will keep ie special casing in one place.
• src/hg/lib/ensemblSource.sql
  • lines changed 7, context: html, text, full: html, text
    cross reference table for ensembl gene biotype (source) from GFF file
• src/hg/lib/fileUi.c
  • lines changed 2, context: html, text, full: html, text
    Under protest, making link from preview browser to RR browser less direct.
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    some changes from code review with Hiram #5049
  • lines changed 10, context: html, text, full: html, text
    don't save the newlines at the end of error messages in the hubStatus table
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release2.notes
  • lines changed 20, context: html, text, full: html, text
    updated notes file
  • lines changed 14, context: html, text, full: html, text
    Changing for the new revoke policy
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyRipSeq.release1.notes
  • lines changed 8, context: html, text, full: html, text
    New broadPeak files
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1, context: html, text, full: html, text
    copy paste mistake wrong date
• src/hg/makeDb/doc/oreNil1.txt
  • lines changed 17, context: html, text, full: html, text
    initial assembly sequence fetch
• src/hg/makeDb/doc/sacCer3.txt
  • lines changed 191, context: html, text, full: html, text
    initial source starting genbank and sgd gene track
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 16, context: html, text, full: html, text
    adding sacCer3
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Replaced mim2gene by omim2gene and relaxed criteria.
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Ooops, I added this line, deleted it on accident, now I'm adding again. These three should not be checked by default per Jim's request.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 36, context: html, text, full: html, text
    Moving HEK293-T-REx into alphabetic order
  • lines changed 4, context: html, text, full: html, text
    put in treatment for haib, dmso 0.02pct 7d
  • lines changed 4, context: html, text, full: html, text
    Fixing md5sum per ticket 5040
  • lines changed 48, context: html, text, full: html, text
    Fixes from code review 5040
  • lines changed 1, context: html, text, full: html, text
    corrected regex pattern so it complies with POSIX regex patterns. (We should consider moving our regex engine to PCRE, so it makes things consistent.
  • lines changed 1, context: html, text, full: html, text
    WERI-Rb-1 is female, not male
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 261, context: html, text, full: html, text
    releasing reviewed beta/cv.ra changes to the public
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 16, context: html, text, full: html, text
    Fixed some grammar, html formatting, and added some explanitory text.
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 13, context: html, text, full: html, text
    Made a couple corrections to citation. Redid the whole box surrounding the note so that it stands out better, looks nicer, and properly uses a div rather than a table to display.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 10, context: html, text, full: html, text
    changed HepG2b > HepG2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 55, context: html, text, full: html, text
    Changed the last Paired away to aligns
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    Removing the replicate 131, 132, 102 and 103
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 85, context: html, text, full: html, text
    Release 3 was merged into release 2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 29, context: html, text, full: html, text
    changed e2f6scWhataver to E2F6 in Haib Tfbs. Also added line for .new in trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 526, context: html, text, full: html, text
    restored V1 metadata
  • lines changed 141, context: html, text, full: html, text
    renamed some v2 files so they are consistent with v1 filenames
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 7, context: html, text, full: html, text
    Changing the Peak Files from bed9 to broadPeak
  • lines changed 7, context: html, text, full: html, text
    Adding the md5sum changes
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyRipSeq.ra
  • lines changed 13, context: html, text, full: html, text
    copied over crickets changes for SUNY Rip-seq, redmine #1709
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Changing the Peak Files from bed9 to broadPeak
  • lines changed 2, context: html, text, full: html, text
    changed e2f6scWhataver to E2F6 in Haib Tfbs. Also added line for .new in trackDb
  • lines changed 2, context: html, text, full: html, text
    modified for trackDb also
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 3, context: html, text, full: html, text
    Miss-spelling of Nuleolus as Nucleolos and nlos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 3, context: html, text, full: html, text
    Fixed long labels and typos according to ticket 2019
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 156, context: html, text, full: html, text
    Fixed long labels and typos according to ticket 2019
  • lines changed 2, context: html, text, full: html, text
    Changed the last Paired away to aligns
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    Miss-spelling of Nuleolus as Nucleolos and nlos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.r3.ra
  • lines changed 2323, context: html, text, full: html, text
    Release 3 was merged into release 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 9, context: html, text, full: html, text
    Miss-spelling of Nuleolus as Nucleolos and nlos
  • lines changed 0, context: html, text, full: html, text
    took out errant tab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 20, context: html, text, full: html, text
    Added two missing tracks
  • lines changed 8, context: html, text, full: html, text
    Release 3 was merged into release 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 13, context: html, text, full: html, text
    changed e2f6scWhataver to E2F6 in Haib Tfbs. Also added line for .new in trackDb
  • lines changed 35, context: html, text, full: html, text
    subgroup error fexed
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
  • lines changed 3, context: html, text, full: html, text
    Mapability release 3 getting some QA love. Minor changes not likely to be the end.
  • lines changed 26, context: html, text, full: html, text
    Added display conventions section at QA's request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 10, context: html, text, full: html, text
    Mapability release 3 getting some QA love. Minor changes not likely to be the end.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 16, context: html, text, full: html, text
    Miss-spelling of Nuleolus as Nucleolos and nlos
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html
  • lines changed 171, context: html, text, full: html, text
    made html for suny gene st release2 modified trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 1, context: html, text, full: html, text
    made html for suny gene st release2 modified trackDb
  • lines changed 2, context: html, text, full: html, text
    Fixing one thing to show matt
  • lines changed 12, context: html, text, full: html, text
    renamed some v2 files so they are consistent with v1 filenames
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 4, context: html, text, full: html, text
    fix a white space between percentage, updated the html, fixed a link that was being redirected, and added a 0 place holder.
  • lines changed 9, context: html, text, full: html, text
    Making description changes for Vanessa
  • lines changed 14, context: html, text, full: html, text
    Fixing git merge
  • lines changed 2, context: html, text, full: html, text
    Adding the Sam/Bam information
  • lines changed 9, context: html, text, full: html, text
    removed breaks and removed a space, redmine# 1709
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.new.ra
  • lines changed 406, context: html, text, full: html, text
    Changing the Peak Files from bed9 to broadPeak
  • lines changed 406, context: html, text, full: html, text
    deleting a file that should never have been added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 8, context: html, text, full: html, text
    Changing the Peak Files from bed9 to broadPeak
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
  • lines changed 147, context: html, text, full: html, text
    Trying to recover this track description
  • lines changed 4, context: html, text, full: html, text
    fixed stuff per QA request
  • lines changed 1, context: html, text, full: html, text
    changed email address to be gersein lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    fixed stuff per QA request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 860, context: html, text, full: html, text
    remade the .new.ra for sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 14, context: html, text, full: html, text
    qa changes to unc protgeno
  • lines changed 16, context: html, text, full: html, text
    Merge branch 'master' into validate
  • lines changed 3, context: html, text, full: html, text
    change data to plural and other minor edits, redmine #141
  • lines changed 16, context: html, text, full: html, text
    moving info about 'Peptide Repeat Count' so that it is listed in the same order as it appears in the hgc details, and other minor edits to that paragrpah, redmine 141
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 1, context: html, text, full: html, text
    qa changes to unc protgeno
  • lines changed 2, context: html, text, full: html, text
    Merge branch 'master' into validate
  • lines changed 1, context: html, text, full: html, text
    added controlledVocabulary line
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 1429, context: html, text, full: html, text
    Added 5 submissions with updated data. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 100, context: html, text, full: html, text
    Added 5 submissions with updated data. Redmine #110.
• src/hg/perf/makefile
  • lines changed 1, context: html, text, full: html, text
    clean should remove local binaries too
• src/hg/protein/pbCalDist/pbCalDist.c
  • lines changed 10, context: html, text, full: html, text
    Added use of the new pbCommon #define. Added hydrophobicity data for the uncommon amino acids. Got rid of the use of a couple magic numbers in the code
  • lines changed 1, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • lines changed 11, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • lines changed 7, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
  • lines changed 1, context: html, text, full: html, text
    Adding a #define that I forgot to add before...
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 2, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 6, context: html, text, full: html, text
    (1) Various updates on the proteome browser code, addressing this week's code review feedback from Jim to ensure that all arrays have all cells initialized (and in the process, guesstimating some hydrophobicity numbers of amino acids such as pyrrolysine and selenocystine), and getting rid of some magic numbers that were doing nothing good to the code. (2) Now that I've learned that there is a FAQ for formats, I've added an entry for peptideMapping, used by wgEncodeUncBsuProt
• src/inc/udc.h
  • lines changed 2, context: html, text, full: html, text
    make udcRead support bit64 request size instead of int
• src/lib/common.c
  • lines changed 9, context: html, text, full: html, text
    using a loop is needed when request size exceeds 2GB
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    adding a little more helpful info about the hostName to the error message
• src/lib/options.c
  • lines changed 8, context: html, text, full: html, text
    make the range checking for the integer return type be real and prevent overflow
• src/lib/udc.c
  • lines changed 8, context: html, text, full: html, text
    make udcRead support bit64 request size instead of int
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v256 final build

• lines changed: 8572
• files changed: 128