CVS changes by file

branch to review (2009-05-12 to 2009-05-19) v206

• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.13 lines changed: 3, context: html, text, full: html, text
    adding variable sort fields from RNA projects
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.96 lines changed: 1, context: html, text, full: html, text
    Sloppy typo
  • 1.95 lines changed: 8, context: html, text, full: html, text
    Added E2F4 fro Yaale/UCD Farnham
• src/hg/encode/hgEncodeSubmit/config/environment.rb.sample
  • 1.4 lines changed: 1, context: html, text, full: html, text
    remove what does not work
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Try to deal with lost Mysql connection after long waits for validate or load
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.13 lines changed: 4, context: html, text, full: html, text
    Try to deal with lost Mysql connection after long waits for validate or load
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Updated URL to Gene Network web site.
• src/hg/hgGene/hgGeneData/Rat/links.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Updated URL to Gene Network site.
• src/hg/hgTracks/config.c
  • 1.78 lines changed: 2, context: html, text, full: html, text
    Added debugging hook for command-line reproduceable forms (&formMethod=GET).
• src/hg/hgTracks/hgTracks.c
  • 1.1566 lines changed: 7, context: html, text, full: html, text
    Restore last position if newly requested position proves invalid.
• src/hg/hgTracks/mafTrack.c
  • 1.64 lines changed: 2, context: html, text, full: html, text
    check for zero size before calling maf score function
• src/hg/hgTracks/simpleTracks.c
  • 1.79 lines changed: 1, context: html, text, full: html, text
    Registered snp130.
  • 1.78 lines changed: 2, context: html, text, full: html, text
    Updated h1n1 tracks.
• src/hg/hgc/hgc.c
  • 1.1544 lines changed: 4, context: html, text, full: html, text
    Could not get DNA from bigBed because bigBed table has only a single column 'fileName' and it cannot be range queried (Easier solution than doign custom code for range query)
  • 1.1543 lines changed: 37, context: html, text, full: html, text
    Replaced multiple sameWord() statements with on startWith() for H1N1 tracks.:wq
  • 1.1542 lines changed: 83, context: html, text, full: html, text
    added prototype support for launching 3D structure browser on H1N1 predicted structures
• src/hg/inc/lsSnpPdbChimera.h
  • 1.3 lines changed: 11, context: html, text, full: html, text
    added prototype support for launching 3D structure browser on H1N1 predicted structures
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.39 lines changed: 12, context: html, text, full: html, text
    Fixed issues with duplicate features by adding internal id
  • 1.38 lines changed: 19, context: html, text, full: html, text
    added border around center cell, made mouseover titles consistent
• src/hg/instinct/bioInt2/pathwayNullDist.c
  • 1.1 lines changed: 778, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.4 lines changed: 19, context: html, text, full: html, text
    Added new features
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.10 lines changed: 22, context: html, text, full: html, text
    Fixed up TCGA clinical data.
• src/hg/js/hui.js
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Oops, change for ChkBoxNormalize had one error
  • 1.27 lines changed: 51, context: html, text, full: html, text
    Reworkd Matrix to subtrack box checking to solve dimZ
• src/hg/lib/cart.c
  • 1.106 lines changed: 6, context: html, text, full: html, text
    Store last position in case new position proves invalid
• src/hg/lib/customFactory.c
  • 1.97 lines changed: 26, context: html, text, full: html, text
    add touching of udc files in cache and reporting of names for the do-not-kill-list with verbose=4
• src/hg/lib/hui.c
  • 1.196 lines changed: 2, context: html, text, full: html, text
    Fixed downloads link bug in entraUiLinks (as seen in hgc)
  • 1.195 lines changed: 1, context: html, text, full: html, text
    Added dimZ class to make javascript handle dimZ properly.
• src/hg/lib/lsSnpPdbChimera.c
  • 1.4 lines changed: 47, context: html, text, full: html, text
    added prototype support for launching 3D structure browser on H1N1 predicted structures
• src/hg/lib/lsSnpPdbChimera.py
  • 1.4 lines changed: 7, context: html, text, full: html, text
    added prototype support for launching 3D structure browser on H1N1 predicted structures
• src/hg/lib/trackDbCustom.c
  • 1.65 lines changed: 4, context: html, text, full: html, text
    In overrideField, ignore the release setting because it was removed from overTd->settingsHash earlier by pruneRelease.
• src/hg/makeDb/doc/aplCal1.txt
  • 1.3 lines changed: 50, context: html, text, full: html, text
    Initial Aplysia californica
  • 1.2 lines changed: 16, context: html, text, full: html, text
    Initial Aplysia californica
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Initial Aplysia californica
• src/hg/makeDb/doc/h1n1.txt
  • 1.6 lines changed: 17, context: html, text, full: html, text
    Added dnaSeq table.
  • 1.5 lines changed: 91, context: html, text, full: html, text
    Added the latest h1n1_0514Seq track build process, with good CDS display.
  • 1.4 lines changed: 61, context: html, text, full: html, text
    Removed old h1n1 track build processes.
• src/hg/makeDb/doc/hg19.txt
  • 1.16 lines changed: 123, context: html, text, full: html, text
    Additional lastz runs started
  • 1.15 lines changed: 135, context: html, text, full: html, text
    lastz runs updated
  • 1.14 lines changed: 157, context: html, text, full: html, text
    lastz runs status updated
  • 1.13 lines changed: 26, context: html, text, full: html, text
    Had some of the SEQ2_LAP mixed up with SEQ1_LAP
  • 1.12 lines changed: 219, context: html, text, full: html, text
    Running lastz alignments
• src/hg/makeDb/genbank/doc/config.html
  • 1.25 lines changed: 1, context: html, text, full: html, text
    added mention of gapToLift
• src/hg/makeDb/genbank/etc/build.crontab
  • 1.12 lines changed: 6, context: html, text, full: html, text
    change frequence of building download files
  • 1.11 lines changed: 3, context: html, text, full: html, text
    rebuild downloads any day of the week
• src/hg/makeDb/genbank/etc/mkdownload
  • 1.10 lines changed: 1, context: html, text, full: html, text
    rebuild downloads any day of the week
  • 1.9 lines changed: 3, context: html, text, full: html, text
    like number of hours download build runs
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • 1.19 lines changed: 1, context: html, text, full: html, text
    fixed typo
  • 1.18 lines changed: 1, context: html, text, full: html, text
    change frequence of building download files
  • 1.17 lines changed: 19, context: html, text, full: html, text
    like number of hours download build runs
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomePartition.py
  • 1.2 lines changed: 1, context: html, text, full: html, text
    minor refactoring that decided not to use
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomeSeqs.py
  • 1.5 lines changed: 3, context: html, text, full: html, text
    minor refactoring that decided not to use
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.76 lines changed: 22, context: html, text, full: html, text
    Fixed IDs on TCGA mutation data.
• src/hg/makeDb/hgFindSpec/hgFindSpec.c
  • 1.10 lines changed: 8, context: html, text, full: html, text
    addVersion: when strict-checking existence of xrefTable, use sqlTableExists instead of hTableOrSplitExists because xrefTable might be db.table.
• src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Fixed a typo and added ref hyperlink.
  • 1.6 lines changed: 17, context: html, text, full: html, text
    Added subscripts and greek letters to make equations easier to follow.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.391 lines changed: 36, context: html, text, full: html, text
    Added snp130 and changed snp12*'s to overrides instead of duplicate def's.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.301 lines changed: 2, context: html, text, full: html, text
    Rearranged RIKEN CAGE
  • 1.300 lines changed: 4, context: html, text, full: html, text
    Adjust visibiltiies on transcriptome tracks so views are visible
  • 1.299 lines changed: 29, context: html, text, full: html, text
    Changes to HudsonAlpha Chip-seq for consistency
  • 1.298 lines changed: 12, context: html, text, full: html, text
    Consistent metadata antibody=Input for Broad
  • 1.297 lines changed: 2, context: html, text, full: html, text
    Changing Duke and Broad's input/control to Input_Control for consistency
  • 1.296 lines changed: 60, context: html, text, full: html, text
    Split uniqueness tracks out of Open Chromatin and made new Mapability composite
  • 1.295 lines changed: 2, context: html, text, full: html, text
    Tweak defaults on Riken CAGE
  • 1.294 lines changed: 66, context: html, text, full: html, text
    Adjust labels and priorities of Riken CAGE for consistency, length
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    minor typo
  • 1.3 lines changed: 107, context: html, text, full: html, text
    Straightening up before pushing to QA.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.1 lines changed: 95, context: html, text, full: html, text
    Initial check-in of mapability which was creating be stripping uniqueness tracks from the Duke/UNC/UTA composite.
• src/hg/makeDb/trackDb/human/hg19/ctgPos2.html
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Adding a supercontigs mapping track
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update NCBI link to Build 37 statistics
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.18 lines changed: 13, context: html, text, full: html, text
    Adding a supercontigs mapping track
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.453 lines changed: 19, context: html, text, full: html, text
    Added a 35-mer uniqueness track
• src/hg/makeDb/trackDb/human/uniqueness.html
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Added a 35-mer uniqueness track
• src/hg/makeDb/trackDb/makefile
  • 1.267 lines changed: 1, context: html, text, full: html, text
    Added aplCal1 to DBS.
  • 1.266 lines changed: 1, context: html, text, full: html, text
    Adding baboon papHam1 to the build
• src/hg/makeDb/trackDb/oreganno.html
  • 1.14 lines changed: 4, context: html, text, full: html, text
    removed reference to broken links
• src/hg/makeDb/trackDb/snp130.html
  • 1.1 lines changed: 227, context: html, text, full: html, text
    Initial description.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.505 lines changed: 8, context: html, text, full: html, text
    Added search def for snp130.
  • 1.504 lines changed: 10, context: html, text, full: html, text
    Adde snp130.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • 1.9 lines changed: 10, context: html, text, full: html, text
    Small tweaks for dbSNP 130: broadened some formats, raised MAX_SNPID.
• src/hg/snp/snpMask/snpMaskCutDeletions.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Removed an old debugging message that confused the heck out of me when I saw it again today.
• src/hg/utils/automation/blastz-run-ucsc
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Tolerate empty results when running lineage specific repeats and tolerate previously existing results
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed typo
  • 1.5 lines changed: 1, context: html, text, full: html, text
    tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSledgeHammer.pl
  • 1.3 lines changed: 1, context: html, text, full: html, text
    handling udc cache files touching
• src/inc/bigBed.h
  • 1.14 lines changed: 30, context: html, text, full: html, text
    Adding clip parameter to bigBed creation. Making a few functions static that don't seem to need to be exposed at the moment.
• src/inc/udc.h
  • 1.10 lines changed: 3, context: html, text, full: html, text
    refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened
• src/lib/bigBed.c
  • 1.18 lines changed: 99, context: html, text, full: html, text
    Adding clip parameter to bigBed creation. Making a few functions static that don't seem to need to be exposed at the moment.
• src/lib/gff3.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed use of non-posix include
• src/lib/htmshell.c
  • 1.48 lines changed: 4, context: html, text, full: html, text
    IE turns out to be a pain. Switched from div.innerHTML to textarea.value in order to preserve newlines.
  • 1.47 lines changed: 19, context: html, text, full: html, text
    Handle html warnings as alerts
• src/lib/udc.c
  • 1.17 lines changed: 71, context: html, text, full: html, text
    refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Adding clip parameter to bigBed creation. Making a few functions static that don't seem to need to be exposed at the moment.
• src/utils/qa/alertBqueue.csh
  • 1.10 lines changed: 12, context: html, text, full: html, text
    improved debugging a little and fixed the case where larrym was being converted to larrymm by adding a space after the substitution
• src/utils/qa/backupCentral.csh
  • 1.14 lines changed: 1, context: html, text, full: html, text
    made dir group writeable
• src/utils/qa/catchBot.csh
  • 1.20 lines changed: 1, context: html, text, full: html, text
    fixed a parameter to sort that was throwing an error
• src/utils/qa/checkBOT.csh
  • 1.13 lines changed: 5, context: html, text, full: html, text
    removed sessionIDs to expose IP itself for getting location of user
• src/utils/qa/checkCoverage.csh
  • 1.10 lines changed: 3, context: html, text, full: html, text
    removed output referring to file that no longer exits
  • 1.9 lines changed: 43, context: html, text, full: html, text
    refactored handling of single chrom. removed extra steps in txStart-assignment pipe. put all rm statements together using else clause. thanks, brooke
• src/utils/qa/checkSync.csh
  • 1.17 lines changed: 1, context: html, text, full: html, text
    put quotes around rm *.out to get rid of annoying error message
• src/utils/qa/compareWholeColumn.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    dropped commas in usage statement to conform to norm
• src/utils/qa/copyExtSeqRows.csh
  • 1.6 lines changed: 10, context: html, text, full: html, text
    a few cosmetic or typo changes
• src/utils/qa/countPerChrom.csh
  • 1.8 lines changed: 65, context: html, text, full: html, text
    made it work for RR. allowed optional arguments to be used singly. allowed use of hgwbeta or hgsqlbeta. simplified logic for doing randoms last. removed tableName variable
• src/utils/qa/doGenbankTests
  • 1.9 lines changed: 37, context: html, text, full: html, text
    Moved gbSanity test to the end, collected table names into variables for each test, clarified error message.
  • 1.8 lines changed: 22, context: html, text, full: html, text
    Added special logic for getting the shortLabels for est and mrna tracks (which are special cases in trackDb). Changed some whitespace stuff.
• src/utils/qa/getChromFieldName.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    added exit after error detect. thanks, brooke.
• src/utils/qa/getSplit.csh
  • 1.12 lines changed: 11, context: html, text, full: html, text
    reset to accept hgwbeta as input. dropped machineName checking as redundant. thanks, brooke
  • 1.11 lines changed: 1, context: html, text, full: html, text
    dropped declaration of varialbe no longer used
  • 1.10 lines changed: 25, context: html, text, full: html, text
    simplified and dropped some variables. caught error state where table does not exist either split or unsplit
• src/utils/qa/makeUniProtFile.csh
  • 1.3 lines changed: 59, context: html, text, full: html, text
    added support for some non-UCSC Gene orgs
  • 1.2 lines changed: 9, context: html, text, full: html, text
    a little clean-up with the file names
  • 1.1 lines changed: 72, context: html, text, full: html, text
    this creates a mapping from UniProtIDs to ucscGeneIDs. UniProt uses it to create links from their web site to our KG details pages
• src/utils/qa/makefile
  • 1.106 lines changed: 1, context: html, text, full: html, text
    new script
• src/utils/qa/runJoiner.csh
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Added an onintr trap and label so that temp files will be removed if the script is killed prematurely.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.59 lines changed: 2, context: html, text, full: html, text
    v207 preview
• src/utils/qa/weeklybld/doNewBranch.csh
  • 1.30 lines changed: 8, context: html, text, full: html, text
    make sure we wait for any background processes before we exit after an error

• lines changed: 3602
• files changed: 78