CVS changes by file

branch to review (2009-04-28 to 2009-05-05) v205

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.3 lines changed: 2, context: html, text, full: html, text
    add natrMaga0; fix multiz for vulcDist0 and joseCoat_042308
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.66 lines changed: 54, context: html, text, full: html, text
    add natrMaga0; fix multiz for vulcDist0 and joseCoat_042308
• src/hg/archaeStuff/data/blat-servers.tab
  • 1.1 lines changed: 6, context: html, text, full: html, text
    blat server host config
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.2 lines changed: 1, context: html, text, full: html, text
    add pog reads
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.16 lines changed: 377, context: html, text, full: html, text
    add mblastx for metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.32 lines changed: 4, context: html, text, full: html, text
    allow comments in blat server file and precomputed track file
  • 1.31 lines changed: 41, context: html, text, full: html, text
    extract blat server host to separate file
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.30 lines changed: 7, context: html, text, full: html, text
    add mblastx for metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/PrecomputedTrack.pm
  • 1.9 lines changed: 3, context: html, text, full: html, text
    allow comments in blat server file and precomputed track file
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.41 lines changed: 6, context: html, text, full: html, text
    add mblastx for metagenomes
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.14 lines changed: 26, context: html, text, full: html, text
    Fixed bug where last chr could be truncated if the previous one was smaller
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.64 lines changed: 50, context: html, text, full: html, text
    add tagAligns as bigbed becuase they are too big to load to mysql
• src/hg/encode/encodeLoad/installSqlSchemas.pl
  • 1.2 lines changed: 26, context: html, text, full: html, text
    also copy .as files
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.94 lines changed: 16, context: html, text, full: html, text
    Added Rad21 and XRCC4 antibodies fro Yale
  • 1.93 lines changed: 8, context: html, text, full: html, text
    Added Pol3 for Yale
  • 1.92 lines changed: 5, context: html, text, full: html, text
    Removed some cut and paste errors
  • 1.91 lines changed: 84, context: html, text, full: html, text
    Added 8 cell lines for Stam lab
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.180 lines changed: 1, context: html, text, full: html, text
    Fixed bug that couldn't find an unzipped file.
  • 1.179 lines changed: 1, context: html, text, full: html, text
    No validator for fragLength
• src/hg/encode/validateFiles/validateFiles.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    fastq sequence names can have # in them.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • 1.35 lines changed: 3, context: html, text, full: html, text
    Updated idSql for links to Jackson Lab, Gepsis, and Gene Card to bypass non-coding genes.
• src/hg/hgGene/hgGeneData/links.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    Updated idSql for links to Stanford Source to bypass non-coding genes.
• src/hg/hgTables/bedList.c
  • 1.67 lines changed: 2, context: html, text, full: html, text
    Performance/memory leak fix: move hTrackDbForTrack (and bedItemRgb, thanks Tim) out of the inner loop of doGetBedOrCt.
• src/hg/hgTracks/cds.c
  • 1.94 lines changed: 6, context: html, text, full: html, text
    Fixed another couple off-by-one problems with insertion lines on the right end of thick portion (thanks Brooke!).
  • 1.93 lines changed: 7, context: html, text, full: html, text
    fixed bug where exons within 3 bases of the start of a chromosome are rendered in solid yellow. No idea why this code was this way
• src/hg/hgTracks/simpleTracks.c
  • 1.77 lines changed: 49, context: html, text, full: html, text
    Rewrote getScoreFilterClause to use hui.c::dyAddFilterAsInt() so that all score filtering uses the same rules
  • 1.76 lines changed: 25, context: html, text, full: html, text
    Added methods for H1N1 (swine flu) sequences.
• src/hg/hgc/hgc.c
  • 1.1532 lines changed: 30, context: html, text, full: html, text
    Put in IF to skip src links, until ORegAnno is fixed.
  • 1.1531 lines changed: 200, context: html, text, full: html, text
    Added details page for H1N1.
• src/hg/hgc/hgdpClick.c
  • 1.7 lines changed: 24, context: html, text, full: html, text
    Remove the working directory after generating images, because the cleaner script does not remove empty dirs (Thx Hiram).
• src/hg/inc/hui.h
  • 1.125 lines changed: 13, context: html, text, full: html, text
    Just changed function comments
  • 1.124 lines changed: 3, context: html, text, full: html, text
    Added a few simple defines
• src/hg/inc/jksql.h
  • 1.83 lines changed: 5, context: html, text, full: html, text
    fixed bug where wrong profile was used for hgcentral
• src/hg/instinct/bioInt2/bioController.c
  • 1.9 lines changed: 22, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioController.h
  • 1.6 lines changed: 16, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntDb.as
  • 1.6 lines changed: 10, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntDb.c
  • 1.8 lines changed: 173, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntDb.h
  • 1.7 lines changed: 79, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntDb.sql
  • 1.6 lines changed: 11, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntDriver.h
  • 1.6 lines changed: 1, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.37 lines changed: 1, context: html, text, full: html, text
    fixed row issue
  • 1.36 lines changed: 13, context: html, text, full: html, text
    Added remove all button
• src/hg/instinct/bioInt2/bioIntFrontend/index.html
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Added remove all button
• src/hg/instinct/bioInt2/bioLevelI.c
  • 1.7 lines changed: 55, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/createTables.c
  • 1.2 lines changed: 18, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/grabData.c
  • 1.5 lines changed: 0, context: html, text, full: html, text
    added factor graph pipeline and code
  • 1.4 lines changed: 104, context: html, text, full: html, text
    fixed grabData for new db structure
• src/hg/instinct/bioInt2/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    added factor graph pipeline and code
• src/hg/instinct/bioInt2/populateDb.c
  • 1.10 lines changed: 77, context: html, text, full: html, text
    added sex correction
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenBio.ra
  • 1.2 lines changed: 486, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenGBMBio.ra
  • 1.1 lines changed: 486, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinGBMBio.ra
  • 1.1 lines changed: 36, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.2 lines changed: 344, context: html, text, full: html, text
    New clinical data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.9 lines changed: 103, context: html, text, full: html, text
    Update to clinical data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAopen.ra
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Commented out bits that might break some browsers.
  • 1.2 lines changed: 26, context: html, text, full: html, text
    Updated clinical data
• src/hg/js/utils.js
  • 1.20 lines changed: 8, context: html, text, full: html, text
    Unintentionally left some exclamations in validateInt messages
• src/hg/lib/encode/tagAlign.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    tagalign files exceed the 4gb mysql data limit
• src/hg/lib/hdb.c
  • 1.402 lines changed: 20, context: html, text, full: html, text
    fixed bug where wrong profile was used for hgcentral
• src/hg/lib/hui.c
  • 1.190 lines changed: 393, context: html, text, full: html, text
    Rewrote score filtering UI and extraWhere to ensure they all play by the same rules.
  • 1.189 lines changed: 1, context: html, text, full: html, text
    NO_VALUE was moved to cheapcgi.h
• src/hg/lib/jksql.c
  • 1.130 lines changed: 19, context: html, text, full: html, text
    fixed bug where wrong profile was used for hgcentral
• src/hg/makeDb/doc/encodeDccHg18.txt
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Removed this empty doc file as all docs are by lab in the encodeDccHg18 subdirectory
• src/hg/makeDb/doc/h1n1.txt
  • 1.2 lines changed: 21, context: html, text, full: html, text
    Added h1n1_0429Seq track using latest data today (4/29/09).
• src/hg/makeDb/genbank/etc/hgdownload.crontab
  • 1.16 lines changed: 3, context: html, text, full: html, text
    can't use --times
  • 1.15 lines changed: 1, context: html, text, full: html, text
    added locking and time preserve download rsync
• src/hg/makeDb/genbank/etc/mkdownload
  • 1.8 lines changed: 5, context: html, text, full: html, text
    prevent bogus stale lock message by doing one database's downloads at a time
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • 1.16 lines changed: 11, context: html, text, full: html, text
    prevent bogus stale lock message by doing one database's downloads at a time
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.74 lines changed: 4, context: html, text, full: html, text
    added updated version of harvard ovarian CGH array
• src/hg/makeDb/schema/all.joiner
  • 1.710 lines changed: 30, context: html, text, full: html, text
    Hopefully fixed wgEncodeGencode and added wgEncodeNhgriBip
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Hide hg19 net by default.
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Moved hg19 net/chain so that it comes after hg18 net/chain.
• src/hg/makeDb/trackDb/human/HInvGeneMrna.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to HInv-DB.
• src/hg/makeDb/trackDb/human/hg16/encodeMlaganCons.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg16/encodeTbaCons.html
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeMavidCons.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeMavidElements.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganCons.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganElements.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeTbaCons.html
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Fixed links to Haussler lab.
• src/hg/makeDb/trackDb/human/hg18/HInvGeneMrna.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to HInv-DB.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.390 lines changed: 1, context: html, text, full: html, text
    removed ability to filter by score for Alt Events track configuration page (all scores are 1000)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.283 lines changed: 583, context: html, text, full: html, text
    UW Stam ChIP-seq track with 40 subtracks: 4 views each of 10 different cell/antibody combos.
  • 1.282 lines changed: 426, context: html, text, full: html, text
    Added Yales resubmitted signals and fixed metadata dates by adding dateResubmitted= value
  • 1.281 lines changed: 118, context: html, text, full: html, text
    Added HL-60, Th2, and SKMC cells to UW Stam DNase track.
  • 1.280 lines changed: 119, context: html, text, full: html, text
    Three more cell lines for the UW DNase-seq track.
  • 1.279 lines changed: 3, context: html, text, full: html, text
    Commented out release alpha to stage on beta.
  • 1.278 lines changed: 275, context: html, text, full: html, text
    Added resubmitted Yale Peaks, though I may be changing unrestructed date yet.
  • 1.277 lines changed: 33, context: html, text, full: html, text
    commented out some "release alpha" blocks
  • 1.276 lines changed: 4, context: html, text, full: html, text
    Added links by trackDb settings to two Gencode tracks
  • 1.275 lines changed: 2, context: html, text, full: html, text
    Fix group assignment for some RNA-seq tracks
  • 1.274 lines changed: 14, context: html, text, full: html, text
    Edit GIS RNA-seq labels for consistency and length
  • 1.273 lines changed: 6, context: html, text, full: html, text
    Fix labels and colors in Helicos
  • 1.272 lines changed: 28, context: html, text, full: html, text
    Prune Caltech track short labels to size
  • 1.271 lines changed: 22, context: html, text, full: html, text
    Affy short labels for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Changes from code review
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed a broken link
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.15 lines changed: 24, context: html, text, full: html, text
    Added panTro2 chain and net blocks.
  • 1.14 lines changed: 10, context: html, text, full: html, text
    Also need a ctgPosNoVersion search (can't expect everyone to always include the .1).
  • 1.13 lines changed: 8, context: html, text, full: html, text
    Added ctgPos search with termRegex for new contig names.
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Small edits for clarity.
• src/hg/makeDb/trackDb/human/sestanBrainAtlas.html
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Turned the link to GEO into an actual link.
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Updated description. citation still to come.
• src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroCali1/trackDb.ra
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/therPend1/trackDb.ra
  • 1.10 lines changed: 22, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.74 lines changed: 237, context: html, text, full: html, text
    add blastx tracks
  • 1.73 lines changed: 19, context: html, text, full: html, text
    add track Pog 454 reads; add scaffold name searching
• src/hg/makeDb/trackDb/nci60.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Changed IMAGE Consortium link to hudsonAlpha, where it now resides.
• src/hg/makeDb/trackDb/oreganno.html
  • 1.13 lines changed: 4, context: html, text, full: html, text
    Added color description
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.36 lines changed: 1, context: html, text, full: html, text
    lowered scoreFilter default to catch min values from table in transRegCode track
• src/hg/makeDb/trackDb/sacCer/transRegCode.html
  • 1.9 lines changed: 2, context: html, text, full: html, text
    fixed redirected link
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changed lower range of score to match reality
• src/hg/makeDb/trackDb/snp.html
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Fixed link to Affymetrix 10K SNP array. Looks like there is only verson 2 now.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.503 lines changed: 1, context: html, text, full: html, text
    shortened the shortLabel to fit within the 16 char maximum
• src/hg/makefile
  • 1.150 lines changed: 3, context: html, text, full: html, text
    do make alpha in the encode dirs
• src/hg/pslStats/pslStats.c
  • 1.8 lines changed: 76, context: html, text, full: html, text
    add queries aligned to overall stats
• src/hg/pslStats/tests/expected/cdna2cdnaOverallTest.stats
  • 1.2 lines changed: 2, context: html, text, full: html, text
    add queries aligned to overall stats
• src/hg/pslStats/tests/expected/untransOverallTest.stats
  • 1.4 lines changed: 2, context: html, text, full: html, text
    add queries aligned to overall stats
• src/hg/pslStats/tests/expected/untransOverallUnalnTest.stats
  • 1.4 lines changed: 2, context: html, text, full: html, text
    add queries aligned to overall stats
• src/hg/stsMarkers/convertPrimerToFA
  • 1.2 lines changed: 29, context: html, text, full: html, text
    Updated with strict and warnings and bugs worked out from that conversion
  • 1.1 lines changed: 85, context: html, text, full: html, text
    Initial source rescued from /cluster/bin/scripts
• src/hg/stsMarkers/findAccession
  • 1.3 lines changed: 274, context: html, text, full: html, text
    Transitioned file to findAccession.pl
• src/hg/stsMarkers/findAccession.pl
  • 1.1 lines changed: 293, context: html, text, full: html, text
    Transition of file from src/utils/findAccession.pl, updated to work with hg19, added strict and warnings and worked out a number of deficiencies
• src/hg/tcga/scripts/createLabTrackTCGA.py
  • 1.1 lines changed: 55, context: html, text, full: html, text
    added script to generate tcga labTrack file
• src/hg/tcga/scripts/labtrack.sql
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added script to generate tcga labTrack file
• src/hg/utils/automation/Encode.pm
  • 1.42 lines changed: 2, context: html, text, full: html, text
    updated message
  • 1.41 lines changed: 2, context: html, text, full: html, text
    add tagAligns as bigbed becuase they are too big to load to mysql
• src/inc/bigBed.h
  • 1.13 lines changed: 50, context: html, text, full: html, text
    splitting bigBedFileCreate() logic to load bed records from a file separately from calculating summary and writing files
• src/inc/cheapcgi.h
  • 1.65 lines changed: 3, context: html, text, full: html, text
    accessor for content_length request header
  • 1.64 lines changed: 6, context: html, text, full: html, text
    more cgi accessors for standard ENV vars
  • 1.63 lines changed: 1, context: html, text, full: html, text
    Added support for a numerical limit having NO_VALUE in the cgiMakeIntWithLimits() and cgiMakeDoubleWithLimits() functions
• src/inc/hash.h
  • 1.49 lines changed: 5, context: html, text, full: html, text
    I take the comemnts back. It seems some poeple like to store hash elements as the value of other hash elemnets in hashes.
  • 1.48 lines changed: 5, context: html, text, full: html, text
    expanding message which lead to a bug somewhere else
• src/lib/bigBed.c
  • 1.17 lines changed: 233, context: html, text, full: html, text
    splitting bigBedFileCreate() logic to load bed records from a file separately from calculating summary and writing files
• src/lib/cheapcgi.c
  • 1.120 lines changed: 6, context: html, text, full: html, text
    accessor for content_length request header
  • 1.119 lines changed: 12, context: html, text, full: html, text
    more cgi accessors for standard ENV vars
  • 1.118 lines changed: 55, context: html, text, full: html, text
    Added support for a numerical limit having NO_VALUE in the cgiMakeIntWithLimits() and cgiMakeDoubleWithLimits() functions
• src/lib/hash.c
  • 1.50 lines changed: 5, context: html, text, full: html, text
    I take the comemnts back. It seems some poeple like to store hash elements as the value of other hash elemnets in hashes.
  • 1.49 lines changed: 5, context: html, text, full: html, text
    expanding message which lead to a bug somewhere else
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.5 lines changed: 8, context: html, text, full: html, text
    sorted option is now automatic in the bigBedFileCreate
• src/utils/findAccession.pl
  • 1.2 lines changed: 269, context: html, text, full: html, text
    Transitioned and updated file to src/hg/stsMarkers/findAccession.pl
• src/utils/qa/backupCentral.csh
  • 1.11 lines changed: 4, context: html, text, full: html, text
    changed single quotes to double so sqlbeta variable can be interpreted
• src/utils/qa/bigPush.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    calling checked-in version of updateTimes script (instead of the one in the user's /bin directory)
• src/utils/qa/checkWigFiles.csh
  • 1.2 lines changed: 7, context: html, text, full: html, text
    a few tweaks based on Bob's code review feedback (thanks Bob)
• src/utils/qa/realTime.csh
  • 1.11 lines changed: 17, context: html, text, full: html, text
    re-enabled sql version checking
• src/utils/qa/runBits.csh
  • 1.15 lines changed: 43, context: html, text, full: html, text
    fixed logic and output to more clearly distinguish betw all gaps and unbridged gaps. it now prints both if there is overlap with both kinds
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.57 lines changed: 2, context: html, text, full: html, text
    v206 preview

• lines changed: 7276
• files changed: 112