CVS changes by file

review to branch (2010-04-27 to 2010-05-04) v230

• src/hg/encode/DAFs/GisChiaPet.daf
  • 1.1 lines changed: 35, context: html, text, full: html, text
    First cut of data agreement for ChIA-PET
• src/hg/encode/DAFs/GisChiaPetExample.ddf
  • 1.1 lines changed: 9, context: html, text, full: html, text
    First cut of data agreement for ChIA-PET
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.38 lines changed: 1, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.236 lines changed: 6, context: html, text, full: html, text
    Forgot to check this one in for Farnham
  • 1.235 lines changed: 1, context: html, text, full: html, text
    IRF-1 to IRF1
  • 1.234 lines changed: 2, context: html, text, full: html, text
    Moved the Ccnt2 antibody entry to uppercase (CCNT2)
  • 1.233 lines changed: 2, context: html, text, full: html, text
    Addd the missing targetId and targetUrl for TFIIB.
  • 1.232 lines changed: 27, context: html, text, full: html, text
    Added antibodies ERalpha(a) and ERalpha(b). Removed some extraneous whitespace on the targetId line for TFIIB.
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    add Tullius
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.223 lines changed: 14, context: html, text, full: html, text
    add support for bigWig's to put min and max in trackDb file
• src/hg/encode/validateFiles/validateFiles.c
  • 1.40 lines changed: 57, context: html, text, full: html, text
    first pass at BAM sequence validation. Only supports alignments with no indels or trimming.
• src/hg/genePredToFakePsl/genePredToFakePsl.c
  • 1.4 lines changed: 79, context: html, text, full: html, text
    Fixed incorrect calculation of CDS refactor
• src/hg/hgGateway/hgGateway.c
  • 1.117 lines changed: 1, context: html, text, full: html, text
    make gene a link to geneSearchBox.html
• src/hg/hgTables/great.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Use 'cartRemove' instead of 'cartSetBoolean'
• src/hg/hgTracks/bedGraph.c
  • 1.22 lines changed: 5, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/bigWigTrack.c
  • 1.10 lines changed: 47, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/hgTracks.c
  • 1.1645 lines changed: 2, context: html, text, full: html, text
    make gene a link to geneSearchBox.html
• src/hg/hgTracks/simpleTracks.c
  • 1.137 lines changed: 1, context: html, text, full: html, text
    fixed breakage noticed by JK during code review
• src/hg/hgTracks/wigCommon.h
  • 1.10 lines changed: 7, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/wigTrack.c
  • 1.106 lines changed: 62, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgc/hgc.c
  • 1.1619 lines changed: 6, context: html, text, full: html, text
    bedPrintPos: added setting bedNameLabel in case 'Item: ' doesn't sound right for a track.
  • 1.1618 lines changed: 26, context: html, text, full: html, text
    include link back to browser in tables of PSL. also fix corner case on PAR were link to wrong chrom
  • 1.1617 lines changed: 27, context: html, text, full: html, text
    add links out of gencode track to yale pseudogenes
• src/hg/hgc/retroClick.c
  • 1.14 lines changed: 8, context: html, text, full: html, text
    fix bug with non human retros, reference ucscRetroSeq instead of gbCdnaInfo for sequence data, to handle different versions
• src/hg/inc/mdb.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/inc/trackDb.h
  • 1.57 lines changed: 6, context: html, text, full: html, text
    Added a couple of functions to determine the viewName for a view level track or a subtrack
• src/hg/inc/versionInfo.h
  • 1.171 lines changed: 1, context: html, text, full: html, text
    "New version number v230"
• src/hg/inc/yaleGencodeAssoc.h
  • 1.1 lines changed: 63, context: html, text, full: html, text
    yale pseudogene association with gencode ids
• src/hg/js/hui.js
  • 1.52 lines changed: 21, context: html, text, full: html, text
    Support for javascript to tie view level and subtrack level controls together in hgTrackUi
• src/hg/lib/extFile.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/gbCdnaInfo.as
  • 1.4 lines changed: 2, context: html, text, full: html, text
    update schema doc
• src/hg/lib/gbSeq.as
  • 1.3 lines changed: 25, context: html, text, full: html, text
    fixed manic editing overwrite of file
  • 1.2 lines changed: 25, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/gbStatus.as
  • 1.1 lines changed: 19, context: html, text, full: html, text
    added gbStatus schema doc
• src/hg/lib/genbankTables.as
  • 1.7 lines changed: 4, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/hgRelate.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    solaris patch for problem reported by user - getPid returns pid_t which is defined as long on solaris - but recommended to cast to int for use with printf
• src/hg/lib/history.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/hui.c
  • 1.282 lines changed: 10, context: html, text, full: html, text
    bamCfgUi: added trackDb setting noColorTag to inhibit the option to color items by user-defined tag (n/a for most tracks including native tracks).
  • 1.281 lines changed: 1, context: html, text, full: html, text
    enabled indel display controls for BAM tracks
  • 1.280 lines changed: 38, context: html, text, full: html, text
    Support for javascript to tie view level and subtrack level controls together in hgTrackUi
• src/hg/lib/makefile
  • 1.408 lines changed: 2, context: html, text, full: html, text
    add yaleGencodeAssoc
• src/hg/lib/mdb.as
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/lib/mdb.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/lib/mdb.sql
  • 1.2 lines changed: 18, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/lib/metaDb.as
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Renaming mdb to metaDb
• src/hg/lib/metaDb.sql
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Renaming mdb to metaDb
• src/hg/lib/metaInfo.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/namedSessionDb.as
  • 1.3 lines changed: 2, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/seq.as
  • 1.3 lines changed: 2, context: html, text, full: html, text
    use bigint for file offsets
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/swInterPro.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/targetDb.as
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/trackDbCustom.c
  • 1.85 lines changed: 27, context: html, text, full: html, text
    Added a couple of functions to determine the viewName for a view level track or a subtrack
• src/hg/lib/trackVersion.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/transRegCodeMotif.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed invalid autoSql that prevented descriptions from being displayed
• src/hg/lib/wiggleCart.c
  • 1.38 lines changed: 4, context: html, text, full: html, text
    Located bug in freeing memeory never allocated.
• src/hg/lib/yaleGencodeAssoc.as
  • 1.1 lines changed: 8, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/lib/yaleGencodeAssoc.c
  • 1.1 lines changed: 132, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/lib/yaleGencodeAssoc.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/makeDb/doc/ailMel1.txt
  • 1.14 lines changed: 5, context: html, text, full: html, text
    run doRecipBest.pl for felCatV17e
• src/hg/makeDb/doc/calJac3.txt
  • 1.8 lines changed: 15, context: html, text, full: html, text
    show how splitMaf is created
• src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt
  • 1.6 lines changed: 1959, context: html, text, full: html, text
    updated change notes
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.10 lines changed: 184, context: html, text, full: html, text
    maf files done
  • 1.9 lines changed: 127, context: html, text, full: html, text
    Add multiz 6 ways support
• src/hg/makeDb/doc/hg18.txt
  • 1.413 lines changed: 2, context: html, text, full: html, text
    Minor edits.
  • 1.412 lines changed: 37, context: html, text, full: html, text
    Documented adding updated data for CRG Mapability track.
• src/hg/makeDb/doc/hg19.txt
  • 1.104 lines changed: 38, context: html, text, full: html, text
    Documented adding updated data for CRG Mapability track.
• src/hg/makeDb/doc/mm9.txt
  • 1.136 lines changed: 45, context: html, text, full: html, text
    Added corrected files for crgMapability subtracks of Mapability track.
• src/hg/makeDb/doc/oryCun2.txt
  • 1.10 lines changed: 27, context: html, text, full: html, text
    Human Proteins
  • 1.9 lines changed: 161, context: html, text, full: html, text
    starting human proteins
• src/hg/makeDb/doc/oviAri1.txt
  • 1.5 lines changed: 79, context: html, text, full: html, text
    blatz tasks
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.122 lines changed: 2, context: html, text, full: html, text
    bad tandem dup example
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.113 lines changed: 1, context: html, text, full: html, text
    adding felCatV17e to list
• src/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra
  • 1.6 lines changed: 22, context: html, text, full: html, text
    Added MouseAtlas3 stuff. Tissue names will need to be abbreviated because they don't fit well in the browser.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Renamed mdb to metaDb
• src/hg/makeDb/schema/all.joiner
  • 1.793 lines changed: 2, context: html, text, full: html, text
    allow chainSelf non-split to work for other dbs too - trying to fix danRer6)
  • 1.792 lines changed: 6, context: html, text, full: html, text
    removed duplicate clause
  • 1.791 lines changed: 218, context: html, text, full: html, text
    adding some things to tablesIgnored and removing redundantentries
  • 1.790 lines changed: 2, context: html, text, full: html, text
    add oryCun2 to Human Protein tracks
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.44 lines changed: 9, context: html, text, full: html, text
    removing stanzas to keep panTro1 genbank tables different on RR from beta (updating panTro1 to not have human RefSeq genes as native chimp)
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGene.html
  • 1.6 lines changed: 55, context: html, text, full: html, text
    removed human-as-chimp xeno refgene hack
• src/hg/makeDb/trackDb/chimp/panTro2/est.html
  • 1.4 lines changed: 108, context: html, text, full: html, text
    removed html related to chimp/human hack
• src/hg/makeDb/trackDb/chimp/panTro2/estWithHs.html
  • 1.2 lines changed: 108, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html
  • 1.6 lines changed: 117, context: html, text, full: html, text
    removed html related to chimp/human hack
• src/hg/makeDb/trackDb/chimp/panTro2/intronEstWithHs.html
  • 1.2 lines changed: 117, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/chimp/panTro2/mrna.html
  • 1.4 lines changed: 73, context: html, text, full: html, text
    removed html related to chimp/human hack
• src/hg/makeDb/trackDb/chimp/panTro2/mrnaWithHs.html
  • 1.2 lines changed: 73, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/chimp/panTro2/refGene.html
  • 1.5 lines changed: 64, context: html, text, full: html, text
    removed html related to chimp/human hack
• src/hg/makeDb/trackDb/chimp/panTro2/refGeneWithHs.html
  • 1.2 lines changed: 64, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.58 lines changed: 63, context: html, text, full: html, text
    removing stanzas that put human mRNAs and Ests in native chimp tracks for genbank
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html
  • 1.5 lines changed: 80, context: html, text, full: html, text
    removed html related to chimp/human hack
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrnaNoHs.html
  • 1.2 lines changed: 80, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGene.html
  • 1.7 lines changed: 55, context: html, text, full: html, text
    removed human-as-chimp xeno refgene hack
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGeneNoHs.html
  • 1.2 lines changed: 55, context: html, text, full: html, text
    removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones
• src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra
  • 1.8 lines changed: 201, context: html, text, full: html, text
    Removed some misleading 'type' vars from Haib Tfbs
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Miss changing antibody from Pol2 to Pol2-4H8
  • 1.6 lines changed: 43, context: html, text, full: html, text
    Krish found 2 fastq files conflicting between release1 and release2. The newer had been loaded with the wronng metadata. This is the correction.
• src/hg/makeDb/trackDb/human/hg18/trackDb.pipeline.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    ENCODE-related data from Weng lab; trying out loading from a new browser pipeline
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.481 lines changed: 1, context: html, text, full: html, text
    ENCODE-related data from Weng lab; trying out loading from a new browser pipeline
  • 1.480 lines changed: 20, context: html, text, full: html, text
    move ucscRetroAli to top level
  • 1.479 lines changed: 20, context: html, text, full: html, text
    add retro track description
  • 1.478 lines changed: 10, context: html, text, full: html, text
    add brTestPlus for test of multiWig
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.961 lines changed: 8, context: html, text, full: html, text
    Insignificant change to Yale input titles and commented out settings for filterComposite code
  • 1.960 lines changed: 4, context: html, text, full: html, text
    Turning on K562 cells by default in the UW DNase DGF track.
  • 1.959 lines changed: 58, context: html, text, full: html, text
    replaced released alpha w/ release alpha,beta
• src/hg/makeDb/trackDb/human/hg18/uMassMedBrainDevHistoneChipSeq.html
  • 1.1 lines changed: 61, context: html, text, full: html, text
    ENCODE-related data from Weng lab; trying out loading from a new browser pipeline
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.25 lines changed: 77, context: html, text, full: html, text
    Flo Pauli updated the methods.
  • 1.24 lines changed: 15, context: html, text, full: html, text
    Extended release notes and changed contact.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Changed cell culture protocols link.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.50 lines changed: 2, context: html, text, full: html, text
    changed link title of contact
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.13 lines changed: 5, context: html, text, full: html, text
    Updated SYDH TFBS: Control variable in factors. To make multiple dimesnions matrix 2x2
  • 1.12 lines changed: 34, context: html, text, full: html, text
    Updated HAIB TFBS track with default track view selected.
  • 1.11 lines changed: 5, context: html, text, full: html, text
    some label changes for RRBS. Some data for link out for Yale pseudo in gencode
  • 1.10 lines changed: 450, context: html, text, full: html, text
    Intial display of Sydh Chip-seq with default track view selected(Tier 1 cells)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.116 lines changed: 20, context: html, text, full: html, text
    move ucscRetroAli to top level
  • 1.115 lines changed: 21, context: html, text, full: html, text
    update retro track entry
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli.html
  • 1.2 lines changed: 66, context: html, text, full: html, text
    move ucscRetroAli.html to top level
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • 1.1 lines changed: 148, context: html, text, full: html, text
    Add prelminary html files for HAIB TFBS track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • 1.1 lines changed: 160, context: html, text, full: html, text
    Add prelminary html files for SYDH TFBS track
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra
  • 1.2 lines changed: 392, context: html, text, full: html, text
    I have added the tracks SYDH_TFBS and SYDH_Hist to the mm9/trackDb.enc.ra. Thedisplay for the Peaks is not working in SYDH_Hist.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.213 lines changed: 21, context: html, text, full: html, text
    move ucscRetroAli to top level
• src/hg/makeDb/trackDb/mouse/ucscRetroAli.html
  • 1.2 lines changed: 66, context: html, text, full: html, text
    move ucscRetroAli to top level
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add extTable
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.627 lines changed: 20, context: html, text, full: html, text
    move ucscRetroAli to top level
• src/hg/makeDb/trackDb/ucscRetroAli.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    updated description for retro track
  • 1.1 lines changed: 66, context: html, text, full: html, text
    move ucscRetroAli to top level
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.47 lines changed: 1, context: html, text, full: html, text
    Turning on fr1 by default in the conservation track.
• src/hg/oneShot/timeGifPng/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a little test program to test gif and png timing
• src/hg/oneShot/timeGifPng/timeGifPng.c
  • 1.1 lines changed: 203, context: html, text, full: html, text
    a little test program to test gif and png timing
• src/hg/pipeline/dafs/1.0/uMassMedBrainDevHistoneChip.daf
  • 1.1 lines changed: 32, context: html, text, full: html, text
    Set up for use of an automated pipeline (ENCODE-like) for browser tracks
• src/hg/ratStuff/mafFilter/mafFilter.c
  • 1.16 lines changed: 19, context: html, text, full: html, text
    Added -maxRow command line option
• src/hg/regulate/regChromiaMergeWindows/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Making a clusterer just for Chromia.
• src/hg/regulate/regChromiaMergeWindows/regChromiaMergeWindows.c
  • 1.1 lines changed: 163, context: html, text, full: html, text
    Making a clusterer just for Chromia.
• src/hg/tcga/pBamBam/pBamBamSNP.c
  • 1.1 lines changed: 1128, context: html, text, full: html, text
    initial commit
• src/inc/errCatch.h
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed incorrect documentation
• src/lib/bbiWrite.c
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Improving error message when chromosome not in chrom.sizes file.
• src/oneShot/rgbaGfxTest/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    A testing area for rgba graphics stuff.
• src/oneShot/rgbaGfxTest/rgbaGfxTest.c
  • 1.2 lines changed: 127, context: html, text, full: html, text
    Making it actually render BigWigs
  • 1.1 lines changed: 368, context: html, text, full: html, text
    A testing area for rgba graphics stuff.
• src/product/README.building.source
  • 1.19 lines changed: 10, context: html, text, full: html, text
    warn_unused_result mentioned
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.8 lines changed: 10, context: html, text, full: html, text
    add minMax option for the ENCODE validator to use
• src/utils/qa/chain.csh
  • 1.32 lines changed: 14, context: html, text, full: html, text
    adjusting message about checking the matrix, chainMinScore and chainLinearGap
• src/utils/qa/qaThis.csh
  • 1.13 lines changed: 19, context: html, text, full: html, text
    fixing spacing issues, reinserting makedoc info
  • 1.12 lines changed: 42, context: html, text, full: html, text
    some usage changes: removed clean, creates a single file. variable name clean up
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.111 lines changed: 3, context: html, text, full: html, text
    v230 final build

• lines changed: 9177
• files changed: 115