All File Changes

v241_preview to v241_base (2010-09-21 to 2010-09-28) v241

• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/dukeExonArray.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/psuMm9RnaSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/ucDHg19Hist.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/DAFs/2.0/uwExonArray.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
  • lines changed 6, context: html, text, full: html, text
    corrected DAF to have the ddf file and the right composite name
• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    making all dataTypes consistant with the CV
• src/hg/encode/encodeMkGeoPkg/README.txt
  • lines changed 39, context: html, text, full: html, text
    Fill out procedure. Add notes for testing
  • lines changed 23, context: html, text, full: html, text
    more details
  • lines changed 1, context: html, text, full: html, text
    fixed filename
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 20, context: html, text, full: html, text
    Replaced a bunch of 'validation RipChip' lines with blank validation lines, to not lead to broken links
  • lines changed 14, context: html, text, full: html, text
    added clusters to dataType
  • lines changed 5, context: html, text, full: html, text
    added treatment AMA50ug9h
  • lines changed 2, context: html, text, full: html, text
    Cluster was a tag not term
  • lines changed 1, context: html, text, full: html, text
    changed treatment for AMA
  • lines changed 2, context: html, text, full: html, text
    Added validation link information for E2F1 and HA-E2F1 targets
  • lines changed 18, context: html, text, full: html, text
    Added links for selected mouse protocols
  • lines changed 1, context: html, text, full: html, text
    Fixed a broken link to a mouse cell protocol
  • lines changed 1, context: html, text, full: html, text
    Fixed one more broken link to a cell protocol
  • lines changed 8, context: html, text, full: html, text
    Finished registration of PBDE cell
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links in antibody validation for Melissa
  • lines changed 1, context: html, text, full: html, text
    Added how PBDE cells were obtained.
  • lines changed 29, context: html, text, full: html, text
    Antibody registration of 2 antibodies, CTCF_(C-20), p300(N-15).
  • lines changed 15, context: html, text, full: html, text
    Registerd antibody for Hardison Lab PAX5-N15
• src/hg/encode/metaCheck/makefile
  • lines changed 20, context: html, text, full: html, text
    first pass at program that checks to see if files, and tables, and trackDb entries exist for everything in metaDb.ra file
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 201, context: html, text, full: html, text
    first pass at program that checks to see if files, and tables, and trackDb entries exist for everything in metaDb.ra file
  • lines changed 54, context: html, text, full: html, text
    more work
  • lines changed 111, context: html, text, full: html, text
    latest and greatest
  • lines changed 19, context: html, text, full: html, text
    add some verbose statements
• src/hg/hgApi/hgApi.c
  • lines changed 13, context: html, text, full: html, text
    Moved mdb queries from hgTracks and hgApi to mdb. Made sure the queries exclude files.
• src/hg/hgCustom/hgCustom.c
  • lines changed 3, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 2, context: html, text, full: html, text
    take link out to bedDetail format until more testing is done
• src/hg/hgGateway/hgGateway.c
  • lines changed 18, context: html, text, full: html, text
    move find tracks button the the front of button list
• src/hg/hgTables/custom.c
  • lines changed 19, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTables/filterFields.c
  • lines changed 19, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTables/joining.c
  • lines changed 1, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTables/schema.c
  • lines changed 52, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Make composite vis go to full if hidden and matrix or subtrack cb is checked
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 9, context: html, text, full: html, text
    rightClick fetch of dense subtrack failed because of conditional label.
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/hgTracks/imageV2.c
  • lines changed 10, context: html, text, full: html, text
    Removed some static style that is now defined in HGStyle.css.
• src/hg/hgTracks/searchTracks.c
  • lines changed 121, context: html, text, full: html, text
    Reformatted tabs and added search toggle
  • lines changed 3, context: html, text, full: html, text
    Bug in js caused many more cart vars to be set than desired. Also made view in browser button reflect whether changes have been made, rather than whether tracks are checked.
  • lines changed 20, context: html, text, full: html, text
    add help links for encode metatada; attempt at cleanup of advanced table layout
  • lines changed 2, context: html, text, full: html, text
    Plugged hole when search value is cleared but search is pressed
  • lines changed 44, context: html, text, full: html, text
    Painful tweaking to get IE FF and Chrome to handle sizing gracefully. Needed to truncated labVersion
  • lines changed 45, context: html, text, full: html, text
    Moved mdb queries from hgTracks and hgApi to mdb. Made sure the queries exclude files.
  • lines changed 3, context: html, text, full: html, text
    Blocking containerChildren from simple search since they do not appear to be displayable outside their container
• src/hg/hgTracks/simpleTracks.c
  • lines changed 202, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 88, context: html, text, full: html, text
    first pass at a cactus bed display
• src/hg/hgc/hgc.c
  • lines changed 136, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 2, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/hgc/hgc.h
  • lines changed 6, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 123, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 83, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/htdocs/images/phylo/ce9_10way.png
  • lines changed 0, context: html, text, full: html, text
    10-way diagram for C. elegans ce9/WS210
• src/hg/htdocs/style/HGStyle.css
  • lines changed 56, context: html, text, full: html, text
    Moved some UI 2.0 classes into this common css file
  • lines changed 1, context: html, text, full: html, text
    Side buttons to be preferred for FF over IE. Rid tabs of zoom
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 1, context: html, text, full: html, text
    Changed tab size in findTracks
  • lines changed 2, context: html, text, full: html, text
    Side buttons to be preferred for FF over IE. Rid tabs of zoom
• src/hg/inc/agpFrag.h
  • lines changed 3, context: html, text, full: html, text
    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/inc/bedDetail.h
  • lines changed 76, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/inc/mdb.h
  • lines changed 6, context: html, text, full: html, text
    add a routine to print metaDb to a file
  • lines changed 9, context: html, text, full: html, text
    Moved mdb queries from hgTracks and hgApi to mdb. Made sure the queries exclude files.
• src/hg/inc/pgSnp.h
  • lines changed 5, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/inc/trackDb.h
  • lines changed 44, context: html, text, full: html, text
    Added support for tdbIsContainer() and tdbIsContainerChild()
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v241
• src/hg/js/ajax.js
  • lines changed 18, context: html, text, full: html, text
    add errorHandler
• src/hg/js/hgTracks.js
  • lines changed 11, context: html, text, full: html, text
    Support for sorting found tracks
  • lines changed 32, context: html, text, full: html, text
    Bug in js caused many more cart vars to be set than desired. Also made view in browser button reflect whether changes have been made, rather than whether tracks are checked.
  • lines changed 43, context: html, text, full: html, text
    add updateMetaDataHelpLinks
  • lines changed 4, context: html, text, full: html, text
    Fixed an inefficiency that was slowing down display of 100 found tracks
  • lines changed 1, context: html, text, full: html, text
    OK not Ok. Okay?
• src/hg/js/hui.js
  • lines changed 14, context: html, text, full: html, text
    Make composite vis go to full if hidden and matrix or subtrack cb is checked
  • lines changed 3, context: html, text, full: html, text
    Again with the Oks not OK. Missed one plase to expose composite when plus button pressed
• src/hg/lib/agpFrag.c
  • lines changed 8, context: html, text, full: html, text
    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/lib/bedDetail.as
  • lines changed 18, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/bedDetail.c
  • lines changed 312, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/bedDetail.sql
  • lines changed 24, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/cart.c
  • lines changed 94, context: html, text, full: html, text
    Changed slPair to hash in anticipation of PLANB being adopted. Fixed bug in plan B
  • lines changed 256, context: html, text, full: html, text
    Lots of rework to the cartTdbTree and Visibility cleanup routines. This code should be passive until findTracks or rightClick are released.
• src/hg/lib/customFactory.c
  • lines changed 316, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/hdb.c
  • lines changed 16, context: html, text, full: html, text
    Added support for tdbIsContainer() and tdbIsContainerChild()
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    Fixed lookup of view vis in tdbVisLimitedByAncestry
  • lines changed 4, context: html, text, full: html, text
    Added support for tdbIsContainer() and tdbIsContainerChild()
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/mdb.c
  • lines changed 29, context: html, text, full: html, text
    add a routine to print metaDb to a file
  • lines changed 59, context: html, text, full: html, text
    Moved mdb queries from hgTracks and hgApi to mdb. Made sure the queries exclude files.
• src/hg/lib/pgSnp.c
  • lines changed 32, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/lib/trackDbCustom.c
  • lines changed 13, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 7, context: html, text, full: html, text
    Made lookup of view optional in tdbIsView
• src/hg/makeDb/doc/bruMal1.txt
  • lines changed 103, context: html, text, full: html, text
    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
  • lines changed 19, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/caeJap3.txt
  • lines changed 120, context: html, text, full: html, text
    done with repeat simple and window masking with kluster scratch ready to copy
  • lines changed 44, context: html, text, full: html, text
    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
  • lines changed 18, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/caePb2.txt
  • lines changed 25, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 25, context: html, text, full: html, text
    fixup gold/gap tables with fixed hgGoldGapGl procedure
• src/hg/makeDb/doc/cb3.txt
  • lines changed 24, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/ce9.txt
  • lines changed 416, context: html, text, full: html, text
    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
  • lines changed 182, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
  • lines changed 229, context: html, text, full: html, text
    initial run of the 10-way multiz done
  • lines changed 88, context: html, text, full: html, text
    added gap annotations
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 25, context: html, text, full: html, text
    Fix gold/gap tables
• src/hg/makeDb/doc/melHap1.txt
  • lines changed 87, context: html, text, full: html, text
    done with repeat simple and window masking with kluster scratch ready to copy
  • lines changed 19, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/melInc1.txt
  • lines changed 81, context: html, text, full: html, text
    done with repeat simple and window masking with kluster scratch ready to copy
  • lines changed 19, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/mm9.txt
  • lines changed 238, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/doc/priPac1.txt
  • lines changed 18, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 98, context: html, text, full: html, text
    adding caeJap3 C. japonica WUGSC 7.0.1, haeCon1 H. contortus WS210, melHap1 M. hapla WS210, melInc1 M. incognita WS210, bruMal1 B. malayi WS210
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 8, context: html, text, full: html, text
    adding haeCon melHap melInc and bruMal nematodes: Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita, Brugia malayi
  • lines changed 1, context: html, text, full: html, text
    melNap is melHap
• src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
  • lines changed 48, context: html, text, full: html, text
    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/makeDb/hgGoldGapGl/hgLoadGap.c
  • lines changed 21, context: html, text, full: html, text
    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 19, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/makeDb/hgLoadBed/makefile
  • lines changed 1, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
  • lines changed 21, context: html, text, full: html, text
    install files should remove the destination before cp -p
• src/hg/makeDb/schema/all.joiner
  • lines changed 13, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/README
  • lines changed 5, context: html, text, full: html, text
    Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type. bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
• src/hg/makeDb/trackDb/cactus/cacTus1/description.html
  • lines changed 129, context: html, text, full: html, text
    Initial descriptions for cacTus1.
• src/hg/makeDb/trackDb/cactus/cacTus1/gap.html
  • lines changed 37, context: html, text, full: html, text
    Initial descriptions for cacTus1.
• src/hg/makeDb/trackDb/cactus/cacTus1/gold.html
  • lines changed 29, context: html, text, full: html, text
    Initial descriptions for cacTus1.
• src/hg/makeDb/trackDb/cactus/cacTus1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Initial descriptions for cacTus1.
  • lines changed 10, context: html, text, full: html, text
    add buildMaf
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 522, context: html, text, full: html, text
    Updated Protocol information for NRSF antibody and 6 cell lines Bugg 1155
  • lines changed 45, context: html, text, full: html, text
    Updated Protocol information for Controls 5 cell lines Bugg 1155
  • lines changed 13, context: html, text, full: html, text
    Updated Protocol information for Control HepG2 cell lines Bug 1155
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 1076, context: html, text, full: html, text
    Change to have ChipSeq
• src/hg/makeDb/trackDb/human/hg18/numtSeq.html
  • lines changed 78, context: html, text, full: html, text
    NumtSeq track description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 24, context: html, text, full: html, text
    Updated Protocol information for NRSF antibody and 6 cell lines Bugg 1155
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    Updated Protocol information for Control HepG2 cell lines Bug 1155
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • lines changed 3, context: html, text, full: html, text
    Changed GEM mapper description.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 400, context: html, text, full: html, text
    FAIRE-seq to FaireSeq and CHiP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    LongRnaSeq to RnaSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    ShortRnaSeq to RnaSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 9, context: html, text, full: html, text
    changed unrestricted date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 305, context: html, text, full: html, text
    Added submission 2348 to meta-data and trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 937, context: html, text, full: html, text
    Added 10 ChIP-seq Experiments to TrackDb and metaDb
  • lines changed 95, context: html, text, full: html, text
    Added submission 2213 for HAIBTFBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 145, context: html, text, full: html, text
    FAIRE-seq to FaireSeq and CHiP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 158, context: html, text, full: html, text
    DNase-seq to DnaseSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 139, context: html, text, full: html, text
    FAIRE-seq to FaireSeq and CHiP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 358, context: html, text, full: html, text
    CAGE to Cage
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    new tracks and metaData added to RikenCage
  • lines changed 441, context: html, text, full: html, text
    Added new tracks to RikenCage
  • lines changed 21, context: html, text, full: html, text
    adding new subtracks
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    added two missing exps
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    revoked and reloaded subs 1813, 1805, 1799
  • lines changed 336, context: html, text, full: html, text
    updated dateSubmitted and origAssembly
  • lines changed 448, context: html, text, full: html, text
    added fastas and fastqs to metaData
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
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    RIP-chip to RipChip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 22, context: html, text, full: html, text
    RIP-chip to RipChip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 70, context: html, text, full: html, text
    ChIP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 623, context: html, text, full: html, text
    ChIP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 554, context: html, text, full: html, text
    ChIP-seq to ChipSeq
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metadata for CSHL Sm RNA-seq on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 892, context: html, text, full: html, text
    staging metadata for CSHL Sm RNA-seq on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
  • lines changed 9, context: html, text, full: html, text
    preparing to push metaDb because Brian fixed the restricted until dates for the Gencode Genes track
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencode.ra
  • lines changed 9, context: html, text, full: html, text
    preparing to push metaDb because Brian fixed the restricted until dates for the Gencode Genes track
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Removed rfamHuman, which isn't needed anymore
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    added the new hg19 UW Affy Exon Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 5, context: html, text, full: html, text
    fixed formatting of contact so it is like other encode tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 3, context: html, text, full: html, text
    Dafault edits for Katrina
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    changed the text to be american english
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    fixed typo
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra
  • lines changed 294, context: html, text, full: html, text
    Added submission 2348 to meta-data and trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 201, context: html, text, full: html, text
    Added 10 ChIP-seq Experiments to TrackDb and metaDb
  • lines changed 20, context: html, text, full: html, text
    Added submission 2213 for HAIBTFBS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 3, context: html, text, full: html, text
    Changed GEM mapper description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 214, context: html, text, full: html, text
    Updated Track Description Pages to recommended information from Lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 200, context: html, text, full: html, text
    Updated Track Description Pages to recommended information from Lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 3, context: html, text, full: html, text
    Updated Track Description Pages to recommended information from Lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 119, context: html, text, full: html, text
    fixed the trackDb to have a description and have replicates for all
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 1305, context: html, text, full: html, text
    new tracks and metaData added to RikenCage
  • lines changed 243, context: html, text, full: html, text
    Added new tracks to RikenCage
  • lines changed 234, context: html, text, full: html, text
    revoked and reloaded subs 1813, 1805, 1799
  • lines changed 176, context: html, text, full: html, text
    fixed the trackDb to have a description and have replicates for all
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
  • lines changed 14, context: html, text, full: html, text
    Added links for selected mouse protocols
  • lines changed 4, context: html, text, full: html, text
    changing case of the s in RNA-seq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 29, context: html, text, full: html, text
    Elaborated on the one-sentence description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 68, context: html, text, full: html, text
    added the new hg19 UW Affy Exon Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 1277, context: html, text, full: html, text
    added the new hg19 UW Affy Exon Track
• src/hg/makeDb/trackDb/human/hg19/wgRna.html
  • lines changed 105, context: html, text, full: html, text
    reflect new version of miRbase
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    adding bit about liftover from hg18 to hg19
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 6, context: html, text, full: html, text
    changing it a bit to make it human centric
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    new url for miRNA
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    add noScoreFilter .
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding caeJap3 to the build
  • lines changed 1, context: html, text, full: html, text
    adding haeCon1 to the build
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    Added cacTus1 to DBS.
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 421, context: html, text, full: html, text
    Use cons13way.html
• src/hg/makeDb/trackDb/marmoset/calJac3/multiz13way.html
  • lines changed 367, context: html, text, full: html, text
    Use cons13way.html
• src/hg/makeDb/trackDb/marmoset/calJac3/phastConsElements13way.html
  • lines changed 96, context: html, text, full: html, text
    Use cons13way.html
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 168, context: html, text, full: html, text
    combined conservation tracks to one track
• src/hg/makeDb/trackDb/mouse/jaxAllele.html
  • lines changed 3, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/mouse/jaxAlleleOld.html
  • lines changed 34, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/mouse/jaxGeneTrap.html
  • lines changed 34, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 1, context: html, text, full: html, text
    Changed glires to euarchontoglire.
• src/hg/makeDb/trackDb/mouse/mm9/mapability.html
  • lines changed 3, context: html, text, full: html, text
    Changed GEM mapper description.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Redmine Track #1091 (MGI/Jackson Lab Tracks update): updated mm9 jaxRepTranscript, jaxAllele and jaxPhenotype; added new track jaxGeneTrap.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    initial 10-way alignment on C. elegans/ce9/WS210
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 504, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
  • lines changed 113, context: html, text, full: html, text
    initial 10-way alignment on C. elegans/ce9/WS210
• src/hg/makeDb/trackDb/worm/caeJap3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 151, context: html, text, full: html, text
    initial 10-way alignment on C. elegans/ce9/WS210
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    added gap annotations
• src/hg/makeDb/trackDb/worm/haeCon1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 158, context: html, text, full: html, text
    done with 10 nematode pair wise alignments
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 9, context: html, text, full: html, text
    turn the quality track into a bigWig instead of wiggle
  • lines changed 12, context: html, text, full: html, text
    use featureBits to verify gold and gap tables cover all bases
• src/hg/utils/bedMergeOverlappingBlocks/bedMergeOverlappingBlocks.c
  • lines changed 140, context: html, text, full: html, text
    Utility to clean up BED 12+ files that have overlapping blocks (exons). Probably can go in src/utils. Compiled it with jkhgap library. Will move it later.
• src/hg/utils/bedMergeOverlappingBlocks/makefile
  • lines changed 18, context: html, text, full: html, text
    Utility to clean up BED 12+ files that have overlapping blocks (exons). Probably can go in src/utils. Compiled it with jkhgap library. Will move it later.
• src/hg/utils/phyloTrees/nematodes.txt
  • lines changed 25, context: html, text, full: html, text
    ten nematodes from NCBI taxonomy
• src/inc/cgi_build_rules.mk
  • lines changed 3, context: html, text, full: html, text
    install files should remove the destination before cp -p
• src/inc/cheapcgi.h
  • lines changed 5, context: html, text, full: html, text
    Added or changed a couple of colors
• src/lib/cheapcgi.c
  • lines changed 5, context: html, text, full: html, text
    A number of class defines were moved to HGStyle.css
• src/product/scripts/trashCleaner.csh
  • lines changed 12, context: html, text, full: html, text
    need to output a status message when all files are done
• src/test/buildTableDescriptions.pl
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    make error message more explicit
• src/utils/qa/weeklybld/buildEnv.csh
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    v241 final build

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• files changed: 247