CVS changes by file

branch to review (2010-03-02 to 2010-03-16) v227

• java/build.xml
  • 1.21 lines changed: 5, context: html, text, full: html, text
    fixing java paths now heather is gone
• java/javaenv
  • 1.5 lines changed: 2, context: html, text, full: html, text
    heather is gone, paths old need updating
• java/src/edu/ucsc/genome/qa/cgiCheck/canFam1.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/ci1.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/hg17.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/mm5.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/quick.props
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• java/src/edu/ucsc/genome/qa/cgiCheck/quickAll.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed references to old location of tables on beta.
• src/blat/blat.c
  • 1.116 lines changed: 1, context: html, text, full: html, text
    fixed typo
• src/blat/test/dupeTargetName/q.fa
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Adding new blat test case.
• src/blat/test/dupeTargetName/t.fa
  • 1.1 lines changed: 34, context: html, text, full: html, text
    Adding new blat test case.
• src/blat/version.doc
  • 1.76 lines changed: 2, context: html, text, full: html, text
    Describing new input sanity check.
• src/cdnaAli/makefile
  • 1.5 lines changed: 3, context: html, text, full: html, text
    need to clean in g2cCheck
• src/fuse/fuse.mk
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Moving the USE_FUSE addition of L += -lfuse to just this directory, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
• src/fuse/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Moving the USE_FUSE addition of L += -lfuse to just this directory, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
• src/fuse/udcFuse/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Moving the USE_FUSE addition of L += -lfuse to just this directory, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
• src/hg/archaeStuff/chooseorg/chooseorg.c
  • 1.1 lines changed: 135, context: html, text, full: html, text
    integrated low lap changes
• src/hg/archaeStuff/chooseorg/makefile
  • 1.1 lines changed: 22, context: html, text, full: html, text
    integrated low lap changes
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.6 lines changed: 1, context: html, text, full: html, text
    change strainA1552 track description
• src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
  • 1.12 lines changed: 4, context: html, text, full: html, text
    fixed GeneMark output parsing
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.27 lines changed: 2, context: html, text, full: html, text
    change dash delimiter to dot for tRNA ID
  • 1.26 lines changed: 3, context: html, text, full: html, text
    add seqname and change tR to tRNA for tRNA track item name
• src/hg/encode/DAFs/2.0/:n
  • 1.1 lines changed: 53, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/affyRnaChip.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/broadMapability.daf
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/buOrchid.daf
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
  • 1.1 lines changed: 135, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • 1.1 lines changed: 47, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/cshlRnaSeq.daf
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • 1.1 lines changed: 48, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • 1.1 lines changed: 42, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/dukeExonArray.daf
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/gisDnaPet.daf
  • 1.1 lines changed: 101, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
  • 1.1 lines changed: 54, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/gisRnaSeq.daf
  • 1.1 lines changed: 68, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • 1.1 lines changed: 42, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/haibCnv.daf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/haibMethyl27.daf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/haibMethylSeq.daf
  • 1.1 lines changed: 32, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
  • 1.1 lines changed: 36, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/helicosRnaSeq.daf
  • 1.1 lines changed: 54, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/nhgriElnitskiBiPro.daf
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/nhgriElnitskiNegReg.daf
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • 1.1 lines changed: 53, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/sangerGencode.daf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
  • 1.1 lines changed: 41, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/stanfordRnaSeq.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/sunyRipChip.daf
  • 1.1 lines changed: 45, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uMassDekker5c.daf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uMassWengTfbsValid.daf
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • 1.1 lines changed: 48, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • 1.1 lines changed: 42, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • 1.1 lines changed: 29, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uwDnaseValid.daf
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/DAFs/2.0/uwExonArray.daf
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Pipeline 2.0
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.72 lines changed: 42, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • 1.5 lines changed: 34, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • 1.2 lines changed: 42, context: html, text, full: html, text
    added flag to output lists of files and tables
  • 1.1 lines changed: 333, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/encode/encodeMkChangeNotes/makefile
  • 1.1 lines changed: 20, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.214 lines changed: 47, context: html, text, full: html, text
    Moved certain terms from 'Control' to explicitly 'input'
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.27 lines changed: 32, context: html, text, full: html, text
    Add compositeSuffix. Also some edits for readability.
  • 1.26 lines changed: 5, context: html, text, full: html, text
    Added 'input'
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.12 lines changed: 5, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.14 lines changed: 61, context: html, text, full: html, text
    Merge in wrangler email (will obsolete labs.ra). Add some new labs and remove some aliases to retire
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.10 lines changed: 12, context: html, text, full: html, text
    Update for pipeline 2.0
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Update for DAF 2.0
• src/hg/encode/makefile
  • 1.12 lines changed: 2, context: html, text, full: html, text
    added script to generate changes notes for ENCODE tracks
• src/hg/hgCustom/hgCustom.c
  • 1.139 lines changed: 1, context: html, text, full: html, text
    added BAM to the list of formats that need an embedded URL.
• src/hg/hgGateway/hgGateway.c
  • 1.115 lines changed: 9, context: html, text, full: html, text
    support "type/paste gene name and click submit without choosing from autosuggest list"
• src/hg/hgSession/hgSession.c
  • 1.53 lines changed: 1, context: html, text, full: html, text
    Oops, forgot a cloneString back in Oct. '08 (thx Pauline).
• src/hg/hgSuggest/hgSuggest.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    safef -> safecpy
  • 1.3 lines changed: 1, context: html, text, full: html, text
    using a format string is recommended
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.516 lines changed: 2, context: html, text, full: html, text
    Code review: ClosestToHome no longer necessary, and format string was hard to read. (thx Jim)
• src/hg/hgTracks/bamTrack.c
  • 1.30 lines changed: 13, context: html, text, full: html, text
    When item labels are suppressed, we still need to draw the leftLabel in dense mode (shortLabel).
  • 1.29 lines changed: 5, context: html, text, full: html, text
    Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles.
  • 1.28 lines changed: 83, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgTracks/cds.c
  • 1.105 lines changed: 1, context: html, text, full: html, text
    Fix for baseColorDrawItem being called w/drawOpt=off.
• src/hg/hgTracks/hgTracks.c
  • 1.1634 lines changed: 2, context: html, text, full: html, text
    utils.js needs to be there whether advancedJavascriptFeatures is on or not
  • 1.1633 lines changed: 54, context: html, text, full: html, text
    refactor code into trackUrl; add track search code within TRACK_SEARCH #define; add ruler entry to trackDbJson; clear suggest field when user hits 'clear' button
  • 1.1632 lines changed: 3, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgTracks/hgTracks.h
  • 1.201 lines changed: 1, context: html, text, full: html, text
    comment out the TRACK_SEARCH #define
  • 1.200 lines changed: 5, context: html, text, full: html, text
    refactor code into trackUrl; add track search code within TRACK_SEARCH #define; add ruler entry to trackDbJson; clear suggest field when user hits 'clear' button
• src/hg/hgTracks/imageV2.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Fix bug with map area clicking
  • 1.25 lines changed: 2, context: html, text, full: html, text
    Move some javascript code into c to speed handling massive images
• src/hg/hgTracks/makefile
  • 1.90 lines changed: 1, context: html, text, full: html, text
    added fogotten build of searchTracks.o
• src/hg/hgTracks/simpleTracks.c
  • 1.128 lines changed: 7, context: html, text, full: html, text
    Change which is currently ifdeffed out, that avoids warning
  • 1.127 lines changed: 3, context: html, text, full: html, text
    Handle empty strings in alleleFreq column of pgSnp tracks
• src/hg/hgc/bamClick.c
  • 1.19 lines changed: 5, context: html, text, full: html, text
    Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles.
  • 1.18 lines changed: 12, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/hgc/bigBedClick.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Doh, there was a segv for rest==0x0 as in any bed3 bigBed.
• src/hg/hgc/encodeClick.c
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Replaced 2 cgiString calls with cartString calls.
• src/hg/hgc/hgc.c
  • 1.1604 lines changed: 1, context: html, text, full: html, text
    Updated the alternate message for tRNAs when image is not available.
  • 1.1603 lines changed: 2, context: html, text, full: html, text
    Minor cosmetic changes.
  • 1.1602 lines changed: 40, context: html, text, full: html, text
    Updated the section for tRNA track to accomodate updated tRNA name format and QA feedback.
  • 1.1601 lines changed: 37, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/hgc/hgcData/links.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Updated dbPEX links.
• src/hg/hgc/lowelab.c
  • 1.44 lines changed: 2, context: html, text, full: html, text
    change lowelab wiki path for track access
• src/hg/inc/bamFile.h
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles.
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/inc/pgPhenoAssoc.h
  • 1.1 lines changed: 65, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/inc/pgPolyphenPred.h
  • 1.1 lines changed: 73, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/inc/pgSiftPred.h
  • 1.1 lines changed: 75, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/inc/pgSnp.h
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/instinct/hgBed15ToArrayVal/hgBed15ToArrayVal.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    updated
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.78 lines changed: 4, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/hgHeatmap2/hgCircleMaps.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.84 lines changed: 1, context: html, text, full: html, text
    Fixed header to be json
  • 1.83 lines changed: 25, context: html, text, full: html, text
    fixed getHeatmaps to look at two databases
  • 1.82 lines changed: 0, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.OLD.ra
  • 1.1 lines changed: 1194, context: html, text, full: html, text
    New version of datasets.ra that uses cancer-pub
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.cancer2.ra
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Fixing line endings... screw you komodo
  • 1.1 lines changed: 348, context: html, text, full: html, text
    New version of datasets.ra that uses cancer-pub
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.36 lines changed: 693, context: html, text, full: html, text
    New version of datasets.ra that uses cancer-pub
  • 1.35 lines changed: 1, context: html, text, full: html, text
    changed back profile entry
  • 1.34 lines changed: 1, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/hgHeatmap2/hgToolTip.c
  • 1.10 lines changed: 5, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/hgMicroscope/microscope/hgMicroscope.c
  • 1.4 lines changed: 49, context: html, text, full: html, text
    multi-word search added
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.c
  • 1.3 lines changed: 373, context: html, text, full: html, text
    Multi-word searching added
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.h
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Multi-word search added
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.41 lines changed: 2, context: html, text, full: html, text
    fixed getHeatmaps to look at two databases
  • 1.40 lines changed: 3, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.67 lines changed: 9, context: html, text, full: html, text
    fixed getHeatmaps to look at two databases
  • 1.66 lines changed: 32, context: html, text, full: html, text
    added profile to gh object for cancer public server
• src/hg/js/hgGateway.js
  • 1.3 lines changed: 18, context: html, text, full: html, text
    support "type/paste gene name and click submit without choosing from autosuggest list"
• src/hg/js/hgTracks.js
  • 1.61 lines changed: 13, context: html, text, full: html, text
    Fix bug with map area clicking
  • 1.60 lines changed: 1, context: html, text, full: html, text
    Fixed postToSaveSettings 'this' should have been 'obj'
  • 1.59 lines changed: 41, context: html, text, full: html, text
    Move some javascript code into c to speed handling massive images
• src/hg/js/loweautocomplete.js
  • 1.1 lines changed: 9, context: html, text, full: html, text
    integrated low lap changes
• src/hg/js/lowetooltip.js
  • 1.3 lines changed: 2, context: html, text, full: html, text
    fixed problem of auto-set width button by Andrew H.
• src/hg/js/makefile
  • 1.15 lines changed: 1, context: html, text, full: html, text
    integrated low lap changes
• src/hg/js/utils.js
  • 1.29 lines changed: 5, context: html, text, full: html, text
    Minor change to clarify, though I don't think postTheForm has ever been called without the href
• src/hg/lib/bamFile.c
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles.
  • 1.21 lines changed: 17, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/lib/customFactory.c
  • 1.118 lines changed: 11, context: html, text, full: html, text
    In bamLoader, report any warnings caught by errCatch even if there was no error.
  • 1.117 lines changed: 1, context: html, text, full: html, text
    Improved an error message.
• src/hg/lib/hdb.c
  • 1.420 lines changed: 3, context: html, text, full: html, text
    find defaultGenome from hg.conf if present
  • 1.419 lines changed: 8, context: html, text, full: html, text
    Fixed loadGrps to handle profiles.
• src/hg/lib/hui.c
  • 1.264 lines changed: 1, context: html, text, full: html, text
    Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist.
• src/hg/lib/knetUdc.c
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Use udcFileMayOpen and warn if it fails, rather than errAborting in udcFileOpen.
  • 1.2 lines changed: 5, context: html, text, full: html, text
    fixing compile error warning: cast from pointer to integer of different size
• src/hg/lib/makefile
  • 1.403 lines changed: 2, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPhenoAssoc.as
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPhenoAssoc.c
  • 1.1 lines changed: 142, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPhenoAssoc.sql
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPolyphenPred.as
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPolyphenPred.c
  • 1.1 lines changed: 220, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgPolyphenPred.sql
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgSiftPred.as
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgSiftPred.c
  • 1.1 lines changed: 259, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgSiftPred.sql
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/pgSnp.c
  • 1.8 lines changed: 34, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks
• src/hg/lib/snp125.as
  • 1.7 lines changed: 11, context: html, text, full: html, text
    Clarifications to comments after user question.
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeqRelease3Lists.txt
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Included index.html and others
• src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt
  • 1.5 lines changed: 13, context: html, text, full: html, text
    Only rep2 for HepG2/SRF so promoting it to rep1
• src/hg/makeDb/doc/encodeDccHg18/mapability.txt
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Notes on the new subtracks added to the mapability track.
  • 1.1 lines changed: 6, context: html, text, full: html, text
    mapability.txt
• src/hg/makeDb/doc/encodeDccHg18/openChromatinR3.notes.txt
  • 1.3 lines changed: 250, context: html, text, full: html, text
    Reworked paths - again
  • 1.2 lines changed: 592, context: html, text, full: html, text
    Reworked paths and included index.html
  • 1.1 lines changed: 1009, context: html, text, full: html, text
    added notes for ENCODE Open Chromatin track
• src/hg/makeDb/doc/encodeDccHg18/rikenCage.release2.notes.txt
  • 1.1 lines changed: 169, context: html, text, full: html, text
    RikenCage Loc release notes
• src/hg/makeDb/doc/encodeDccHg18/uwAffyExonArray.release2.notes.txt
  • 1.1 lines changed: 95, context: html, text, full: html, text
    another attempt to capture what's changed between releases. We need a script to make these consistent
• src/hg/makeDb/doc/encodeDccHg18/uwDgfStamm.release2.notes.txt
  • 1.1 lines changed: 105, context: html, text, full: html, text
    added notes for wgEncodeUwDGF release 2
• src/hg/makeDb/doc/encodeDccHg18/uwDnaseSeq.release3.notes.txt
  • 1.4 lines changed: 3, context: html, text, full: html, text
    fixed totaly of untouched wibs and removed a file from untouched files that is actually being replaced and is already accounted for in the replaced files section.
  • 1.3 lines changed: 32, context: html, text, full: html, text
    Making sure all of Jurkat files/tables are treated as if new. Thanks Katrina for noticing this problem.
• src/hg/makeDb/doc/encodeDccHg18/yaleChIPseq.release3.notes.txt
  • 1.1 lines changed: 1558, context: html, text, full: html, text
    added notes for wgEncodeYaleChIPseq release 3
• src/hg/makeDb/doc/encodeHg18.txt
  • 1.32 lines changed: 5, context: html, text, full: html, text
    Added more information about the CRG alignablity subtracks.
  • 1.31 lines changed: 5, context: html, text, full: html, text
    added CRG Alignability subtracks to Mapability track.
• src/hg/makeDb/doc/encodeHg19.txt
  • 1.1 lines changed: 14, context: html, text, full: html, text
    added Mapability track with CRG alignability data.
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.1 lines changed: 105, context: html, text, full: html, text
    New support for felCatV17e
• src/hg/makeDb/doc/hg18.txt
  • 1.404 lines changed: 7, context: html, text, full: html, text
    Re-built hg18 tRNAs track using updated source data.
  • 1.403 lines changed: 6, context: html, text, full: html, text
    Adding phenotype tables for pgSnp track hgc clicks, and new genomes
  • 1.402 lines changed: 16, context: html, text, full: html, text
    Add H-InvDB_7.0 support
• src/hg/makeDb/doc/hg19.txt
  • 1.90 lines changed: 5, context: html, text, full: html, text
    Updated tRNAs track build.
  • 1.89 lines changed: 86, context: html, text, full: html, text
    Undo Add H-InvDB_7.0 support
  • 1.88 lines changed: 86, context: html, text, full: html, text
    Add H-InvDB_7.0 support
• src/hg/makeDb/doc/mm9.txt
  • 1.127 lines changed: 7, context: html, text, full: html, text
    Re-built mm9 tRNAs track.
• src/hg/makeDb/doc/rn4.txt
  • 1.39 lines changed: 7, context: html, text, full: html, text
    Rebuilt rn4 tRNAs track using updated data files from Todd Lowe.
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.100 lines changed: 1, context: html, text, full: html, text
    added ignore entry
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.87 lines changed: 2, context: html, text, full: html, text
    turning on genbank updates for both aplCal1 and tetNig2
• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/hgBedsToBedExps/bToBeCfg.sql
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
  • 1.3 lines changed: 26, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/hgBedsToBedExps/tests/first/in.cfg
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Small tweaking to get it to work with real rather than pretend data.
• src/hg/makeDb/makefile
  • 1.45 lines changed: 3, context: html, text, full: html, text
    need to clean hgTomRough
• src/hg/makeDb/trackDb/README
  • 1.102 lines changed: 25, context: html, text, full: html, text
    Added notes about release public.
• src/hg/makeDb/trackDb/affyExonTissues.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Finally committing an old ref update change.
• src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/canHg10/trackDb.ra
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/canHg11/trackDb.ra
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra
  • 1.8 lines changed: 7, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/canHg4/trackDb.ra
  • 1.13 lines changed: 4, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/canHg9/trackDb.ra
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/car46/trackDb.ra
  • 1.10 lines changed: 4, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/catArr1/trackDb.ra
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/euaGli13/trackDb.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/gliRes13/trackDb.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/homIni13/trackDb.ra
  • 1.9 lines changed: 12, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/homIni14/trackDb.ra
  • 1.8 lines changed: 8, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/homIni20/trackDb.ra
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/homPan20/trackDb.ra
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/priMat13/trackDb.ra
  • 1.8 lines changed: 10, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/rodEnt13/trackDb.ra
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/ancestor/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/anopheles/trackDb.ra
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra
  • 1.28 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/apis/trackDb.ra
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.15 lines changed: 24, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/blatFr1.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/cat/felCatV17e/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Initial files for felCatV17e
• src/hg/makeDb/trackDb/cat/felCatV17e/gap.html
  • 1.1 lines changed: 64, context: html, text, full: html, text
    Initial files for felCatV17e
• src/hg/makeDb/trackDb/cat/felCatV17e/gold.html
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Initial files for felCatV17e
• src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Initial files for felCatV17e
• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/chainAnoCar1.html
  • 1.5 lines changed: 94, context: html, text, full: html, text
    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainBosTau1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainBosTau2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainBosTau3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainBosTau4.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainBraFlo1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainCalJac1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainCanFam1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainCanFam2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainCavPor3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainDanRer1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainDanRer2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainDanRer3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainDanRer4.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainDanRer5.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainEquCab1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainEquCab2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainFelCat3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainFr1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainFr2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainGalGal2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainGalGal3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainGasAcu1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainHg15.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainHg16.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainHg17.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainHg18.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainHg19.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm4.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm5.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm6.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm7.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm8.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMm9.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMonDom1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMonDom2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMonDom4.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainMonDom5.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainNet.html
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/chainOrnAna1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainOryCun1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainOryLat1.html
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• src/hg/makeDb/trackDb/chainOryLat2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainPanTro1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainPanTro2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainPetMar1.html
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• src/hg/makeDb/trackDb/chainPonAbe1.html
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• src/hg/makeDb/trackDb/chainPonAbe2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainRheMac1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainRheMac2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainRn3.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainRn4.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainStrPur2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainTaeGut1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainTetNig1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainXenTro1.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chainXenTro2.html
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    dropping top-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chicken/galGal1/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/chicken/galGal2/chainPanTro2.html
  • 1.5 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
  • 1.4 lines changed: 90, context: html, text, full: html, text
    testing cvs delete to see if hirsotry is retained when replaced
  • 1.3 lines changed: 90, context: html, text, full: html, text
    testing cvs delete to see if hirsotry is retained when replaced
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.79 lines changed: 6, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/chimp/chainHg16.html
  • 1.5 lines changed: 100, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chimp/panTro1/netHg16.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.41 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/chimp/panTro2/chainGalGal2.html
  • 1.3 lines changed: 86, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.55 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/cow/bosTau1/chainHg17.html
  • 1.6 lines changed: 86, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • 1.41 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/dog/canFam2/chainMm6.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/dog/canFam2/netMm6.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/dog/chainBosTau2.html
  • 1.4 lines changed: 90, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/drosophila/dm1/trackDb.ra
  • 1.63 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • 1.63 lines changed: 7, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/dp1/trackDb.ra
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.16 lines changed: 11, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/drosophila/dp2/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/dp3/trackDb.ra
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droAna1/trackDb.ra
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.15 lines changed: 11, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droGri1/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droMoj1/trackDb.ra
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.14 lines changed: 11, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/drosophila/droMoj2/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droSim1/trackDb.ra
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droVir1/trackDb.ra
  • 1.15 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.14 lines changed: 11, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/drosophila/droVir2/trackDb.ra
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/droYak1/trackDb.ra
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.17 lines changed: 11, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/drosophila/droYak2/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • 1.88 lines changed: 37, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.87 lines changed: 13, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/fugu/chainDanRer3.html
  • 1.4 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/fugu/chainDanRer4.html
  • 1.6 lines changed: 93, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/fugu/netDanRer2.html
  • 1.5 lines changed: 80, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/fugu/netDanRer3.html
  • 1.3 lines changed: 93, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.81 lines changed: 7, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.80 lines changed: 1, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/human/chainMonDom4.html
  • 1.3 lines changed: 99, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg10/trackDb.ra
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/human/hg12/trackDb.ra
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/human/hg13/trackDb.ra
  • 1.49 lines changed: 8, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/human/hg15/trackDb.ra
  • 1.87 lines changed: 17, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/human/hg16/chainPt0.html
  • 1.17 lines changed: 105, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg16/chainRxBestPt0.html
  • 1.14 lines changed: 124, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg16/netPanTro1.html
  • 1.5 lines changed: 122, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.590 lines changed: 31, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.457 lines changed: 31, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.456 lines changed: 2, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/human/hg18/chainDanRer3.html
  • 1.5 lines changed: 99, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/chainOrnAna1Pre.html
  • 1.3 lines changed: 88, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/chainPanTro1.html
  • 1.3 lines changed: 95, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/chainRheMac2.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/chainTetNig1.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/chainXenTro1.html
  • 1.3 lines changed: 91, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/netDanRer3.html
  • 1.4 lines changed: 95, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/netOrnAna1Pre.html
  • 1.2 lines changed: 83, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • 1.2 lines changed: 236, context: html, text, full: html, text
    This includes all pgSnp tracks so it can be used when updating the pgSnp track to include these additions.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.475 lines changed: 15, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.474 lines changed: 8, context: html, text, full: html, text
    Added search term for tRNAs track.
  • 1.473 lines changed: 9, context: html, text, full: html, text
    Adding a new experimental track.
  • 1.472 lines changed: 27, context: html, text, full: html, text
    Add phenotype tables to hg18 pgSnp tracks where available
  • 1.471 lines changed: 1, context: html, text, full: html, text
    Adding URL for H-Inv(V7.0)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.922 lines changed: 495, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
  • 1.921 lines changed: 1, context: html, text, full: html, text
    fix a missing color for HeLa rep2 in UwAffyExon trakc
  • 1.920 lines changed: 10, context: html, text, full: html, text
    Changing shortLabels to be consistent across a cell line
  • 1.919 lines changed: 30, context: html, text, full: html, text
    Forgot to commit this removal of alphas.
  • 1.918 lines changed: 57, context: html, text, full: html, text
    removed alphas for the wgEncodeUwAffyExonArray track
  • 1.917 lines changed: 235, context: html, text, full: html, text
    removed release alpha lines for wgEncodeUwDnaseSeq release3 in preparation for release to RR
  • 1.916 lines changed: 1148, context: html, text, full: html, text
    removed release beta blocks for wgEncodeUwDnaseSeq release3 in preparation for release to RR
  • 1.915 lines changed: 10, context: html, text, full: html, text
    Shortened the short label for the CRG Alignability subtrack of the Mapability track.
  • 1.914 lines changed: 1384, context: html, text, full: html, text
    reverted back to version with release alphas and release beta blocks in wgEncodeDnaseSeq track because I am not ready to release as I thought I was
  • 1.913 lines changed: 235, context: html, text, full: html, text
    removed release alphas from wgEncodeDnaseSeq parent, sub-tracks, and view-in-the-middle blocks
  • 1.912 lines changed: 1149, context: html, text, full: html, text
    removed release beta blocks of wgEncodeUwDnaseSeq in preparation to stage and then release release 3 of this track
  • 1.911 lines changed: 25, context: html, text, full: html, text
    Removed revoked crud and set up html for YDH TFSB release2 so that Release3 can proceed
  • 1.910 lines changed: 21, context: html, text, full: html, text
    Added HeLa/Brg1/IgG-mus as last holdout from Jan 2010 freeze to YDH TFBS
  • 1.909 lines changed: 75, context: html, text, full: html, text
    Unrevoked HUVEC for YDH TFBS now that input is loaded.
  • 1.908 lines changed: 870, context: html, text, full: html, text
    extract GIS RNA-loc to its own file
  • 1.907 lines changed: 44, context: html, text, full: html, text
    Renamed tables and files to match metadata on Yale TFSB
  • 1.906 lines changed: 203, context: html, text, full: html, text
    Loaded in missing IgG-rab input for Yale TFBS
  • 1.905 lines changed: 1657, context: html, text, full: html, text
    alpha/beta ize Yale TFBS
  • 1.904 lines changed: 1, context: html, text, full: html, text
    Getting ready for release3
  • 1.903 lines changed: 1, context: html, text, full: html, text
    Fixed reference to html file to restore description to RR version of track.
  • 1.902 lines changed: 12, context: html, text, full: html, text
    Noticed some more discrepencies
  • 1.901 lines changed: 157, context: html, text, full: html, text
    Changed a whole lot of Seqs to seqs
  • 1.900 lines changed: 10, context: html, text, full: html, text
    HAIB TFBS HepG2/SRF has only one replicate which has been renamed rep1
  • 1.899 lines changed: 2, context: html, text, full: html, text
    change default visible tables for MethylSeq
  • 1.898 lines changed: 1, context: html, text, full: html, text
    fix up some metadata for H9ES cell in MethylSeq
  • 1.897 lines changed: 1, context: html, text, full: html, text
    turn off the nextItem arrows by default for the MethylSeq track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.22 lines changed: 7, context: html, text, full: html, text
    trying to clear this up
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra
  • 1.3 lines changed: 144, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.29 lines changed: 42, context: html, text, full: html, text
    Getting ready for release3
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMapRelease2.html
  • 1.1 lines changed: 331, context: html, text, full: html, text
    Getting ready for release3
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra
  • 1.1 lines changed: 1077, context: html, text, full: html, text
    extract GIS Pet tracks to separte include file
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Release 2 should go out in March 2010 hopefully
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.19 lines changed: 18, context: html, text, full: html, text
    change the mailto: links and removed contact:
  • 1.18 lines changed: 13, context: html, text, full: html, text
    fixed typo and changed the way the mailto:'s were displayed
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • 1.5 lines changed: 39, context: html, text, full: html, text
    take out colorByStrand on signal tracks which aren't colored by strand
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.beta.ra
  • 1.2 lines changed: 61, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.17 lines changed: 2, context: html, text, full: html, text
    add some release notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.16 lines changed: 2, context: html, text, full: html, text
    trying to clarify the release name of this batch
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
  • 1.6 lines changed: 13, context: html, text, full: html, text
    add release policy paragram, and release notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    changed number of new cell lines in release notes to the correct number, 19
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseqRelease2.html
  • 1.1 lines changed: 217, context: html, text, full: html, text
    Getting ready for Release3
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added missing closing A tag
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • 1.5 lines changed: 7, context: html, text, full: html, text
    adding shortLabels for stanzas for tetngi1
  • 1.4 lines changed: 1, context: html, text, full: html, text
    swapping tetNig1 c/n for tetNig2 c/n.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    reverting Hiram's change. It would have caused tetNig1 chains and nets on the RR to switch from 'Tetraodon' to 'tetNig1'.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    replace tetNig1 with tetNig2 chainNet
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.4 lines changed: 5, context: html, text, full: html, text
    Shortened the short label for the CRG Alignability subtrack of the Mapability track.
  • 1.3 lines changed: 135, context: html, text, full: html, text
    add gencode
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.104 lines changed: 88, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.103 lines changed: 6, context: html, text, full: html, text
    swapping tetNig1 c/n for tetNig2 c/n.
  • 1.102 lines changed: 8, context: html, text, full: html, text
    Added search term for tRNAs track.
  • 1.101 lines changed: 6, context: html, text, full: html, text
    backing out Hiram's last change. Mary noticed that if this trackDb was pushed to the RR before the tetNig chain/net tables are released, then the tetNig1 chainNet track would go away.
  • 1.100 lines changed: 6, context: html, text, full: html, text
    replace tetNig1 with tetNig2 in vertebrate chainNet
• src/hg/makeDb/trackDb/human/netMonDom4.html
  • 1.2 lines changed: 95, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.527 lines changed: 1, context: html, text, full: html, text
    Added a restriction for the maximum window size for the alignments tracks of the Burge RNA-seq track.
  • 1.526 lines changed: 23, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.525 lines changed: 1, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
  • 1.524 lines changed: 134, context: html, text, full: html, text
    Adding new personal genomes to the pgSnp track (Hgwdev only for now)
  • 1.523 lines changed: 26, context: html, text, full: html, text
    Getting rid of some records that mix releases at different levels.
• src/hg/makeDb/trackDb/loadTracks
  • 1.20 lines changed: 1, context: html, text, full: html, text
    make it so tdbQuery is called with -release option
• src/hg/makeDb/trackDb/makefile
  • 1.286 lines changed: 5, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
  • 1.285 lines changed: 2, context: html, text, full: html, text
    Changed beta target to buildBeta in preparation for changing to alpha/beta/public trackDb makes. It does not seem to be used anywhere.
  • 1.284 lines changed: 1, context: html, text, full: html, text
    Initial support for felCatV17e
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.3 lines changed: 37, context: html, text, full: html, text
    adding 13-way definition
• src/hg/makeDb/trackDb/medaka/oryLat1/trackDb.chainNet.ra
  • 1.2 lines changed: 9, context: html, text, full: html, text
    this is the only way we could get oryLat1 and 2 to place nicely with the new tetNig2 c/n shortLabels.
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    this is the only way we could get oryLat1 and 2 to place nicely with the new tetNig2 c/n shortLabels.
• src/hg/makeDb/trackDb/mouse/chainBosTau2.html
  • 1.4 lines changed: 90, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainCanFam2.html
  • 1.3 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainDanRer3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainDanRer4.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainFr1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainGalGal2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainHg18.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainOryLat1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainPanTro1.html
  • 1.3 lines changed: 95, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainTetNig1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/chainXenTro1.html
  • 1.3 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm2/trackDb.ra
  • 1.21 lines changed: 5, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm2X/trackDb.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm3/trackDb.ra
  • 1.43 lines changed: 12, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm3X/trackDb.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm4/trackDb.ra
  • 1.29 lines changed: 9, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm5/trackDb.ra
  • 1.54 lines changed: 11, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm6/chainCanFam2u1.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/chainGalGal2u1.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/chainHg17u1.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/chainRn3u1.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/netCanFam2u1.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/netDanRer3.html
  • 1.5 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/netGalGal2u1.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/netHg17u1.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm6/netRn3u1.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/chainHg17.html
  • 1.4 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/chainRheMac1.html
  • 1.4 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/chainRn3.html
  • 1.4 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/netDanRer3.html
  • 1.3 lines changed: 92, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/netFr1.html
  • 1.3 lines changed: 78, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.68 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm8/chainGalGal2.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.69 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/mouse/mm9/chainRn4Test.html
  • 1.3 lines changed: 97, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    overriding old tetNig1 c/n
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.88 lines changed: 5, context: html, text, full: html, text
    Shortened short labels for Mapability subtracks for CRG data.
  • 1.87 lines changed: 4, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
  • 1.86 lines changed: 8, context: html, text, full: html, text
    Added search term for tRNAs track.
• src/hg/makeDb/trackDb/mouse/netHg17.html
  • 1.6 lines changed: 88, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.34 lines changed: 1, context: html, text, full: html, text
    added shortLabel so that db name rather than org for danRer5
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.210 lines changed: 6, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/netAnoCar1.html
  • 1.2 lines changed: 82, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netBosTau1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netBosTau2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netBosTau3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netBosTau4.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netBraFlo1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netCalJac1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netCanFam1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netCanFam2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netCavPor3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netDanRer1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netDanRer2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netDanRer3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netDanRer4.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netDanRer5.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netEquCab1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netEquCab2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netFelCat3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netFr1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netFr2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netGalGal2.html
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• src/hg/makeDb/trackDb/netGalGal3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netGasAcu1.html
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• src/hg/makeDb/trackDb/netHg15.html
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• src/hg/makeDb/trackDb/netHg16.html
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• src/hg/makeDb/trackDb/netHg17.html
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• src/hg/makeDb/trackDb/netHg18.html
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• src/hg/makeDb/trackDb/netHg19.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netMacEug1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netMm3.html
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• src/hg/makeDb/trackDb/netMm4.html
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• src/hg/makeDb/trackDb/netMm5.html
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• src/hg/makeDb/trackDb/netMm6.html
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• src/hg/makeDb/trackDb/netMm7.html
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• src/hg/makeDb/trackDb/netMm8.html
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• src/hg/makeDb/trackDb/netMm9.html
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• src/hg/makeDb/trackDb/netMonDom1.html
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• src/hg/makeDb/trackDb/netMonDom2.html
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• src/hg/makeDb/trackDb/netMonDom4.html
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• src/hg/makeDb/trackDb/netMonDom5.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netOrnAna1.html
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• src/hg/makeDb/trackDb/netOryCun1.html
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• src/hg/makeDb/trackDb/netOryLat1.html
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• src/hg/makeDb/trackDb/netOryLat2.html
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• src/hg/makeDb/trackDb/netPanTro1.html
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• src/hg/makeDb/trackDb/netPanTro2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/netPetMar1.html
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• src/hg/makeDb/trackDb/netPonAbe1.html
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• src/hg/makeDb/trackDb/netPonAbe2.html
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• src/hg/makeDb/trackDb/netRheMac1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
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• src/hg/makeDb/trackDb/netRn3.html
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• src/hg/makeDb/trackDb/netTetNig1.html
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• src/hg/makeDb/trackDb/netXenTro1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/chainDanRer2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/chainGalGal2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/chainHg17.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/monDom2/chainDanRer3.html
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    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/monDom2/netDanRer3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/opossum/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/rat/chainHg17.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/rat/chainHg18.html
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• src/hg/makeDb/trackDb/rat/rn2/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/rat/rn4/chainDanRer3.html
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    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/rat/rn4/chainXenTro1.html
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    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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    Added search term for rn4 tRNAs track.
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
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    Initial edit of this file -- still have to fix up a few things.
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/squirt/cioSav1/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/stickleback/chainOryLat1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/stickleback/netOryLat1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
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    overriding old tetNig1 c/n
• src/hg/makeDb/trackDb/tagTypes.tab
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    Added tags for additions to genome variants track
• src/hg/makeDb/trackDb/tetraodon/chainDanRer3.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/tetraodon/chainDanRer4.html
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• src/hg/makeDb/trackDb/tetraodon/chainFr1.html
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• src/hg/makeDb/trackDb/tetraodon/chainHg17.html
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• src/hg/makeDb/trackDb/tetraodon/chainMm7.html
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• src/hg/makeDb/trackDb/tetraodon/chainMm8.html
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• src/hg/makeDb/trackDb/tetraodon/netDanRer3.html
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• src/hg/makeDb/trackDb/tetraodon/netFr1.html
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• src/hg/makeDb/trackDb/tetraodon/netHg17.html
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• src/hg/makeDb/trackDb/tetraodon/netMm5.html
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• src/hg/makeDb/trackDb/tetraodon/netMm7.html
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• src/hg/makeDb/trackDb/tetraodon/netMm8.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/tetraodon/tetNig2/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Edited.
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    Edited this file.
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    Deleting a sample position query that was didn't work
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    replacing non-fuctional sample position queries with fuctional ones
• src/hg/makeDb/trackDb/tetraodon/tetNig2/gap.html
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    moved sentence. added period.
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.622 lines changed: 6, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/worm/caeRem1/trackDb.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/cb1/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/cb2/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/ce1/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/ce2/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/ce3/trackDb.ra
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    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.43 lines changed: 2, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.44 lines changed: 28, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.43 lines changed: 6, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makeDb/trackDb/xenTro/chainDanRer4.html
  • 1.4 lines changed: 84, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/chainMm6.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/chainMm7.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/netDanRer1.html
  • 1.4 lines changed: 81, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/netGalGal2.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/netHg17.html
  • 1.4 lines changed: 88, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/netMm5.html
  • 1.4 lines changed: 88, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/netMm7.html
  • 1.2 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/chainDanRer1.html
  • 1.6 lines changed: 83, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/chainGalGal2.html
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    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/chainHg17.html
  • 1.7 lines changed: 84, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/xenTro/xenTro1/chainMm5.html
  • 1.6 lines changed: 84, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/chainMm8.html
  • 1.3 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/chainTetNig1.html
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    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer1/trackDb.ra
  • 1.39 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/zebrafish/danRer2/trackDb.ra
  • 1.37 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainFr1.html
  • 1.5 lines changed: 85, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainHg18.html
  • 1.3 lines changed: 99, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainMm6.html
  • 1.7 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainMm7.html
  • 1.6 lines changed: 89, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainMm8.html
  • 1.3 lines changed: 89, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainMonDom2.html
  • 1.4 lines changed: 89, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainTetNig1.html
  • 1.6 lines changed: 92, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netFr1.html
  • 1.4 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netHg18.html
  • 1.2 lines changed: 95, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netMm6.html
  • 1.6 lines changed: 90, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netMm7.html
  • 1.3 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netMm8.html
  • 1.2 lines changed: 91, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netMonDom2.html
  • 1.3 lines changed: 85, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/netTetNig1.html
  • 1.4 lines changed: 86, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • 1.62 lines changed: 1, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
• src/hg/makeDb/trackDb/zebrafish/danRer4/chainFr1.html
  • 1.7 lines changed: 94, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer4/chainPanTro2.html
  • 1.3 lines changed: 90, context: html, text, full: html, text
    dropping bot-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/danRer4/netPanTro2.html
  • 1.2 lines changed: 87, context: html, text, full: html, text
    dropping mid-level html files no longer needed since the consolidation into chainNet composites
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.79 lines changed: 6, context: html, text, full: html, text
    Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie.
  • 1.78 lines changed: 4, context: html, text, full: html, text
    Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public).
• src/hg/makefile
  • 1.156 lines changed: 1, context: html, text, full: html, text
    integrated low lap changes
• src/hg/mouseStuff/makefile
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Well, we need a clean in simpleChain
  • 1.22 lines changed: 2, context: html, text, full: html, text
    fixed clean target to recurse correct, but it doesn't matter, since many sub-makefiles don't have clean
• src/hg/pslCDnaFilter/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    need to clean algo.msg for clean target
• src/hg/pslMap/tests/makefile
  • 1.12 lines changed: 8, context: html, text, full: html, text
    temporarily disabling tests to clean up large wasteful cvs history
• src/hg/pslPartition/makefile
  • 1.6 lines changed: 3, context: html, text, full: html, text
    needed a clean target
• src/hg/regulate/regBedStats/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Little program to calculate mean/std and quartile stats for a bunch of bed files.
• src/hg/regulate/regBedStats/regBedStats.c
  • 1.2 lines changed: 35, context: html, text, full: html, text
    Moving doubleBoxWhiskerCalc to library.
  • 1.1 lines changed: 144, context: html, text, full: html, text
    Little program to calculate mean/std and quartile stats for a bunch of bed files.
• src/hg/regulate/regCluster/makefile
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Making it so that it will break up clusters that are weakly linked.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/regulate/regCluster/regCluster.c
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    Making it so that it will break up clusters that are weakly linked.
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    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/regulate/regCluster/tests/needBreak/a.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/b.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/c.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/d.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/e.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/expected.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/expected.cluster
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/f.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/g.bed
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regCluster/tests/needBreak/in.tab
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    Making it so that it will break up clusters that are weakly linked.
• src/hg/regulate/regClusterBedExpCfg/makefile
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    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
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    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/regulate/regClusterMakeTableOfTables/makefile
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    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
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    Removing -two option.
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    First cut of some code to combine ENCODE regulatory tracks into a single track done.
• src/hg/snp/makefile
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    add clean target and use curly braces on variables
• src/hg/tcga/bamToFastQ/bamToFastQ.c
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    updated to correctly output paired ends
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    updated
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    initial commit
• src/hg/tcga/bamToFastQ/makefile
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    updated
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    initial commit
• src/hg/tcga/pBamBam/asBamBam.c
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    updated
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    updated
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    updated
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    updated
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    updated
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    updated
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    updated
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    updated
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    initial commit
• src/hg/tcga/pBamBam/makefile
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    updated
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    initial commit
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    updated
• src/hg/tcga/pBamBam/pBamBamMuts.c
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    initial commit
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    updated
• src/hg/utils/automation/Encode.pm
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    Tweak error msg
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    Update DAF version to 2.0, freeze to June 2010, assemblies to hg19 and mm9, table/file name prefix to 'enc'. Add warning for beta testing.
• src/hg/utils/tdbQuery/tdbQuery.c
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    update to understand tri-state release mechanims
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    Improving handling of release tags. Case where have alpha and beta in composite tracks works better.
• src/hg/utils/tdbQuery/tdbRecord.c
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    Improving handling of release tags. Case where have alpha and beta in composite tracks works better.
• src/hg/utils/tdbQuery/tdbRecord.h
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    a new function
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    Improving handling of release tags. Case where have alpha and beta in composite tracks works better.
• src/inc/common.h
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    Adding doubleBoxWhiskerCalc to library.
• src/inc/common.mk
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    Moving the USE_FUSE addition of L += -lfuse to src/fuse only, so execs created in the rest of the tree don't crash on machines that don't have libfuse.
• src/inc/genoFind.h
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    Bumping version number.
• src/inc/https.h
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    Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
• src/inc/net.h
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    Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
• src/isPcr/makefile
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    need a clean target
• src/jkOwnLib/genoFind.c
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    Putting in check for uniqueness of target sequence names.
• src/lib/basicBed.c
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    allow bedLoadAll to read from pipe by not closing and reopening
• src/lib/cheapcgi.c
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    halfVis not ready for primetime, because ff and ie can't agree
  • 1.132 lines changed: 1, context: html, text, full: html, text
    Fixed halfVis style
• src/lib/common.c
  • 1.145 lines changed: 2, context: html, text, full: html, text
    Fixing compile errors under Linux.
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    Adding doubleBoxWhiskerCalc to library.
• src/lib/errCatch.c
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    fixed incorrect assumption about pthread_t being an int
• src/lib/https.c
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    Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
• src/lib/internet.c
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    Taking untranslated h_errno out of warning message -- IMO it adds confusion instead of clarification when 99.99999% of the time, the problem is a typo in host name. man h_errno says that herror and hstrerror are obsolete, bummer.
• src/lib/net.c
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    Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
• src/lib/osunix.c
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    fix semiUniqName when host name includes : as in: localhost:8080 (from 41,000 ft)
• src/lib/udc.c
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    Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values.
• src/product/README.udc
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    adding some documentation about udc, bbi, bam, udc.cacheDir hg.conf setting
• src/product/ex.hg.conf
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    add defaultGenome variable discussion, pointer to README.udc and fixup comments for downloadsServer
• src/utils/qa/chain.csh
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    only for vertebrate assemblies.
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    added disclaimer about findLevel output since all chainNets now use top-level chainNet.html file
• src/utils/qa/checkOffend.csh
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    added error message for non-chrom-based tables
• src/utils/qa/comparePublic.csh
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    added support for second trackDb field. settings not yet supported. html will probably never be
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    added support for comparing to trackD on beta, too. still doesn't work for second field
  • 1.1 lines changed: 61, context: html, text, full: html, text
    utility to compare trackDb_public on beta to trackDb on RR. first rough cut
• src/utils/qa/findLevel
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    Added changes to work with updated tdbQuery that recognizes multiple release tags (like beta,public).
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    Do db check with hgsql instead of tdbQuery, as unrelated errors there will mess with the db check. Also give an error if nothing tdbQuery only gives errors.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Changed html file lookup so that it actually starts at the assembly level, like it says it does. Thanks, Ann.
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Changed dependency on symlink in home directory to dependency on the kent source tree in home directory. Also moved this check closer to the top, as tdbQuery run by default also depends on the tree being in the home dir.
• src/utils/qa/knownGene.csh
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Fixing a bug I introduced. Oops!
  • 1.17 lines changed: 7, context: html, text, full: html, text
    Editing usage statement for clarity
  • 1.16 lines changed: 13, context: html, text, full: html, text
    Fixed some typos, an unmatched quote and clarified description statement.
• src/utils/qa/makefile
  • 1.121 lines changed: 1, context: html, text, full: html, text
    utility to compare trackDb_public on beta to trackDb on RR. first rough cut
• src/utils/qa/net.csh
  • 1.24 lines changed: 1, context: html, text, full: html, text
    only for vertebrate assemblies.
  • 1.23 lines changed: 4, context: html, text, full: html, text
    added disclaimer about findLevel output since all chainNets now use top-level chainNet.html file
• src/utils/qa/qaEncodeTracks.csh
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    un-hard-coded hg18 from script
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    Added the other two file formats implied by bbi for clarity.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.104 lines changed: 2, context: html, text, full: html, text
    v227 preview
  • 1.103 lines changed: 2, context: html, text, full: html, text
    fix paths now heather is gone
• src/utils/qa/weeklybld/buildUtils.csh
  • 1.17 lines changed: 1, context: html, text, full: html, text
    trying to get it to run faster
• src/utils/qa/weeklybld/defaultBuildSettings.mk
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated for bamsam
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    adding pauline
• src/utils/qa/weeklybld/doNewReview.csh
  • 1.17 lines changed: 1, context: html, text, full: html, text
    adding pauline and ann
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated for bamsam
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • 1.8 lines changed: 4, context: html, text, full: html, text
    jim added keyword Warning which was triggering as an error, but its not serious enough to stop the build for
• src/xenoAli/bwana/makefile
  • 1.8 lines changed: 3, context: html, text, full: html, text
    need clean targets everywhere here
• src/xenoAli/dynAlign/makefile
  • 1.9 lines changed: 3, context: html, text, full: html, text
    need a clean target
• src/xenoAli/makefile
  • 1.4 lines changed: 5, context: html, text, full: html, text
    need clean targets everywhere here
• src/xenoAli/stitcher/makefile
  • 1.8 lines changed: 3, context: html, text, full: html, text
    need clean targets everywhere here

• lines changed: 46829
• files changed: 574