All File Changes

origin/v233_branch to v234_preview (2010-06-07 to 2010-06-15) v234

• .gitignore
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    adding .gitignore to itself at the highest level
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    do not want to see .a files either
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    first quick attempt to change major makefiles from cvs to git.
• build/dosEolnCheck
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    converted to git using gitFiles the script that checks for CRLF line terminators
• src/aladdin/aladdin/makefile
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    fixing makefiles to have clean targets
• src/aladdin/makefile
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    fixing makefiles to have clean targets
• src/ameme/makefile
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    fixing makefiles to have clean targets
• src/blat/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/.gitignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/throwback/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/throwback/.gitignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/v29skips/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/v29skips/.gitignore
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    renaming .cvsignore files to .gitignore
• src/dnaDust/makefile
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    fixing makefiles to have clean targets
• src/fuse/makefile
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    fixing makefiles to have clean targets
• src/getgene/makefile
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    fixing makefiles to have clean targets
• src/hg/autoSql/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/checkTableCoords/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/checkTableCoords/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
  • lines changed 59, context: html, text, full: html, text
    update for hg19
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
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    New daf for remapped hg18
• src/hg/encode/DAFs/2.0/cshlRnaSeq.daf
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    This is redundant with cshlLongRnaSeq.daf
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
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    New daf for remapped hg18 data
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
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    Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/DAFs/2.0/gisDnaPet.daf
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    Work in progress, trying to get it in boefore the freeze
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
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    hanged the requirement for the .ddf
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    Changed the wigs to bigWigs
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    New daf for remapped from hg18 data
• src/hg/encode/DAFs/2.0/gisRnaSeq.daf
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    New daf for remapped from hg18 data
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
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    Changed -Seq to -seq in all non-conforming files
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
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    change validationSettings
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    add treatment and growthProtocol
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
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    Changed -Seq to -seq in all non-conforming files
• src/hg/encode/DAFs/2.0/helicosRnaSeq.daf
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    Changed -Seq to -seq in all non-conforming files
• src/hg/encode/DAFs/2.0/renMm9Tfbs.daf
  • lines changed 7, context: html, text, full: html, text
    Modifed Lab to LICR and grant to Ren, consistent with pi.ra. Changed compiste suffix to LicrChipSeq(not enought data to support just Tfbs) and changed long labels to Ren -> LICR
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    Changed -Seq to -seq in all non-conforming files
• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • lines changed 11, context: html, text, full: html, text
    New daf for remapped from hg18 data
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Changed fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 11, context: html, text, full: html, text
    Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/encodeCharts/June2010-Freeze.html
  • lines changed 147, context: html, text, full: html, text
    Initial checkin of html file which generates the ENCODE June 2010 Freeze update chart
• src/hg/encode/encodeCharts/encodeDist.py
  • lines changed 3, context: html, text, full: html, text
    Updated to latest renderHtml and changed color orange to RGB to fix IE8 problems
• src/hg/encode/encodeCharts/encodeDistUnrelease.py
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    Updated to latest renderHtml and changed color orange to RGB to fix IE8 problems
• src/hg/encode/encodeCharts/encodeJune2010-Freeze.py
  • lines changed 80, context: html, text, full: html, text
    Initial checkin. Scripts produces the ENCODE report file as a JSON object to be consumed by the June2010-Freeze.html webpage
• src/hg/encode/encodeCharts/encodeReport.py
  • lines changed 23, context: html, text, full: html, text
    Script can now report the latest report file date as json and jsonp objects
  • lines changed 13, context: html, text, full: html, text
    Added output as Google JSON Query Response
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    Updated to latest renderHtml
• src/hg/encode/encodeCharts/encodeReportFilter.py
  • lines changed 28, context: html, text, full: html, text
    Improved behavior when key and value are not specified based on suggestion from Krish. Also added freeze=all as option
  • lines changed 2, context: html, text, full: html, text
    Fixed bug found by Kate dealing with Jan2010 freeze date
• src/hg/encode/encodeCharts/encodeReportLib.py
  • lines changed 19, context: html, text, full: html, text
    Added another option to renderHtml function and added DOCTYPE tag to fix IE8 problems
• src/hg/encode/encodeCharts/encodeStatus.py
  • lines changed 3, context: html, text, full: html, text
    Updated to latest renderHtml and changed color orange to RGB to fix IE8 problems
• src/hg/encode/encodeCharts/encodeTimeline.py
  • lines changed 2, context: html, text, full: html, text
    Updated to latest renderHtml and added px to fix IE8 problems
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 64, context: html, text, full: html, text
    Documented most stanza types
  • lines changed 26, context: html, text, full: html, text
    Added a header comment block describing the tissue type section
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    Added line validatio missing to cv.ra
  • lines changed 12, context: html, text, full: html, text
    Added Antibody STAT3 from Snyder lab to cv.ra
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    Fixed the protocol names for ECC1 and T47D
  • lines changed 3, context: html, text, full: html, text
    Added a few more fiends for ECC1 and T47D
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 5, context: html, text, full: html, text
    added the field growthProtocol to distinguish which growth protocl is being used
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • lines changed 55, context: html, text, full: html, text
    Add support for new metaDb. Protect against missing data
• src/hg/encode/encodeValidate/doEncodeValidate.pl
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    Commented out the specific check for a lab inorder to write replicate to subgroups. The code has been checked in the unit test and will now write replicate as a subgroup regardless of lab. Have discussed with Brian about changes.
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    Swap '.' for offending ';' in ddf fields
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
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    Updated file names
• src/hg/encode/encodeValidate/test/expected/chipseq/fileDb.ra
  • lines changed 16, context: html, text, full: html, text
    Added fileDb.ra as this is generated by the pipeline at the moment
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • lines changed 4, context: html, text, full: html, text
    Upated tablenames to include wgEncode
• src/hg/encode/encodeValidate/test/expected/chipseq/mdb.txt
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    Added mdb.txt to check the mdb.txt, might still need to update make file to verify everything in the file
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
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    Updated the metadata line to include only subId and dateSubmitted. updated track and subtrack names to include wgEncode and appropriate abreviations. Lastly updated type wig line to update to ENC-> WGENCODE
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.wig
  • lines changed 10995, context: html, text, full: html, text
    restoring some large files that had already become small enough to add back
• src/hg/encode/encodeValidate/test/input/duke/GM12878_DNase_peaks.bed
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    restoring some old test file in non-huge form
• src/hg/encode/encodeValidate/test/input/genes/known.jan08.gff
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    restoring some old test file in non-huge form
• src/hg/encode/encodeValidate/test/makefile
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    Added mdb.txt and fileDb.ra files to check between expected and actual. Uncommented line to print the file name
• src/hg/encode/hgEncodeSubmit/README.FTP
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    adding FTP notes
• src/hg/encode/hgEncodeSubmit/runforever.sample
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    changing qateam to encodeteam
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 31, context: html, text, full: html, text
    some little fixups
• src/hg/geneBounds/bedThickToCds/makefile
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    fixup makefiles to be OK with parallel make
• src/hg/geneBounds/clusterGenes/makefile
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    fixup makefiles to be OK with parallel make
• src/hg/geneBounds/clusterPsl/makefile
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    fixup makefiles to be OK with parallel make
• src/hg/geneBounds/orfCompare/makefile
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    fixup makefiles to be OK with parallel make
• src/hg/geneBounds/orfEnum/makefile
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    fixup makefiles to be OK with parallel make
• src/hg/hgBlat/hgBlat.c
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    Making it so bot delay is only called every other sequence when user has multiple sequences.
• src/hg/hgGene/hgGeneData/Human/links.ra
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    Updated OMIM URL.
• src/hg/hgTracks/hgTracks.c
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    remove searchTracks cartRemove
• src/hg/hgTracks/multiWig.c
  • lines changed 5, context: html, text, full: html, text
    Improved a few more comments.
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    Improved header comment.
• src/hg/hgTracks/searchTracks.c
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    improve isDescriptionMatch so it finds matches only at the start of words
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    use trix search for simple search; style related code review changes per jim
• src/hg/hgc/hgc.c
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    Use long long not long in getSnpSeqFileOffset, so it will work on 32-bit systems as well. Contributed by John Hayward @ Wheaton.
• src/hg/hgc/hgc.h
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    make motifHitSection and loadDnaMotif public; use a table for motif section to avoid problem where bases in image and text did not line up; fix typo (occurence => occurrence)
• src/hg/hgc/regMotif.c
  • lines changed 39, context: html, text, full: html, text
    make motifHitSection and loadDnaMotif public; use a table for motif section to avoid problem where bases in image and text did not line up; fix typo (occurence => occurrence)
• src/hg/htdocs/ENCODE/releaseLog.html
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    "Encode release log update"
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    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
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    "Encode release log update"
• src/hg/htdocs/admin/exe/README.txt
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    moving this to hgdownload repo where it belongs
• src/hg/htdocs/goldenPath/help/bam.html
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    changed the path of data files to be under the examples directory
• src/hg/htdocs/goldenPath/help/bigBed.html
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    changed the path of data files to be under the examples directory
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    moved more examples to examples dir
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    changed the path of data files to be under the examples directory
• src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
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    moved more examples to examples dir
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
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    moved more examples to examples dir
• src/hg/htdocs/goldenPath/help/wiggle.html
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    changed the path of data files to be under the examples directory
• src/hg/htdocs/goldenPath/pubs.html
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    moved some publications, fixed links
• src/hg/htdocs/goldenPath/releaseLog.html
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    "Release log update"
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    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/makefile
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    tweaking git pull to be safer, fixing checkbeta target
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    first quick attempt to change major makefiles from cvs to git.
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    moved training
• src/hg/htdocs/style/jquery-ui.css
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    remove dos newlines
• src/hg/inc/mdb.h
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    Added mdbObjsPrintUpdateLines and mdbObjsSortOnVars to aid special advanced mdbPrint options
• src/hg/js/hgTracks.js
  • lines changed 53, context: html, text, full: html, text
    support tabbed ui in searchTracks
• src/hg/js/makefile
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    tweaking git pull to be safer
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    conversion to git
• src/hg/lib/mdb.c
  • lines changed 145, context: html, text, full: html, text
    Added mdbObjsPrintUpdateLines and mdbObjsSortOnVars to aid special advanced mdbPrint options
• src/hg/lib/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/lib/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/liftUp/test/.cvsignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/liftUp/test/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/doc/ailMel1.txt
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    rework felCat4
• src/hg/makeDb/doc/bosTau4P2.txt
  • lines changed 371, context: html, text, full: html, text
    Initial bosTau4P2
• src/hg/makeDb/doc/calJac3.txt
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    start phyloP
• src/hg/makeDb/doc/canFam2.txt
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    Multiz with felCat4
• src/hg/makeDb/doc/danRer6.txt
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    adding needed downloads for phastCons6way
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    not needed
• src/hg/makeDb/doc/dm3.txt
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    Added AFFYMETRIX TIMECOURSE tracks using the data on dm2.
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
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    These are running docs that I need to check in before git
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • lines changed 311, context: html, text, full: html, text
    These are running docs that I need to check in before git
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • lines changed 1647, context: html, text, full: html, text
    These are running docs that I need to check in before git
• src/hg/makeDb/doc/encodeDccHg18/myers.txt
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    These are running docs that I need to check in before git
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
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    These are running docs that I need to check in before git
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeCaltechRnaSeq.release2.notes.txt
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    fixed problems with different files. Turns out that both of the release2 files were truncated. Hmm... disk exhaustion?
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
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    These are running docs that I need to check in before git
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 37, context: html, text, full: html, text
    rework felCat4
• src/hg/makeDb/doc/hg19.txt
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    Multiz with felCat4
• src/hg/makeDb/doc/mm9.txt
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    Multiz with felCat4
• src/hg/makeDb/doc/monDom5.txt
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    rework felCat4
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
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    Executing a bit further...
  • lines changed 9, context: html, text, full: html, text
    Finished one more stage of execution
• src/hg/makeDb/hgTrackDb/.cvsignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/makeDb/hgTrackDb/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 66, context: html, text, full: html, text
    Added special option to print mdbUpdate lines to assist in importing vars from one db.mdb to another.
• src/hg/makeDb/trackDb/.cvsignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/makeDb/trackDb/.gitignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevSignal.html
  • lines changed 83, context: html, text, full: html, text
    Added affyDrosDevSignal.html based on dm2 affyDrosDevSignal.html.
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevTransfrags.html
  • lines changed 73, context: html, text, full: html, text
    Added affyDrosDevTransfrags.html based on dm2 affyDrosDevTransfrags.html.
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 189, context: html, text, full: html, text
    Added affyDrosDevTransfrags and affyDrosDevSignal tracks with their sub-tracks for dm3.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 99, context: html, text, full: html, text
    Fixed RawSignal fileNames which should point to their Alignments parent
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 99, context: html, text, full: html, text
    updating metaDb on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    adding wgEncodeHudsonalphaChipSeq.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaChipSeq.ra
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    creating metaDb for release
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    committing this on aamp's behalf. He altered the hg18 polyaDb table accordingly
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    fixed typo in include line just added
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    added include line for wgEncodeBroadChipSeq.new.ra
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    removed include statement for wgEncodeHudsonalphaChipSeq.new.ra in prep for release on rr
  • lines changed 95, context: html, text, full: html, text
    Adding another mark to regulatory track and improving a viewLimit.
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    added commented out heading to make the include statement for BU ORChID easier to find and consistent with other include statements
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    take out wgEncodeBuOrchid
  • lines changed 2, context: html, text, full: html, text
    removed include for wgEncodeCaltechRnaSeq.new.ra
  • lines changed 2, context: html, text, full: html, text
    Yale Poly A was renamed Yale RNA-seq
  • lines changed 3, context: html, text, full: html, text
    Took out special character in the long label (-)
  • lines changed 4, context: html, text, full: html, text
    Changed the labels for the BU ORChID tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 180, context: html, text, full: html, text
    added release alpha,beta liness
  • lines changed 48, context: html, text, full: html, text
    modified all Signal track spanList to spanList first, via the View level, and changed the view limit to 1:50 as Jim requested
  • lines changed 1626, context: html, text, full: html, text
    creating a .new.ra file for use with release 3 display update
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
  • lines changed 1, context: html, text, full: html, text
    added html line pointing to Release3 original html
  • lines changed 180, context: html, text, full: html, text
    added release public tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease3original.html
  • lines changed 123, context: html, text, full: html, text
    html page for RR so I can modify the html page for the release3 display update
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.html
  • lines changed 7, context: html, text, full: html, text
    Reworded the methods section
  • lines changed 1, context: html, text, full: html, text
    fixed typo
  • lines changed 1, context: html, text, full: html, text
    fixed typo: changed preditions to predictions
  • lines changed 12, context: html, text, full: html, text
    removed extra spaces and fixed several of the citation formats
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
  • lines changed 1, context: html, text, full: html, text
    Changed a bit more of the long label to comply with Katrina requests
  • lines changed 4, context: html, text, full: html, text
    Changed long labels to include Boston University
  • lines changed 1, context: html, text, full: html, text
    fix labels
  • lines changed 55, context: html, text, full: html, text
    split out into its own include file
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • lines changed 9, context: html, text, full: html, text
    add some text about the Plus and Minus Raw Signal views
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 144, context: html, text, full: html, text
    removed release alpha,beta tags for release
  • lines changed 143, context: html, text, full: html, text
    change default view to include all of the K562 and GM12878 tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 647, context: html, text, full: html, text
    copied new trackDb file with no release tags for release to RR
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDNAseSuper.html
  • lines changed 103, context: html, text, full: html, text
    Supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • lines changed 1, context: html, text, full: html, text
    fix contact email address
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHistoneSuper.html
  • lines changed 87, context: html, text, full: html, text
    Supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • lines changed 1, context: html, text, full: html, text
    revised # of experiments because it was incorrect
  • lines changed 14, context: html, text, full: html, text
    HudsonAlpha responded that the 2007 paper is the right ref.
  • lines changed 1, context: html, text, full: html, text
    removed extra .
  • lines changed 1, context: html, text, full: html, text
    Tiny change
  • lines changed 26, context: html, text, full: html, text
    Adjustments/fixes requested by Katrina
  • lines changed 2, context: html, text, full: html, text
    changed links from pointing at inaccessible full text to summary/abstract
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 362, context: html, text, full: html, text
    removed release tags to get ready for release
  • lines changed 81, context: html, text, full: html, text
    Changed the default subtracks and a couple of short labels as well
  • lines changed 2, context: html, text, full: html, text
    The new longLabelClip setting is definitely not ready to go out
  • lines changed 4, context: html, text, full: html, text
    Tightened the signal range as per Katrina's request
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 2659, context: html, text, full: html, text
    updated to be for release 2, which I am releasing
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 5, context: html, text, full: html, text
    Adding a little to doc.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTxn.html
  • lines changed 1, context: html, text, full: html, text
    Elaborating description just a little.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRnaSubcellLocSuper.html
  • lines changed 53, context: html, text, full: html, text
    Supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSuper.ra
  • lines changed 7, context: html, text, full: html, text
    Restore ENC prefix
  • lines changed 50, context: html, text, full: html, text
    *** empty log message ***
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    Added missing mdb RA files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 533, context: html, text, full: html, text
    Initial checkin of Methyl that leaked in during mini-freeze of TFBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2555, context: html, text, full: html, text
    Post mini-freeze update with wigs removed and dates updated
  • lines changed 6250, context: html, text, full: html, text
    Updated metaDb to include new bam and broad peak files from June 7th freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 145, context: html, text, full: html, text
    Adding the new meta data file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 253, context: html, text, full: html, text
    New metadata .ra for the SunyAlbany track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    Updated the standardized lab UCD(Farnham) -> UCD
  • lines changed 599, context: html, text, full: html, text
    Checking in the file with the correct information. revision 1.4 was empty accidently. Updated Lab for submission 1122 and 1123 to UCD. Updated UCDavis -> UCD
  • lines changed 599, context: html, text, full: html, text
    Made Lab name consistent for all variants of UCD% -> UCD
  • lines changed 7, context: html, text, full: html, text
    Clensed semicolons from labVersion
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 10654, context: html, text, full: html, text
    Added new metaData from 58 new submissions
  • lines changed 12, context: html, text, full: html, text
    Removed ; (semicolns) accidently reintrodcued in labVersion
  • lines changed 81, context: html, text, full: html, text
    Made Lab name consistent for all variants of UCD% -> UCD and Harvard(Weissman) -> Harvard
  • lines changed 12, context: html, text, full: html, text
    Clensed semicolons from labVersion
  • lines changed 4, context: html, text, full: html, text
    Imported dateSubmitted from hg18 for one remapped submission
  • lines changed 25, context: html, text, full: html, text
    Updated metaData with metaData for bam from sbumission 1246
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 25, context: html, text, full: html, text
    More dates have been imported
  • lines changed 156, context: html, text, full: html, text
    Imported dates from hg18
  • lines changed 1825, context: html, text, full: html, text
    Initial check in of Uw Histone( ChIP-seq) metadata file.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    hopefully the last time we will have to touch snp131. Making snp131 on by default and hiding snp130 by default
  • lines changed 2, context: html, text, full: html, text
    making snp131 hidden by default as temp fix for CGI error with new func field
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    More supertrack descriptions, thanks melissa
  • lines changed 1, context: html, text, full: html, text
    Added a new composite for Suny
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSuny.ra
  • lines changed 2, context: html, text, full: html, text
    Minor typos
  • lines changed 3, context: html, text, full: html, text
    I fixed the controlled vocab line to have the right tag and I also removed view from the sort as there is only one view.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSunyAlbanyTiling.ra
  • lines changed 111, context: html, text, full: html, text
    Added a new composite for Suny
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
  • lines changed 103, context: html, text, full: html, text
    More supertrack descriptions, thanks melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDnaMethylSuper.html
  • lines changed 63, context: html, text, full: html, text
    More supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
  • lines changed 67, context: html, text, full: html, text
    More supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
  • lines changed 87, context: html, text, full: html, text
    More supertrack descriptions, thanks melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
  • lines changed 98, context: html, text, full: html, text
    More supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSubcellLocSuper.html
  • lines changed 53, context: html, text, full: html, text
    More supertrack descriptions, thanks melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneST.html
  • lines changed 31, context: html, text, full: html, text
    A new track description as the old one was for Tiling Arrays
  • lines changed 142, context: html, text, full: html, text
    The correct track name for the .html file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
  • lines changed 142, context: html, text, full: html, text
    Track Description for the next Suny Track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyGeneST.html
  • lines changed 142, context: html, text, full: html, text
    It had the wrong track name
  • lines changed 142, context: html, text, full: html, text
    New Track Description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
  • lines changed 7, context: html, text, full: html, text
    Restore ENC prefix
  • lines changed 50, context: html, text, full: html, text
    Adding supertracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 65, context: html, text, full: html, text
    More supertrack descriptions from Melissa
• src/hg/makeDb/trackDb/makefile
  • lines changed 5, context: html, text, full: html, text
    tweaking git pull to be safer, fixing checkbeta target
  • lines changed 6, context: html, text, full: html, text
    first quick attempt to change major makefiles from cvs to git.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Adding longLabelClip now even though the feature is not ready for prime time. Just trying to beat git.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    hopefully the last time we will have to touch snp131. Making snp131 on by default and hiding snp130 by default
  • lines changed 6, context: html, text, full: html, text
    remove old search spec ucscRetroInfo (base table is now ucscRetroAli)
  • lines changed 2, context: html, text, full: html, text
    making snp131 hidden by default as temp fix for CGI error with new func field
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 4, context: html, text, full: html, text
    fixing GeneTrack list
  • lines changed 250, context: html, text, full: html, text
    adding track description page
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    oops
• src/hg/mouseStuff/mafRanges/makefile
  • lines changed 3, context: html, text, full: html, text
    do not have all:: target making the test target
• src/hg/mouseStuff/mafRanges/tests/.cvsignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/mouseStuff/mafRanges/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/hg/oneShot/rmDupCol1/makefile
  • lines changed 11, context: html, text, full: html, text
    Created makefile.
• src/hg/oneShot/rmDupCol1/rmDupCol1.c
  • lines changed 51, context: html, text, full: html, text
    Created rmDupCol1.c, which removes duplicated lines with identical col1.
• src/hg/pslMap/tests/input/kgProtMRna.blast
  • lines changed 2239, context: html, text, full: html, text
    restoring some large files that had already become small enough to add back
• src/hg/pslMap/tests/input/negQ.chain
  • lines changed 632, context: html, text, full: html, text
    restoring some large files that had already become small enough to add back
• src/hg/pslPseudo/pslPseudo.c
  • lines changed 21, context: html, text, full: html, text
    trying to fix the compiler warnings
• src/hg/pslPseudo/tests/input/pseudoEst5MrnaOrf100.psl
  • lines changed 993, context: html, text, full: html, text
    adding big test data back smaller
• src/hg/utils/automation/Encode.pm
  • lines changed 0, context: html, text, full: html, text
    trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 0, context: html, text, full: html, text
    trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty
• src/hg/utils/automation/HgDb.pm
  • lines changed 0, context: html, text, full: html, text
    trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • lines changed 18, context: html, text, full: html, text
    include long descriptions of metadata; don't propogate html to children
• src/idbQuery/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    first quick attempt to change major makefiles from cvs to git.
• src/inc/linefile.h
  • lines changed 4, context: html, text, full: html, text
    add a function to remove initial browser and track lines
• src/index/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/lib/bbiWrite.c
  • lines changed 3, context: html, text, full: html, text
    skip browser and track lines at the begining of bedGraphs and wigs when creating bigWigs (added function in linefile to do this)
• src/lib/bwgCreate.c
  • lines changed 11, context: html, text, full: html, text
    skip browser and track lines at the begining of bedGraphs and wigs when creating bigWigs (added function in linefile to do this)
• src/lib/cheapcgi.c
  • lines changed 2, context: html, text, full: html, text
    Minor change to waitMask CSS definition. Avoids silent warnings in some browsers.
• src/lib/linefile.c
  • lines changed 17, context: html, text, full: html, text
    skip browser and track lines at the begining of bedGraphs and wigs when creating bigWigs (added function in linefile to do this)
• src/makefile
  • lines changed 14, context: html, text, full: html, text
    fixing makefiles to have clean targets
  • lines changed 2, context: html, text, full: html, text
    safer to be agnostic about the git pull for now
  • lines changed 4, context: html, text, full: html, text
    first quick attempt to change major makefiles from cvs to git.
• src/parasol/inc/paraVersion.h
  • lines changed 1, context: html, text, full: html, text
    next version increment
• src/parasol/paraHub/paraHub.c
  • lines changed 5, context: html, text, full: html, text
    handle -1 fileSize means does not exist so skip output
• src/parasol/parasol/parasol.c
  • lines changed 3, context: html, text, full: html, text
    adding help for pstat2
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    allowing pstat2 command to optionally use -result=path/results.txt, i.e. for jobTree use
• src/parasol/version.doc
  • lines changed 6, context: html, text, full: html, text
    added info about jobtree pstat2 and parahub results fileSize checks
• src/primeMate/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    improved dbProfile in trackDb example
• src/protDust/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/reformat/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/scanIntrons/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/test/.cvsignore
  • lines changed 1, context: html, text, full: html, text
    renaming .cvsignore files to .gitignore
• src/test/.gitignore
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    renaming .cvsignore files to .gitignore
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    skip browser and track lines at the beginning of a bedGraph. Add better error message
• src/utils/qa/makefile
  • lines changed 3, context: html, text, full: html, text
    tweaking git pull to be safer
  • lines changed 2, context: html, text, full: html, text
    first quick attempt to change major makefiles from cvs to git.
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    Added idHitter.csh.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v234 preview
  • lines changed 2, context: html, text, full: html, text
    removing test area GBUILDDIR
  • lines changed 2, context: html, text, full: html, text
    creating BUILDHOME variable
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    new location for things under git build - no partial sandbox checkouts available
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 9, context: html, text, full: html, text
    added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push
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    hgcentral.sql is in new hgdownload git build repo
  • lines changed 3, context: html, text, full: html, text
    updates
• src/utils/qa/weeklybld/buildUtils.csh
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    conversion of buildUtils.csh to using git
• src/utils/qa/weeklybld/coBranch.csh
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    converting to git
• src/utils/qa/weeklybld/configureSandbox.csh
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    print working dir before exit 1 for additional troubleshooting info
• src/utils/qa/weeklybld/doJavaUtilBuild.csh
  • lines changed 9, context: html, text, full: html, text
    convert to git
• src/utils/qa/weeklybld/doNewReview.csh
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    convert to git
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 9, context: html, text, full: html, text
    convert to git
  • lines changed 1, context: html, text, full: html, text
    updates
• src/utils/qa/weeklybld/makeZip.csh
  • lines changed 31, context: html, text, full: html, text
    convert to git
• src/utils/qa/weeklybld/tagBeta.csh
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    convert to git
• src/utils/qa/weeklybld/tagNewBranch.csh
  • lines changed 10, context: html, text, full: html, text
    convert to git
• src/utils/qa/weeklybld/tagPreview.csh
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    git convert, rename review to preview as that is more common usage now
• src/utils/qa/weeklybld/tagReview.csh
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    git convert, rename review to preview as that is more common usage now
• src/utils/qa/weeklybld/updateCgiVersion.csh
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    added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push
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    convert to git
• src/utils/scaffoldFaToAgp/test/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/utils/scaffoldFaToAgp/test/.gitignore
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    renaming .cvsignore files to .gitignore
• src/weblet/counter/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to have clean targets
• src/weblet/hitreport/makefile
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    fixing makefiles to have clean targets
• src/weblet/makefile
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    fixing makefiles to have clean targets
• src/wormAli/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to have clean targets

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