All File Changes

v234_preview to v234_base (2010-06-15 to 2010-06-22) v234

• git-reports.c
  • lines changed 848, context: html, text, full: html, text
    moving files to new home under kent
  • lines changed 13, context: html, text, full: html, text
    making author use email account name by request
  • lines changed 1, context: html, text, full: html, text
    tags are global so do not get automatic origin/ prefix
  • lines changed 1, context: html, text, full: html, text
    fixed tiny bug - added check that h output file was actually open
  • lines changed 4, context: html, text, full: html, text
    shorthand git is simpler
  • lines changed 1, context: html, text, full: html, text
    fixing end-li tag
  • lines changed 88, context: html, text, full: html, text
    removed redundancy in html generation, and in mkdir, tidied up tags a bit for consistency
  • lines changed 28, context: html, text, full: html, text
    added error checking for system() call, removed some uglyf prints, cleaned up some comments
  • lines changed 38, context: html, text, full: html, text
    suppress commitIds as too-much-info, add UL/LI tags to allow text to wrap, htmlEncode the commit-comment, also substitute <br> for newlines in comment
  • lines changed 8, context: html, text, full: html, text
    added a copyright and my name and MarkDs name
  • lines changed 9, context: html, text, full: html, text
    fixing link formatting regarding position of pre-tag section
  • lines changed 82, context: html, text, full: html, text
    fixed bug with calling makeDiffAndSplit in wrong loopfixed tempfilename in case multiple users run it at same time
    added main index page
    made titles and headers consistent
    removed sed to clean weird unwanted context lines saving 20 seconds
    
  • lines changed 107, context: html, text, full: html, text
    changed from git show to git diff to have more control over output options like suppressing whitespace. Also in order to get the diff for a deleted file, I had to change it to dump the entire diff for the commit and then parse it into parts
  • lines changed 2, context: html, text, full: html, text
    getting rid of word Git in title
  • lines changed 42, context: html, text, full: html, text
    adding all-files view
  • lines changed 2, context: html, text, full: html, text
    added bottom navigation links to files and commits views
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    added navigation links to files and commits views
  • lines changed 148, context: html, text, full: html, text
    added files view for user
  • lines changed 3, context: html, text, full: html, text
    adding commitNumber for fileview sorting
  • lines changed 42, context: html, text, full: html, text
    fixed colors, fixed counts on new files when there is no context line to finish the block, fixed bug in output of git show in diff part where odd and variable extra context appeared after @@ .* @@, currently just using sed to trim the diff file so html file inherits automatically
  • lines changed 33, context: html, text, full: html, text
    added users-page
  • lines changed 19, context: html, text, full: html, text
    add counts for lines and files changed for user and grand total
  • lines changed 100, context: html, text, full: html, text
    fixed bugs in output paths, added htmlEncode
  • lines changed 32, context: html, text, full: html, text
    adding linesChanged
  • lines changed 48, context: html, text, full: html, text
    adding html processing
  • lines changed 87, context: html, text, full: html, text
    fixed bugs, got diffs working
  • lines changed 12, context: html, text, full: html, text
    mkdir more various subdir levels needed
  • lines changed 16, context: html, text, full: html, text
    mkdir various subdir levels needed
  • lines changed 7, context: html, text, full: html, text
    mkdir outPrefix in case
  • lines changed 6, context: html, text, full: html, text
    adding outPrefix to dir or url
  • lines changed 7, context: html, text, full: html, text
    using slNameSort
  • lines changed 26, context: html, text, full: html, text
    adding userHash and users list
  • lines changed 97, context: html, text, full: html, text
    add parsing for main commits list from startTag to endTag
  • lines changed 96, context: html, text, full: html, text
    initial commit of git-reports
• makefile
  • lines changed 27, context: html, text, full: html, text
    moving files to new home under kent
  • lines changed 2, context: html, text, full: html, text
    fix relative path in makefile for integration
  • lines changed 31, context: html, text, full: html, text
    getting ready to integrate into kent source
  • lines changed 2, context: html, text, full: html, text
    making author use email account name by request
  • lines changed 1, context: html, text, full: html, text
    tags are global so do not get automatic origin/ prefix
  • lines changed 3, context: html, text, full: html, text
    fixing makefile
  • lines changed 1, context: html, text, full: html, text
    fixed bug with calling makeDiffAndSplit in wrong loopfixed tempfilename in case multiple users run it at same time
    added main index page
    made titles and headers consistent
    removed sed to clean weird unwanted context lines saving 20 seconds
    
  • lines changed 1, context: html, text, full: html, text
    changed from git show to git diff to have more control over output options like suppressing whitespace. Also in order to get the diff for a deleted file, I had to change it to dump the entire diff for the commit and then parse it into parts
  • lines changed 2, context: html, text, full: html, text
    fixed bugs, got diffs working
  • lines changed 39, context: html, text, full: html, text
    initial commit of git-reports
• src/ai/paraFlow/aceTools/makefile
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    last bunch of makefiles that need a clean target
• src/ai/paraFlow/compiler/makefile
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    last bunch of makefiles that need a clean target
• src/ai/paraFlow/runAsm/makefile
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    last bunch of makefiles that need a clean target
• src/ai/paraFlow/runtime/makefile
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    last bunch of makefiles that need a clean target
• src/blat/test/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/blatTheory/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/cbAli/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/ali2alx/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/aliGlue/makefile
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• src/cdnaAli/binGood/makefile
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• src/cdnaAli/cdnaOff/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/cluster/makefile
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• src/cdnaAli/exonAli/makefile
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• src/cdnaAli/findCdna/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/lib/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/pairClo/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/patCount/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/patSpace/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/refineAli/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/sortFilt/makefile
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    last bunch of makefiles that need a clean target
• src/cdnaAli/stitchea/makefile
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    last bunch of makefiles that need a clean target
• src/fuzzyFind/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/gfClient/makefile
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    last bunch of makefiles that need a clean target
• src/gfServer/makefile
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    last bunch of makefiles that need a clean target
• src/hg/affyTransciptome/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/agpAllToFaFile/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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• src/hg/agpCloneCheck/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/agpCloneList/makefile
  • lines changed 3, context: html, text, full: html, text
    adding clean targets to makefiles reached via clean_utils
• src/hg/agpToGl/makefile
  • lines changed 3, context: html, text, full: html, text
    adding clean targets to makefiles reached via clean_utils
• src/hg/altGraph/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/altSplice/affySplice/makefile
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    last bunch of makefiles that need a clean target
• src/hg/altSplice/axtCountBeds/makefile
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    last bunch of makefiles that need a clean target
• src/hg/altSplice/spliceWalk/makefile
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    last bunch of makefiles that need a clean target
• src/hg/autoXml/t/makefile
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    last bunch of makefiles that need a clean target
• src/hg/bedIntersect/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • lines changed 1, context: html, text, full: html, text
    change usage message to be more clear
• src/hg/bedOverlap/makefile
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    last bunch of makefiles that need a clean target
• src/hg/bedToGenePred/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/bioImage/hgBioImage/makefile
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    last bunch of makefiles that need a clean target
• src/hg/borfBig/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/cgiExample/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/checkHgFindSpec/makefile
  • lines changed 3, context: html, text, full: html, text
    adding clean targets to makefiles reached via clean_utils
• src/hg/chimpStuff/chimpChromContigAgp/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/chimpStuff/chimpHiQualDiffs/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/chimpStuff/chimpSuperQuals/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/ctgFaToFa/makefile
  • lines changed 3, context: html, text, full: html, text
    adding clean targets to makefiles reached via clean_utils
• src/hg/ctgToChromFa/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/encode/DAFs/2.0/:n
  • lines changed 53, context: html, text, full: html, text
    removing mistaken file, Cricket confirms is just a dupe anyway
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 1, context: html, text, full: html, text
    make mismatches 7
  • lines changed 1, context: html, text, full: html, text
    make mismatches 7
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • lines changed 5, context: html, text, full: html, text
    New dafs for HAIB project
• src/hg/encode/DAFs/2.0/haibMethylSeq.daf
  • lines changed 5, context: html, text, full: html, text
    New dafs for HAIB project
  • lines changed 2, context: html, text, full: html, text
    fix up a few problems
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 37, context: html, text, full: html, text
    Renamed file to follow pattern of lab name first in daf instead of pi
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 37, context: html, text, full: html, text
    Renamed file to follow pattern of lab name first in daf instead of pi
• src/hg/encode/DAFs/2.0/renMm9Histone.daf
  • lines changed 37, context: html, text, full: html, text
    Renamed file to follow pattern of lab name first in daf instead of pi
  • lines changed 37, context: html, text, full: html, text
    Seperated Ren Lab Chip-Seq daf into TFBS and Histone Dafs. Added preliminary BAM validation
• src/hg/encode/DAFs/2.0/renMm9Tfbs.daf
  • lines changed 37, context: html, text, full: html, text
    Renamed file to follow pattern of lab name first in daf instead of pi
  • lines changed 6, context: html, text, full: html, text
    Seperated Ren Lab Chip-Seq daf into TFBS and Histone Dafs. Added preliminary BAM validation
• src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
  • lines changed 1, context: html, text, full: html, text
    Validated all changes in daf
  • lines changed 3, context: html, text, full: html, text
    Appended daf, as validating setting got placed on an extra line
  • lines changed 9, context: html, text, full: html, text
    Updated DAF for SYDH Histone to the one they have been using as well as updating a line to the lab names that they may use.
• src/hg/encode/encodeDownloadsPage/makefile
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• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 92, context: html, text, full: html, text
    fix up to handle BAM files and to remove bigWig downloads
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 29, context: html, text, full: html, text
    fix up to handle BAM files and to remove bigWig downloads
• src/hg/encode/encodeLoad/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
  • lines changed 2, context: html, text, full: html, text
    Improving some comments.
  • lines changed 49, context: html, text, full: html, text
    Adding uniqueName option.
  • lines changed 78, context: html, text, full: html, text
    Adding threshold, maxMin, and addMin options.
  • lines changed 36, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
  • lines changed 168, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Add.narrowPeak
  • lines changed 36, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
• src/hg/encode/encodeMergeReplicates/expRep1Rep2AddAddMin.narrowPeak
  • lines changed 30, context: html, text, full: html, text
    Adding another test case
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Agree.narrowPeak
  • lines changed 18, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Default.narrowPeak
  • lines changed 36, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Threshold10.narrowPeak
  • lines changed 28, context: html, text, full: html, text
    Adding threshold, maxMin, and addMin options.
• src/hg/encode/encodeMergeReplicates/makefile
  • lines changed 5, context: html, text, full: html, text
    Adding another test case
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    Adding threshold, maxMin, and addMin options.
  • lines changed 6, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
  • lines changed 29, context: html, text, full: html, text
    Adding some test cases
• src/hg/encode/encodeMergeReplicates/rep1.narrowPeak
  • lines changed 32, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/rep2.narrowPeak
  • lines changed 25, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMkChangeNotes/makefile
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• src/hg/encode/encodeStatus/makefile
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    fixup makefiles to have clean targets
• src/hg/encode/encodeValidate/config/cv.ra
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    Did I say 76. No it is H3K479me2
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    Added 2 antibodies provisionally
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    CKM is male, not female
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    try this again, add ilNA field
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    take out NA for insert length since it was interfering with NA for mapAlgorithm
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    Changed Sex of LHSR cell line from F to M to be accurate according to OpenChrom Labs
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    added some words for Wold. New insert lengths and a code for TopHat as aligner
  • lines changed 4, context: html, text, full: html, text
    Fixed the mapAlgorithm TopHat to be TH1014
  • lines changed 21, context: html, text, full: html, text
    Added more insertLenth Information for the WOld Lab and added a mapAlgorithm calll TopHat that needs a description
• src/hg/encode/encodeValidate/config/fields.ra
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    Adding protocolID
• src/hg/encode/encodeValidate/doEncodeValidate.pl
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    add junction type that isn't validate (yet) for Caltech junction beds.
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    No more fileDb.ra, stopped obsolete RawSignals generation, made trackDb templates children of views
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    Add comments to code as per Cricket in doEncodeValidate.pl. Code commented out is better explained.
  • lines changed 22, context: html, text, full: html, text
    No more fileDb.ra, stopped obsolete RawSignals generation, made trackDb templates children of views
  • lines changed 3, context: html, text, full: html, text
    Add comments to code as per Cricket in doEncodeValidate.pl. Code commented out is better explained.
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    added new file types for Caltech FPKM and insert distribution. At this point these file types are *not* validated
• src/hg/encode/encodeValidate/makefile
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• src/hg/encode/hgEncodeDataVersions/makefile
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• src/hg/encode/hgEncodeVocab/makefile
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• src/hg/encode/ldGencodeIntron/makefile
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• src/hg/encode/makefile
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• src/hg/encode/regionAgp/makefile
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• src/hg/encode/regionOrtho/makefile
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• src/hg/encode/validateFiles/validateFiles.c
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    don't check for mismatches in unmapped reads, put number of alignments on positive and negative strands out to stdout for BAM's with verbose >=2.
• src/hg/fakeFinContigs/makefile
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• src/hg/fakeOut/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/ffaToFa/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/fqToQa/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/fqToQac/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/fragPart/makefile
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• src/hg/gbGetEntries/tests/makefile
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• src/hg/gbOneAcc/makefile
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• src/hg/geneBounds/assessLibs/makefile
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• src/hg/geneBounds/averagExp/makefile
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• src/hg/geneBounds/axtForEst/makefile
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• src/hg/geneBounds/bedCons/makefile
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    removed Smear8 in favor of making Smears always take Colors. There are still some problems with 32 bit smears not getting the same colors as it's 8bit analog. I'm thinking this is something to do with the 0 and 1 being white and black in eight bit
• src/hg/hgTracks/gbrowseTest.c
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    Making hgTrackRender - a program that renders one track quickly - currently from the command line in postscript only.
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    combining Jims 2 commits into one. Making hgTrackRender and Rearranging things
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• src/hg/hgTracks/hgTracks.h
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    combining Jims 2 commits into one. Making hgTrackRender and Rearranging things
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    Making hgTrackRender - a program that renders one track quickly - currently from the command line in postscript only.
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    removed Smear8 in favor of making Smears always take Colors. There are still some problems with 32 bit smears not getting the same colors as it's 8bit analog. I'm thinking this is something to do with the 0 and 1 being white and black in eight bit
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    combining Jims 2 commits into one. Making hgTrackRender and Rearranging things
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    Making hgTrackRender - a program that renders one track quickly - currently from the command line in postscript only.
• src/hg/hgTracks/renderMain.c
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    Making hgRenderTracks look up default track settings before layering on stuff passed in .
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    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
• src/hg/hgTracks/simpleTracks.c
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    change a 1 to MG_BLACK, shame on me for having done this in the first place
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    removed Smear8 in favor of making Smears always take Colors. There are still some problems with 32 bit smears not getting the same colors as it's 8bit analog. I'm thinking this is something to do with the 0 and 1 being white and black in eight bit
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    add maxWindowToQuery setting for bigWigs.
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    "Encode release log update"
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    change the link so it does not reference hgwdev to the public
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    added info about bigWigToWig utilities
• src/hg/htdocs/goldenPath/help/pbTracksHelpFiles/makefile
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    last bunch of makefiles that need a clean target
• src/hg/htdocs/goldenPath/newsarch.html
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    fixing broken link
• src/hg/htdocs/goldenPath/pubs.html
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    Added Vaske pub
• src/hg/htdocs/goldenPath/releaseLog.html
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    "Release log update"
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    "Release log update"
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    "Release log update"
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    "Release log update"
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    "Release log update"
• src/hg/htdocs/robots.txt
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    allowed the w3c link checker
• src/hg/htdocs/staff.html
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    adding the new encode data wranglers
• src/hg/htdocs/training.html
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    Added link to Grisham tutorial, fixed some capitalization for consistency.
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    Added link to Grisham tutorial, fixed some capitalization for consistency.
• src/hg/inc/cart.h
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
• src/hg/inc/hdb.h
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    adding hTrackDbForTrackAndAncestors
• src/hg/inc/hvGfx.h
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    removed Smear8 in favor of making Smears always take Colors. There are still some problems with 32 bit smears not getting the same colors as it's 8bit analog. I'm thinking this is something to do with the 0 and 1 being white and black in eight bit
• src/hg/inc/trackDb.h
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
• src/hg/inc/versionInfo.h
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    "New version number v234"
• src/hg/intronEnds/makefile
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    adding clean targets to makefiles reached via clean_utils
• src/hg/intronSizes/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/js/hgTracks.js
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    fix error message which occurrs when the search tabs aren't defined
• src/hg/lfsOverlap/makefile
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    fixup makefiles to have clean targets
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    fixup makefiles to have clean targets
• src/hg/lib/cart.c
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
• src/hg/lib/hdb.c
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    adding hTrackDbForTrackAndAncestors
• src/hg/lib/knownToKeggEntrez.sql
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/lib/trackDbCustom.c
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
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    Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
    
• src/hg/liftFrags/makefile
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    fixup makefiles to have clean targets
• src/hg/logCrawl/hgAccessCrawl/makefile
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    fixup makefiles to have clean targets
• src/hg/makeDb/doc/cavPor3.txt
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    reenable panTro1/2 on rr
• src/hg/makeDb/doc/danRer6.txt
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    adding phastConsElements html description page
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeYaleRnaSeq.release1.notes.txt
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    notes for release1
• src/hg/makeDb/doc/felCat4.txt
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    felCat4 vs monDom5 swap
• src/hg/makeDb/doc/hg17.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/doc/hg18.txt
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    reload genomicSuperDups;
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    Starting to work on integrating Hudsonalpha ChIP data. Describing how to call encodeMergeReplicates and convert from broad to narrow peak.
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/doc/hg19.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/doc/mm7.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/doc/mm8.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/doc/mm9.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
• src/hg/makeDb/doc/monDom5.txt
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    complete LASTZ with felCat4
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    Testing git
• src/hg/makeDb/doc/rn4.txt
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    Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4).
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    added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4
• src/hg/makeDb/genbank/etc/align.dbs
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    add native refseqs to cavPor3
• src/hg/makeDb/genbank/etc/genbank.conf
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    add native refseqs to cavPor3
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    re-enabling cavPor3
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    add native refseqs to cavPor3
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    add native refseqs to cavPor3
• src/hg/makeDb/genbank/etc/rr.dbs
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    re-enabling cavPor3
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    reenable panTro1/2 on rr
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    add native refseqs to cavPor3
• src/hg/makeDb/genbank/makefile
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    fix rsync for installing etc targets
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    git conversion, manage etc dir with rsync install
• src/hg/makeDb/hgAar/makefile
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    last bunch of makefiles that need a clean target
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    last bunch of makefiles that need a clean target
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    Improving usage statement.
• src/hg/makeDb/hgExperiment/makefile
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    last bunch of makefiles that need a clean target
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    add maxWindowToQuery setting for bigWigs.
• src/hg/makeDb/trackDb/human/decipher.html
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    typo
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    backing out last change that I made on aamp's behalf -- the data is incorrect
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
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    removed release alpha tags and added release alpha,beta tags to stage yaleRna-seq
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    Prep to release update of track: removed release tags, cp *.new.ra to *.ra, removed include line for *.new.ra
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    Polishing names and labels for enhancer subtracks of wgEncodeReg.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
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    pointed Bernstein lab link to website w/o login requirement; changed contact link to name
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    adding update to release 3 to release notes section
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
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    Prep to release update of track: removed release tags, cp *.new.ra to *.ra, removed include line for *.new.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
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    Prep to release update of track: removed release tags, cp *.new.ra to *.ra, removed include line for *.new.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
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    add view range
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    removing release tags
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    add maxWindowToQuery setting for bigWigs.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
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    added a link, changed capitalization
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    added a link, changed capitalization
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
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    UW DGF metadata for June 2010 freeze
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    blank in wrong spot screwed this one up
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    Displaying UW DNase submissions for Jun 2010 freeze
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    Adding wgEncodeUwHistone to hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
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    Added new submissions for SYDH Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
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    Removed metaData for Histone submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
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    UW DGF metadata for June 2010 freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
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    Displaying UW DNase submissions for Jun 2010 freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
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    Adding wgEncodeUwHistone to hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    Adding UW DGF after Jun 2010 freeze. Reordered UW Histine and Uw Dnase
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    Displaying UW DNase submissions for Jun 2010 freeze
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    Adding wgEncodeUwHistone to hg19
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    add CSHL RNA short
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    Seperated out the Encode compsite tracks, SYDH Tfbs, SYDH Histone and HAIB Tfbs into 3 seperate trackDb files. Added include statements to trackDb.wgEncode.ra to accomadate the newly generated trackDb files.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra
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    Seperated out the Encode compsite tracks, SYDH Tfbs, SYDH Histone and HAIB Tfbs into 3 seperate trackDb files. Added include statements to trackDb.wgEncode.ra to accomadate the newly generated trackDb files.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra
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    Added new submissions for SYDH Histone
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    Seperated out the Encode compsite tracks, SYDH Tfbs, SYDH Histone and HAIB Tfbs into 3 seperate trackDb files. Added include statements to trackDb.wgEncode.ra to accomadate the newly generated trackDb files.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
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    Added new submission data to composite, previously available as downloads only
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    Removed submission 1144, revoked submission, Lab has provided replacement
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    Seperated out the Encode compsite tracks, SYDH Tfbs, SYDH Histone and HAIB Tfbs into 3 seperate trackDb files. Added include statements to trackDb.wgEncode.ra to accomadate the newly generated trackDb files.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
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    Incorporating feedback from Jim
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
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    Incorporating feedback from Jim
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwChIPSeq.ra
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    Minor update
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
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    Adding UW DGF after Jun 2010 freeze. Reordered UW Histine and Uw Dnase
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
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    Adding UW DGF after Jun 2010 freeze. Reordered UW Histine and Uw Dnase
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
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    Preliminary descrition page from hg18
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
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    Adding UW DGF after Jun 2010 freeze. Reordered UW Histine and Uw Dnase
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    Displaying UW DNase submissions for Jun 2010 freeze
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
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    Adding wgEncodeUwHistone to hg19
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