All File Changes

v281_base to v282_preview (2013-03-25 to 2013-04-02) v282

• src/ameme/makefile
  • lines changed 26, context: html, text, full: html, text
    testing new makefile organization refs #9104
• src/cdnaAli/ali2alx/makefile
  • lines changed 9, context: html, text, full: html, text
    testing new makefile organization refs #9104
• src/cdnaAli/aliGlue/makefile
  • lines changed 12, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
  • lines changed 1, context: html, text, full: html, text
    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/binGood/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/cdnaOff/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/cluster/makefile
  • lines changed 12, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/exonAli/makefile
  • lines changed 15, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
  • lines changed 1, context: html, text, full: html, text
    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/findCdna/makefile
  • lines changed 11, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/g2cCheck/makefile
  • lines changed 16, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/introns/makefile
  • lines changed 12, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/pairClo/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/patCount/makefile
  • lines changed 9, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/patSpace/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/refineAli/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
  • lines changed 1, context: html, text, full: html, text
    correct relative reference to jkOwnLib refs #9104
• src/cdnaAli/sortFilt/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/cdnaAli/stitchea/makefile
  • lines changed 10, context: html, text, full: html, text
    using new minimal makefile construction refs #9104
• src/dnaDust/makefile
  • lines changed 19, context: html, text, full: html, text
    minimal makefile for kentUtils build refs #9104
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 51, context: html, text, full: html, text
    Adding a new output - the list of files that we are changing, and what they get changed to.
• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
  • lines changed 39, context: html, text, full: html, text
    Making bit where it checks sizes and prints out validation fields and option.
• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/encode2Md5UpdateManifest.c
  • lines changed 16, context: html, text, full: html, text
    Moving hashMd5File to library.
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 1, context: html, text, full: html, text
    Suppressing hoisting of fileNames.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/encode2MetaPatchRenamed.c
  • lines changed 169, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
  • lines changed 5, context: html, text, full: html, text
    Reducing verbosity of a warning. Making it pass through if it has same name after patch rather than suppressing it.
  • lines changed 42, context: html, text, full: html, text
    Making it create subobjects when patching multiples in place of single old one, rather than creating siblings.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/expected.out
  • lines changed 134, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/makefile
  • lines changed 22, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.ra
  • lines changed 121, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.rename
  • lines changed 3, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 16, context: html, text, full: html, text
    using bigBed in ENCODE3 instead of bed for bed and bed-variant types
• src/hg/featureBits/makefile
  • lines changed 18, context: html, text, full: html, text
    using new minimal makefile refs #9104
  • lines changed 2, context: html, text, full: html, text
    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/genePredToBed/makefile
  • lines changed 1, context: html, text, full: html, text
    genePred test program should call /genePredToBed.
• src/hg/hgLogin/hgLogin.c
  • lines changed 30, context: html, text, full: html, text
    Redmine Bug #9662 Use wiki.userNameCookie and wiki.loggedInCookie values as name of cookie.
• src/hg/hgLogin/hgLogin.h
  • lines changed 2, context: html, text, full: html, text
    Redmine Bug #9662 Use wiki.userNameCookie and wiki.loggedInCookie values as name of cookie.
• src/hg/hgTracks/multiWig.c
  • lines changed 4, context: html, text, full: html, text
    multiWig.c
  • lines changed 10, context: html, text, full: html, text
    Removing magic number per Kate's suggestion. Ref #10370
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Minor fix in GAD details: if publication title etc. are missing, don't display them. refs #10449
  • lines changed 1, context: html, text, full: html, text
    changed the hard-coded snp132 to snp137 in omim AV SNPs track. refs #10501
• src/hg/hgsql/makefile
  • lines changed 15, context: html, text, full: html, text
    using new minimal makefile refs #9104
  • lines changed 2, context: html, text, full: html, text
    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Changing data is to data are, Code Review refs# 10472
  • lines changed 20, context: html, text, full: html, text
    Adding MLQ #10478 to ENCODE FAQ following Kate's suggesion refs# 9712
  • lines changed 2, context: html, text, full: html, text
    Correcting name mispelling, Darryl, when adding MLQ #10478 to ENCODE FAQ following Kate's suggesion refs #9712
  • lines changed 35, context: html, text, full: html, text
    Adding a MLQ.10494 to ENCODE FAQ refs #10494 #9712
  • lines changed 7, context: html, text, full: html, text
    Making edits to added MLQ.10494, such as making data plural,to ENCODE FAQ refs #10494 #9712
  • lines changed 16, context: html, text, full: html, text
    Additional references. Some clarifications and copy-edits. refs #9712 Portal: ENCODE FAQ
  • lines changed 23, context: html, text, full: html, text
    Rearranging FAQ top links for new ENCODE FAQ ref# 9712
  • lines changed 30, context: html, text, full: html, text
    Adding MLQ #10494 about Software Tools to ENCODE FAQ page refs #10494 #9712
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 2, context: html, text, full: html, text
    Made some wording changes suggested by Pauline in code review (redmine #10473)
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    Changed button name to match reality (from 'Display' to 'Use').
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    Made slight changes to the wording for the PDF/PS printing instructions (redmine #1077)
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 31, context: html, text, full: html, text
    Added a few PMIDs + PMCIDs in conjunction with doing ENCODE progress report. Will complete this work as time permits.
• src/hg/htdocs/images/Amazona_vittata.jpg
  • lines changed 0, context: html, text, full: html, text
    photo for amaVit1 browser, Tom MacKenzie, U.S. Fish and Wildlife Service www.fws.gov/caribbean/ES/Parrot-Gallery.html refs #10144
• src/hg/inc/encode3/encode2Manifest.h
  • lines changed 11, context: html, text, full: html, text
    Adding sveral new functions to handle short form manifests.
• src/hg/inc/meta.h
  • lines changed 58, context: html, text, full: html, text
    Writing some utility functions for meta files and related structures. I debated just using existing .ra infrastructure, but decided something smaller and more specialized would be helpful.
  • lines changed 20, context: html, text, full: html, text
    Adding several new functions to meta library.
  • lines changed 76, context: html, text, full: html, text
    Added test case.
• src/hg/lib/encode3/encode2Manifest.c
  • lines changed 39, context: html, text, full: html, text
    Adding sveral new functions to handle short form manifests.
• src/hg/lib/gadAll.as
  • lines changed 49, context: html, text, full: html, text
    GAD data update. Refactored gadPos program and extended it to alsouse Gencode tables if available. Added gadAll.as for documentation.
    refs #10449
    
• src/hg/lib/gadAll.sql
  • lines changed 8, context: html, text, full: html, text
    GAD data update. Refactored gadPos program and extended it to alsouse Gencode tables if available. Added gadAll.as for documentation.
    refs #10449
    
• src/hg/lib/geoMirror.c
  • lines changed 2, context: html, text, full: html, text
    removed the word Use from the mirror pulldown for US Server and European Server
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding meta to makefile.
  • lines changed 1, context: html, text, full: html, text
    Moving meta module to different library.
• src/hg/lib/meta.c
  • lines changed 295, context: html, text, full: html, text
    Writing some utility functions for meta files and related structures. I debated just using existing .ra infrastructure, but decided something smaller and more specialized would be helpful.
  • lines changed 44, context: html, text, full: html, text
    Adding several new functions to meta library.
  • lines changed 339, context: html, text, full: html, text
    Added test case.
• src/hg/makeDb/doc/amaVit1.txt
  • lines changed 486, context: html, text, full: html, text
    initial browser done, masking in progress, refs #10144
  • lines changed 72, context: html, text, full: html, text
    done with masking, ready for genbank refs #10144
  • lines changed 15, context: html, text, full: html, text
    done with genscan and cpgIslandExt refs #10144
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 62, context: html, text, full: html, text
    Add back the good quality University of Chicago datasets (based on Anshul's quality curation) to the ENCODE Uniform TFBS track. refs #10024
  • lines changed 26, context: html, text, full: html, text
    Remove 10 low quality datasets from Uniform TFBS. These failed IDR according to Anshul's quality metric curation. refs #10042
  • lines changed 44, context: html, text, full: html, text
    Add quality from Anshul's spreadsheet to metadata of Uniform TFBS track. Also swap two datasets (mistakenly removed good and left in bad: CBEBP vs. CBEBZ (bad). #refs 10042
• src/hg/makeDb/doc/go.txt
  • lines changed 31, context: html, text, full: html, text
    rebuild GO database fixed #10492
• src/hg/makeDb/doc/hg19.txt
  • lines changed 47, context: html, text, full: html, text
    GAD data update. Refactored gadPos program and extended it to alsouse Gencode tables if available. Added gadAll.as for documentation.
    refs #10449
    
  • lines changed 10, context: html, text, full: html, text
    addes hg19 micMur1 swap for lift over refs #10485
  • lines changed 2, context: html, text, full: html, text
    Updating makedoc with chain re-run steps. refs #9812
  • lines changed 6, context: html, text, full: html, text
    More small updates to the makedoc wrt the new Gibbon chain track. refs #9812
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 40, context: html, text, full: html, text
    genscan work.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 100, context: html, text, full: html, text
    per user request refs #10398
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 10, context: html, text, full: html, text
    Updating windowmasker section as per Hiram's comments refs #9812
  • lines changed 24, context: html, text, full: html, text
    reset default position slightly and add hg19 chain net swap procedure, refs #9812
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 208, context: html, text, full: html, text
    genscan work.
• src/hg/makeDb/doc/rn5.txt
  • lines changed 35, context: html, text, full: html, text
    per user request refs #10398
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 5, context: html, text, full: html, text
    add some notes from braney's UCSC gene talk
• src/hg/makeDb/doc/uniProt/sp120323.txt
  • lines changed 1, context: html, text, full: html, text
    add some notes from braney's UCSC gene talk
• src/hg/makeDb/genbank/etc/dbload
  • lines changed 1, context: html, text, full: html, text
    finally get around to changing hgnfs1 to rrnfs1.... probably this means we'll switch back ;-)
• src/hg/makeDb/genbank/etc/rr-dbload
  • lines changed 1, context: html, text, full: html, text
    finally get around to changing hgnfs1 to rrnfs1.... probably this means we'll switch back ;-)
• src/hg/makeDb/genbank/src/copy/gbCopyStep
  • lines changed 4, context: html, text, full: html, text
    UDR doesn't want the rsync port options specified, and barfs in grand fashion it you do set them. Also, sleep inbetween connections is no longer necessary.
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    a few changes to clean up the errors that Steve got in the big all.joiner checking
  • lines changed 42, context: html, text, full: html, text
    Added extra stanzas for Retroposed Genes (ucscRetro) rules as chopAfter doesn't work with the macro.
  • lines changed 1, context: html, text, full: html, text
    Per Mark D, lowered the hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck threshold from 0.30 to 0.25 which fixed an hg19 joinerCheck error
  • lines changed 2, context: html, text, full: html, text
    make these changes again because Rachel accidently removed them
  • lines changed 1, context: html, text, full: html, text
    Per Braney, excluded hg19 from spMrna.mrnaID which fixed an hg19 joinerCheck error
  • lines changed 18, context: html, text, full: html, text
    Mark D thought GENCODE V4 was too old to fix the joinerCheck errors; per discussion with Ann, commented out the GENCODE V4 sections
  • lines changed 19, context: html, text, full: html, text
    Per Mark D, just deleted the GENCODE V4 sections
  • lines changed 2, context: html, text, full: html, text
    Added felCat5 and petMar2 to ensGeneDb section; removed petMar2 from notEnsemblTranscriptId; joinerCheck runs fine on both (redmine #10503)
• src/hg/makeDb/trackDb/birds/amaVit1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/gold.html
  • lines changed 33, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/birds/amaVit1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10144
• src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html
  • lines changed 1, context: html, text, full: html, text
    NHGRI is changing their photo links refs #9812
  • lines changed 26, context: html, text, full: html, text
    add notes about chromosome names refs #9812
  • lines changed 9, context: html, text, full: html, text
    order the chrM contigs numerically refs #9812
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    add search rule for gold table refs #9812
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • lines changed 2, context: html, text, full: html, text
    protect nomLeu1 chain on public with the release tag and add Gibbon to the primate chain net description page
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra
  • lines changed 91, context: html, text, full: html, text
    Add back the good quality University of Chicago datasets (based on Anshul's quality curation) to the ENCODE Uniform TFBS track. refs #10024
  • lines changed 190, context: html, text, full: html, text
    Remove 10 low quality datasets from Uniform TFBS. These failed IDR according to Anshul's quality metric curation. refs #10042
  • lines changed 708, context: html, text, full: html, text
    Add quality from Anshul's spreadsheet to metadata of Uniform TFBS track. Also swap two datasets (mistakenly removed good and left in bad: CBEBP vs. CBEBZ (bad). #refs 10042
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    The trackDb override for gad applies only to beta,public now, andneeds to be phased out as QA progresses. refs #10449
    
  • lines changed 19, context: html, text, full: html, text
    Adding entry for new gibbon chain/net track. refs #9812
  • lines changed 2, context: html, text, full: html, text
    protect nomLeu1 chain on public with the release tag and add Gibbon to the primate chain net description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 1, context: html, text, full: html, text
    Remove 10 low quality datasets from Uniform TFBS. These failed IDR according to Anshul's quality metric curation. refs #10042
  • lines changed 1, context: html, text, full: html, text
    Add quality from Anshul's spreadsheet to metadata of Uniform TFBS track. Also swap two datasets (mistakenly removed good and left in bad: CBEBP vs. CBEBZ (bad). #refs 10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 46, context: html, text, full: html, text
    Add back the good quality University of Chicago datasets (based on Anshul's quality curation) to the ENCODE Uniform TFBS track. refs #10024
  • lines changed 73, context: html, text, full: html, text
    Remove 10 low quality datasets from Uniform TFBS. These failed IDR according to Anshul's quality metric curation. refs #10042
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    adding amaVit1 parrot to the build refs #10144
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 4, context: html, text, full: html, text
    added a couple of hyphens and thanks to Giacomo Bernardi for help with fish
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Add genePredToBed to UTIL_DIRS list.
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
  • lines changed 1, context: html, text, full: html, text
    fixes #10481 updating url to kegg in hgNear
• src/hg/near/hgNear/hgNearData/columnDb.ra
  • lines changed 1, context: html, text, full: html, text
    fixes #10481 updating url to kegg in hgNear
• src/hg/oneShot/freen/freen.c
  • lines changed 18, context: html, text, full: html, text
    Testing some meta stuff.
• src/hg/protein/gadPos/gadPos.c
  • lines changed 1, context: html, text, full: html, text
    Use mustOpen not fopen so that stdout works correctly.
  • lines changed 185, context: html, text, full: html, text
    GAD data update. Refactored gadPos program and extended it to alsouse Gencode tables if available. Added gadAll.as for documentation.
    refs #10449
    
• src/hg/utils/automation/mkConfigRa.sh
  • lines changed 84, context: html, text, full: html, text
    prototype for new config.ra template creation, refs #10144
  • lines changed 29, context: html, text, full: html, text
    correct usage message, refs #10144
• src/hg/utils/automation/unplacedScaffolds.pl
  • lines changed 122, context: html, text, full: html, text
    processing genbank unplaced scaffold assemblies into AGP and UCSC named fasta files, refs #10144
• src/hg/utils/gapToLift/makefile
  • lines changed 17, context: html, text, full: html, text
    adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
  • lines changed 2, context: html, text, full: html, text
    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
• src/hg/utils/gffToBed/gffToBed.c
  • lines changed 1, context: html, text, full: html, text
    Adding a high verbosity message that may alleviate some mysteriousness.
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing from makefile because it won't build.
• src/hg/utils/metaFlatten/expected.out
  • lines changed 116, context: html, text, full: html, text
    Adding test case.
  • lines changed 116, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/makefile
  • lines changed 18, context: html, text, full: html, text
    Seems to work.
  • lines changed 4, context: html, text, full: html, text
    Adding test case.
  • lines changed 22, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/metaFlatten.c
  • lines changed 82, context: html, text, full: html, text
    Seems to work.
  • lines changed 82, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/test.in
  • lines changed 38, context: html, text, full: html, text
    Adding test case.
  • lines changed 38, context: html, text, full: html, text
    Added test case.
• src/hg/utils/oligoMatch/makefile
  • lines changed 14, context: html, text, full: html, text
    using minimal makefile to allow build in kentUtils refs #9104
• src/hg/utils/phyloTrees/97way.commonNames.nh
  • lines changed 77, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/97way.nh
  • lines changed 3, context: html, text, full: html, text
    jerboa moved closer to mouse rat before squirrel and kangaroo rat refs #10272
  • lines changed 23, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/97way.scientificNames.nh
  • lines changed 77, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    restore distances to the same as they were in the mm10 60-way refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 4, context: html, text, full: html, text
    removed redundant mention of spotted gar. shortened tetNig lineage at top end to match other fishes - starting at Euteleostomi
• src/idbQuery/makefile
  • lines changed 18, context: html, text, full: html, text
    minimal makefile for kentUtils build refs #9104
• src/inc/bbiFile.h
  • lines changed 1, context: html, text, full: html, text
    Improved readability and removed unused function parameter. Ref #10428.
• src/inc/gff.h
  • lines changed 1, context: html, text, full: html, text
    Unrolling gff changes that broke some of Mark's tests.
  • lines changed 1, context: html, text, full: html, text
    Small conservative change to gff/gtf reader, just to count # of each feature in file.
• src/inc/md5.h
  • lines changed 3, context: html, text, full: html, text
    Making function that puts an md5sum file into a hash.
• src/inc/meta.h
  • lines changed 76, context: html, text, full: html, text
    Added test case.
• src/inc/userApp.mk
  • lines changed 35, context: html, text, full: html, text
    testing new makefile organization refs #9104
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    eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
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    minimal makefiles for kentUtils build refs #9104
• src/index/bptForTwoBit/makefile
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    using new minimal makefile construction refs #9104
• src/index/bptLookupStringToBits64/makefile
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• src/index/bptMakeStringToBits64/makefile
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• src/lib/bbiWrite.c
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    Improved readability and removed unused function parameter. Ref #10428.
• src/lib/bigBed.c
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    Improved readability and removed unused function parameter. Ref #10428.
• src/lib/gff.c
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    Unrolling gff changes that broke some of Mark's tests.
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    Small conservative change to gff/gtf reader, just to count # of each feature in file.
• src/lib/makefile
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• src/lib/md5.c
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    Making function that puts an md5sum file into a hash.
• src/lib/meta.c
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• src/makefile
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    Moving meta stuff out of hg. It's not really browser specific yet.
• src/meta/makefile
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    Moving meta stuff out of hg. It's not really browser specific yet.
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    Added -f flag to rm, so it won't abort when there's nothing to remove.
• src/meta/metaFlatten/expected.out
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    Moving meta stuff out of hg. It's not really browser specific yet.
• src/meta/metaFlatten/metaFlatten.c
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• src/product/ex.hg.conf
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    Bug #9662 Use wiki.userNameCookie and wiki.loggedInCookie values as name of cookie in hgLogin.c
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• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    Improved readability and removed unused function parameter. Ref #10428.
• src/utils/bedRemoveOverlap/makefile
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• src/utils/bedToBigBed/bedToBigBed.c
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    Adding whitespace to improve readability. Ref #10370
• src/utils/bestThreshold/makefile
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• src/utils/cCp/cCp.c
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    broken compile refs #9104
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• src/utils/faCat/makefile
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    cleanup and proper DESTDIR for refs #9104
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• src/utils/newProg/makefile
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    using new style minimal makefile for ordinary programs, not fixing CGI rules yet, removing obsolete CVS business, refs #9104
• src/utils/newProg/newProg.c
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    using new style minimal makefile for ordinary programs, not fixing CGI rules yet, removing obsolete CVS business, refs #9104
• src/utils/qa/updateTimes.csh
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    removed unused variable, verbosity; removed some status checking that never fails; moved output to right after info obtained, so it doesn't have to wait for all the processing before giving up some info. refs #10471
• src/utils/qa/weeklybld/buildEnv.csh
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