All File Changes

v271_base to v272_preview (2012-08-07 to 2012-08-14) v272

• python/lib/ucscGb/encode/mkChangeNotes.py
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    added a warning for new and revoked files at the same time
• src/hg/hgCustom/hgCustom.c
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    Feature #3265 (nightly cron job should build utils and cgis with various USE_* options):Tim found that build breaks with USE_BAM=0 USE_TABIX=1 USE_KNETFILE_HOOKS=1 -- fixing.
    
• src/hg/hgLogin/hgLogin.c
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    Upper case all mysql keywords in query statements.
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    remove include of crypt.h. It's not needed, and it's not present in MacOSX (#8746)
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 28, context: html, text, full: html, text
    fixed breaking control over gene labels when gencode track was refactored
• src/hg/hgTracks/hgTracks.h
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    fixed breaking control over gene labels when gencode track was refactored
• src/hg/hgTracks/simpleTracks.c
  • lines changed 19, context: html, text, full: html, text
    fixed breaking control over gene labels when gencode track was refactored
• src/hg/htdocs/ENCODE/dataSummary.html
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    #8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 16, context: html, text, full: html, text
    #8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
• src/hg/htdocs/ENCODE/downloadsMouse.html
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    Adding link to downloads for new mouse ENCODE track PSU RNA-Seq (Release 1) RM#107
• src/hg/htdocs/ENCODE/index.html
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    #8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
• src/hg/htdocs/ENCODE/integrativeAnalysis/VM/index.html
  • lines changed 10, context: html, text, full: html, text
    #8740: Portal redirect to Galaxy for analysis virtual machines
  • lines changed 2, context: html, text, full: html, text
    Improvements to user message. Shorten and add links
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 1, context: html, text, full: html, text
    Made absolte path to relative path to style sheet, as it should be.
• src/hg/htdocs/goldenPath/help/geneSearchBox.html
  • lines changed 3, context: html, text, full: html, text
    center the suggest image
  • lines changed 18, context: html, text, full: html, text
    rewording to match new comboBox functionality
  • lines changed 1, context: html, text, full: html, text
    turns out that the button is labeled 'go' in hgTracks and 'submit' in hgGateway. I decided that people would probably come to this page more often from hgGateway.
• src/hg/htdocs/goldenPath/help/mysql.html
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    Fixed path for two links.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    Filling out documentation of wgEncode setting (prompted by Redmine that Rachel will file re use on hub)
• src/hg/htdocs/images/autoselect.jpg
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    update image to reflect merged gene suggest
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    remove white-space at the bottom
• src/hg/htdocs/style/HGStyle.css
  • lines changed 8, context: html, text, full: html, text
    center the suggest image
• src/hg/inc/cart.h
  • lines changed 16, context: html, text, full: html, text
    remove some routines used only by the proteome browser (#5740)
• src/hg/lib/cart.c
  • lines changed 47, context: html, text, full: html, text
    remove some routines used only by the proteome browser (#5740)
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release3.notes
  • lines changed 6294, context: html, text, full: html, text
    updated notes
  • lines changed 348, context: html, text, full: html, text
    updated notes again
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release3.notes
  • lines changed 826, context: html, text, full: html, text
    add notes file
  • lines changed 69, context: html, text, full: html, text
    created notes file
  • lines changed 43, context: html, text, full: html, text
    update notes file after removing the *Plac* input only file that have not been released that was revoked previously using the procedure of released dataset
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHist.release2.notes
  • lines changed 274, context: html, text, full: html, text
    renaming file to proper composite name
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release2.notes
  • lines changed 274, context: html, text, full: html, text
    first pass at notes for sydh histone
  • lines changed 274, context: html, text, full: html, text
    renaming file to proper composite name
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 992, context: html, text, full: html, text
    7-way done and ready for downloads
  • lines changed 143, context: html, text, full: html, text
    download files ready to go
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    done with hgPal downloads for 7-way
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    completed upstream maf files
• src/hg/makeDb/genbank/etc/genbank.conf
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    adding upstream definition to geoFor1
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Reinstating panTro1 after beginning to archive it. It is the only chimp with a BAC End Pairs track.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Reinstating panTro1 after beginning to archive it. It is the only chimp with a BAC End Pairs track.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 8, context: html, text, full: html, text
    It was necessary to make the warnings silent on make strict. Otherwise the current trackDbs for beta cause warnings that prevents the beta build.
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    Jeeeezzz it seems make strict on beta cannot survive any of the tag validation.
• src/hg/makeDb/schema/all.joiner
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    adding geoFor to the xenoRefGene definitions
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Use the same picture as papHam1, since the two assemblies are both from the same animal
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 416, context: html, text, full: html, text
    initial contents
  • lines changed 29, context: html, text, full: html, text
    finalize this 7-way description document
  • lines changed 1, context: html, text, full: html, text
    adding Zebra finch to the list of species
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra
  • lines changed 2, context: html, text, full: html, text
    default vis
  • lines changed 7, context: html, text, full: html, text
    default visibilities and correct range on the phyloP overall
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    add correct search spec for gold table
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    add gold table search rule
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Shortening target for REST in CV
  • lines changed 175, context: html, text, full: html, text
    Adding targetClass variable to CV
  • lines changed 1, context: html, text, full: html, text
    Adding H1 derived neuron protocols to CV
  • lines changed 12, context: html, text, full: html, text
    Adding targetClass typeOfTerm to CV
  • lines changed 1, context: html, text, full: html, text
    Adding targetClass typeOfTerm to CV
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 4, context: html, text, full: html, text
    add Medium ground finch to the matrix notes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1787, context: html, text, full: html, text
    added in expIds
  • lines changed 4306, context: html, text, full: html, text
    fixed controls naming and removed duplicate controls
  • lines changed 82, context: html, text, full: html, text
    added in md5sums
  • lines changed 4, context: html, text, full: html, text
    didn't revoke the originals last time
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 1598, context: html, text, full: html, text
    last metadata for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1820, context: html, text, full: html, text
    added in last SydhTfbs tracks hg19
  • lines changed 161, context: html, text, full: html, text
    added in all but one ControlId
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 43, context: html, text, full: html, text
    Restaging on beta for GIS RNA PET (Release 2) RM#5942
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 1454, context: html, text, full: html, text
    Releasing Caltech RNA-seq (Release 4) to the RR (redmine #8537)
• src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
  • lines changed 54, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Describe Function categories still in use in the coloring section (thx Brooke).
    
  • lines changed 7, context: html, text, full: html, text
    Feature #8551: Coloring function category names according to default coloring scheme (thx Brooke).
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing Caltech RNA-seq (Release 4) to the RR (redmine #8537)
  • lines changed 6, context: html, text, full: html, text
    Changed release tags to move new highlighting feature to beta (redmine #8634)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.html
  • lines changed 218, context: html, text, full: html, text
    Corrected formatting of html and made appropriate grammar/content corrections (redmine #8537)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.ra
  • lines changed 2, context: html, text, full: html, text
    Adding missing parens
  • lines changed 105, context: html, text, full: html, text
    Removing the maxWindows as it is not needed anymore and fixing the long labels to get rid of the parens ticket 8537
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
  • lines changed 47, context: html, text, full: html, text
    Changing the html according to code review of Steve
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release3.ra
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    fixed problem where gencode V7 and were referencing table that were not in that release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 1, context: html, text, full: html, text
    fixed problem where gencode V7 and were referencing table that were not in that release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
  • lines changed 10, context: html, text, full: html, text
    Fixing the issues in ticket 5942. Trying to add references
  • lines changed 48, context: html, text, full: html, text
    Fixes in ticket 5942
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing the issues in ticket 5942. Trying to add references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 10, context: html, text, full: html, text
    Adding release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 450, context: html, text, full: html, text
    long labels first pass
  • lines changed 452, context: html, text, full: html, text
    short labels first attempt
  • lines changed 500, context: html, text, full: html, text
    fixed controls issue in haib tfbs trackDb
  • lines changed 73, context: html, text, full: html, text
    added in twiers for h1neruons and fixed long and short labels
  • lines changed 14, context: html, text, full: html, text
    removing bad stanzas
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 272, context: html, text, full: html, text
    added in last open chrom chip tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
  • lines changed 227, context: html, text, full: html, text
    added in last SydhTfbs tracks hg19
  • lines changed 121, context: html, text, full: html, text
    cleaning up trackDb
  • lines changed 26, context: html, text, full: html, text
    added back tracks that were erroneously pulled out, and pulled out bad ones
  • lines changed 4, context: html, text, full: html, text
    correcting tags
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 1, context: html, text, full: html, text
    Removed redundant table data and row closing tags found by hgTablesTest.
  • lines changed 2, context: html, text, full: html, text
    Updated tables to use our nice table class. Thanks, Greg.
  • lines changed 1, context: html, text, full: html, text
    Removed comma that made squirrel monkey sound like two organisms.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 3, context: html, text, full: html, text
    Shortened shortLabels greater than 17 chars.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 19, context: html, text, full: html, text
    adding geoFor1 to the Vertebrate chain net grouping
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    set revoke status to two CH12 entries missed earlier
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    set controlId for those V2 datasets
  • lines changed 71, context: html, text, full: html, text
    update expId for V2 datasets
  • lines changed 6, context: html, text, full: html, text
    add revoke status to the input only dataset (Plac)
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    delete input only datasets
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    modified V2 statement based on Steve's input, note 83, #7502
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 169, context: html, text, full: html, text
    added in last sydh histone mouse track
  • lines changed 7, context: html, text, full: html, text
    adding in md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1585, context: html, text, full: html, text
    update new datasets submitted before the freeze
  • lines changed 273, context: html, text, full: html, text
    adding md5sums and restoring some stanzas
  • lines changed 147, context: html, text, full: html, text
    added in last metadata for mm9 sydh tfbs
  • lines changed 7, context: html, text, full: html, text
    adding md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1304, context: html, text, full: html, text
    update the new datasets submitted before the freeze
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging on beta mm9 PSU RNA-Seq (Release 1/Final) RM#107
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
  • lines changed 998, context: html, text, full: html, text
    Staging LICR TFBS (Release 3) on beta (redmine #7502)
  • lines changed 25, context: html, text, full: html, text
    Ruihua made some corrections to the metadata (redmine #7502)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuRnaSeq.ra
  • lines changed 4301, context: html, text, full: html, text
    Staging on beta mm9 PSU RNA-Seq (Release 1/Final) RM#107
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
  • lines changed 1810, context: html, text, full: html, text
    Staging on beta PSU TFBS mm9 (Release 2) RM#7516
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
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    Staging on public, PSU RNA-Seq (Release 1) RM#107
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
  • lines changed 998, context: html, text, full: html, text
    Releasing LICR TFBS (Release 3) to the RR (redmine #7502)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuRnaSeq.ra
  • lines changed 4301, context: html, text, full: html, text
    Staging on public, PSU RNA-Seq (Release 1) RM#107
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
  • lines changed 1810, context: html, text, full: html, text
    Staging on Public PSU TFBS mm9 (Release 2) RM#7516
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging on beta PSU TFBS mm9 (Release 2) RM#7516
  • lines changed 2, context: html, text, full: html, text
    Staging on Public PSU TFBS mm9 (Release 2) RM#7516
  • lines changed 2, context: html, text, full: html, text
    Staging LICR TFBS (Release 3) on beta (redmine #7502)
  • lines changed 2, context: html, text, full: html, text
    Releasing LICR TFBS (Release 3) to the RR (redmine #7502)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.html
  • lines changed 1, context: html, text, full: html, text
    update release note
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    modify release note
  • lines changed 1, context: html, text, full: html, text
    modified release notes
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    add TFBS and LICR in the text
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    Added link to Bowtie (redmine #7502)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.ra
  • lines changed 22, context: html, text, full: html, text
    comment out stanzas whose datasets are revoked
  • lines changed 77, context: html, text, full: html, text
    remove the digit that appearred in the beginning of age and celltype
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    fix labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Redmine #107. Q5. Added missing parethesis and removed extra ones.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
  • lines changed 0, context: html, text, full: html, text
    Fixed typo found in code review. Redmine #8720.
  • lines changed 2, context: html, text, full: html, text
    Redmine #107. Q1. Fixed long and short labels to reflect label convention.
  • lines changed 1, context: html, text, full: html, text
    Fixed alphabetical ordering. Redmine #107.
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    Redmine #107. Q4. Fixed typo in shortLabel using O instead of 0.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixes for Redmine #7516. Q3. Added period at end of sentence in Release Notes 2nd paragraph.
  • lines changed 122, context: html, text, full: html, text
    Redmine #7516. Q5. Fixed references to link to pubmed.
  • lines changed 1, context: html, text, full: html, text
    Fixed link that was going to the wrong track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Redmine #7516. Q2. Fixed Treatment cv linkage.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
  • lines changed 18, context: html, text, full: html, text
    added in last sydh histone mouse track
  • lines changed 36, context: html, text, full: html, text
    long ahd short labels fix
  • lines changed 1, context: html, text, full: html, text
    fixed html line
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 199, context: html, text, full: html, text
    update new datasets submitted before the freeze
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 89, context: html, text, full: html, text
    clean up long labels
  • lines changed 7, context: html, text, full: html, text
    clean up long labels
  • lines changed 92, context: html, text, full: html, text
    added age to long labels
  • lines changed 23, context: html, text, full: html, text
    added Signal to Raw which suppose to be Raw Signal
  • lines changed 5, context: html, text, full: html, text
    clean up long labels
  • lines changed 7, context: html, text, full: html, text
    clean up short labels
  • lines changed 6, context: html, text, full: html, text
    clean up short labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 300, context: html, text, full: html, text
    update the new datasets submitted before the freeze
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    changed a129=129 to S129=129 where S129 is listed as the tag for term 129 in cv
  • lines changed 5, context: html, text, full: html, text
    add a letter a in front of strain 129DLCR which started with digit
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    changed S129=129 back to a129=129, otherwise it would be messy to try to get right sort order with those strains share 129 prefix, I think the tag S129 for the term 129 should be changed to 129
• src/hg/makeDb/trackDb/snp131.html
  • lines changed 3, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
    Also adding caveat about similar situation in snp135.
    
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 3, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
    Also adding caveat about similar situation in snp135.
    
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 5, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
    Also adding caveat about similar situation in snp135.
    
• src/hg/makeDb/trackDb/worm/ce10/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/worm/ce4/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/worm/ce6/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 189, context: html, text, full: html, text
    Put v67 definitions back into EnsGeneAutomate.pm.
• src/inc/dsPrint.h
  • lines changed 77, context: html, text, full: html, text
    rewrote/renamed some dsPrint functions based upon Angie's advice in code review. Also added support for some print buffer surgery. However, the regex version is ifdef'd out for now, as I am not sure it is a good idea to check in a requirement for including <regex.h> into src/lib.
• src/lib/dsPrint.c
  • lines changed 7, context: html, text, full: html, text
    The casting failed in the 32bit build, due to pointer size issues. This version works in both 32 and 64 bit compiles and functionally changes nothing. Since this is a patch request, let me be clear that no checked in code yet calls any of these functions in this new module. The only affect this change has is that the 32bit build should now complete.
  • lines changed 213, context: html, text, full: html, text
    rewrote/renamed some dsPrint functions based upon Angie's advice in code review. Also added support for some print buffer surgery. However, the regex version is ifdef'd out for now, as I am not sure it is a good idea to check in a requirement for including <regex.h> into src/lib.
• src/lib/knetUdc.c
  • lines changed 2, context: html, text, full: html, text
    Feature #3265 (nightly cron job should build utils and cgis with various USE_* options):Tim found that build breaks with USE_BAM=0 USE_TABIX=1 USE_KNETFILE_HOOKS=1 -- fixing.
    
• src/lib/linefile.c
  • lines changed 6, context: html, text, full: html, text
    oops - some sort of editing error left sizes/types incorrect - easily fixed here.
• src/utils/bedToBigBed/bedToBigBed.c
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    incrementing version # because of bugfix to integer parsing routines in linefile.c
• src/utils/qa/makefile
  • lines changed 2, context: html, text, full: html, text
    trying to remove git pull from makefiles
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v272 preview1

• lines changed: 44234
• files changed: 167