All File Changes

v290_base to v291_preview (2013-09-30 to 2013-10-07) v291

• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 7, context: html, text, full: html, text
    Row 1 to 36 of edwFile.submitId are all equal to 1. And the userId of edwSubmit row 1 is 0. the edwUserNameFromFileId() will cause the 500 server error when looking for email of the the non-exist user 0. In this case, edwUserNameFromFileId() should return "an unknown user" instead.
• src/hg/hgBlat/hgBlat.c
  • lines changed 16, context: html, text, full: html, text
    trying to find reasonable limits for warning for protein and translated dnax; improving warn message; fixes #5798
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    making the cmpReal operator actually check for valid allowed operators, and not just being not "ignored"
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Refining a 10-year-old kludge for a few tracks that have thickStart=thickEnd=0,but want thick items. There aren't many, but they include wgRna in hg18 and hg19,
    and hg18.ncRna. Without this additional check for item start != 0, it's possible
    for the kludge to falsely trigger on items that have thickStart=thickEnd=chromStart
    when chromStart just happens to be 0, for example in DGV. Of the remaining tracks
    that need this kludge, none seem to have chromStart=0, so this seems to take care of
    both new and old tracks. In the long term, it would be best for all tables to
    just have thickStart=chromStart and thickEnd=chromEnd if they want thick items.
    fixes #11870
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    update to Glenn's new API
  • lines changed 28, context: html, text, full: html, text
    add chromosome color mode to snakes that uses a hash of the chrom to geta color ffrom a fixed palette. Also make pack mode a little more dense
    
  • lines changed 3, context: html, text, full: html, text
    fix a crash in snake drawing code when there are no blocks in a speciesin pack mode.
    
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    When user selects Artificial Example Variants, force genome-wide searchbecause the example variants often fall outside of the cart position range.
    refs #11110
    
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    Code review feedback from Brian - use trackDb instead of hardcoding accessory URL.refs #11763
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 27, context: html, text, full: html, text
    Adding a useful real-world example of BLAT on the negative strand.
  • lines changed 39, context: html, text, full: html, text
    oops: fixing off-by-one error on target coordinates.
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Correcting pre-emptive news entry, code review #11840
• src/hg/inc/jsHelper.h
  • lines changed 8, context: html, text, full: html, text
    Added jsonFindNameRecurse() and jsonFindName() to extract the email address from JSON file.
  • lines changed 8, context: html, text, full: html, text
    Use slNameAddHead() instead of slNameAddTail() in jsonFindNameRecurse(). Added jsonFindNameUniq() to filter out duplicate name.
• src/hg/lib/annoStreamDb.c
  • lines changed 3, context: html, text, full: html, text
    Fixing corner case: if we hit the end of rowBuf in nextRowFromBuffer,then discover in asdDoQueryChunking that we don't need to query again,
    then we need to reset rowBuf because when we return to nextRowFromBuffer,
    we check rowBuf->size which should be 0. We could also check self->eof,
    but I think it's cleaner to have the correct rowBuf state.
    
• src/hg/lib/dgvPlus.as
  • lines changed 1, context: html, text, full: html, text
    Fixing incorrect comment found by Brian L. refs #11200
• src/hg/lib/gpFx.c
  • lines changed 58, context: html, text, full: html, text
    Fix for crash found by Jonathan in http://redmine.soe.ucsc.edu/issues/11775#note-60 ;more careful error-checking and corner-case handling in getTxCoords.
    When CDS starts out of frame, we were getting early truncation of
    coding sequence, leading to some strange characters in output; the
    ideal fix would be to take exonFrames into account, but for now we can
    just bail if coding sequence ends before the variant hits it. Also
    fixing a couple bone-headed incorrect invocations of slAddTail, and
    making sure that an exon's splice_region_variant is listed with an
    exon number, not an intron number.
    refs #11775, #11771
    
• src/hg/lib/gwasCatalog.sql
  • lines changed 1, context: html, text, full: html, text
    change a varchar field to a longblob in gwasCatalog because it wasn'tbig enough to hold the data in the flat files.
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    make a buffer larger to accomodate longer track names
• src/hg/lib/jsHelper.c
  • lines changed 62, context: html, text, full: html, text
    Added jsonFindNameRecurse() and jsonFindName() to extract the email address from JSON file.
  • lines changed 22, context: html, text, full: html, text
    Use slNameAddHead() instead of slNameAddTail() in jsonFindNameRecurse(). Added jsonFindNameUniq() to filter out duplicate name.
• src/hg/lib/rgdQtlLink.sql
  • lines changed 1, context: html, text, full: html, text
    mysql 5.6 doesn't accept TYPE= anymore, we must use ENGINE=.
• src/hg/makeDb/doc/rn4.txt
  • lines changed 3, context: html, text, full: html, text
    Steve found a joinerCheck error about a duplicate ID in rn4.rgdQtl.Comments in doc/rn4.txt indicated that the dupe should have been
    resolved, but somehow the database tables on hgwdev did not reflect
    the fix. So I followed the same steps in rn4.txt to fix the dupe,
    and the joinerCheck error is resolved on hgwdev.
    
• src/hg/makeDb/genbank/etc/dbload
  • lines changed 2, context: html, text, full: html, text
    get genbank utils to use etc/.hg.genome-browser-mirror.conf
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    turn CCDS off for braNey1
  • lines changed 19, context: html, text, full: html, text
    Added upstreamGeneTbl and upstreamMaf fields for those assemblies whose /multiz#way/maf directories were either missing or outdated (redmine #11575)
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • lines changed 1, context: html, text, full: html, text
    get genbank utils to use etc/.hg.genome-browser-mirror.conf
• src/hg/makeDb/genbank/src/lib/gbFileOps.c
  • lines changed 1, context: html, text, full: html, text
    fix problem with very slow loads on eurotoad. Always use local timeinstead of sometimes gm time and sometimes local time.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 35, context: html, text, full: html, text
    Resolving various joinerCheck errors found by Steve.
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • lines changed 10, context: html, text, full: html, text
    Adding percentages to reports of hits and misses so we don't have to manually calculate those.
• src/hg/makeDb/trackDb/human/dgvPlus.html
  • lines changed 26, context: html, text, full: html, text
    Making some minor punctuation, rephrasing changes to dgvPlus.html refs #11200
  • lines changed 2, context: html, text, full: html, text
    Adding a helpful FAQ link to DGV about their process refs #11200
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 3, context: html, text, full: html, text
    Mentioning alligator on human vertChainNet html page, adding a comma refs #8750
• src/hg/makeDb/trackDb/human/hg19/snp138.html
  • lines changed 36, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/human/hg19/snp138Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/human/hg19/snp138FlaggedMention.html
  • lines changed 4, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Adding search specs for snp138 tracks (thx Luvina!) refs #11438
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Code review feedback from Brian - use trackDb instead of hardcoding accessory URL.refs #11763
    
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    adding a track with the matches of the repeatmasker proteins to the repeatmasker sequences to repeats2
• src/hg/makeDb/trackDb/snp138.html
  • lines changed 31, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/snp138.shared.html
  • lines changed 460, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/snp138Common.html
  • lines changed 28, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/snp138Mult.html
  • lines changed 25, context: html, text, full: html, text
    Adding details pages for snp138* tracks. refs #11438
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Code review feedback from Brian - use trackDb instead of hardcoding accessory URL.refs #11763
    
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
  • lines changed 24, context: html, text, full: html, text
    add some test tracks that show XM_ and XR_ alignments
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    Adding search specs for snp138 tracks (thx Luvina!) refs #11438
• src/hg/qaPushQ/makefile
  • lines changed 1, context: html, text, full: html, text
    minor improvement to preserve the timestamp when copying the executable to hgwbeta
• src/inc/annoAssembly.h
  • lines changed 2, context: html, text, full: html, text
    Make annoAssemblySeqSize cache sequence sizes, because twoBitSeqSizedoes a seek and read, and some annoStreams check sequence size pretty often.
    
• src/lib/annoAssembly.c
  • lines changed 18, context: html, text, full: html, text
    Make annoAssemblySeqSize cache sequence sizes, because twoBitSeqSizedoes a seek and read, and some annoStreams check sequence size pretty often.
    
• src/lib/annoStreamVcf.c
  • lines changed 16, context: html, text, full: html, text
    When reading a VCF file without a tabix index, make sure we stopafter regionEnd (if there is one).
    
  • lines changed 5, context: html, text, full: html, text
    f8bcbbee didn't go far enough to completely fix #11787 -- I forgot toaccount for changing chromosomes.
    fixes #11787
    refs #11775
    
• src/lib/annoStreamer.c
  • lines changed 2, context: html, text, full: html, text
    In annoStreamerSetRegion, if we're given (chrom, 0, 0), treat that as(chrom, 0, chromSize).
    
• src/lib/net.c
  • lines changed 15, context: html, text, full: html, text
    Revert "net.c: Adding read and write timeouts to the tcp open. One site was connecting but then failing to send a response and hanging indefinitely."
    This reverts commit b1daa872c111d286d607213ce0ba97d74133b9dd.
    
    Although the relatively short 10 second read/write timeout works for bigDataUrl connections,
    it does not work for robots accessing html sites that can take a long time to return a response.
    This approach was too simple. It is being reverted.
    
• src/utils/calc/calc.c
  • lines changed 40, context: html, text, full: html, text
    adding -h flag to calc for more readable numbers
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v291 preview1

• lines changed: 1188
• files changed: 55