All File Changes

v292_preview2 to v292_base (2013-11-04 to 2013-11-11) v292

• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
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    Fixing bad cut
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 30, context: html, text, full: html, text
    Adding hyperlink into Stanford on experiment.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 6, context: html, text, full: html, text
    oops must allow "10" which is 2 digits long
• src/hg/genePredCheck/genePredCheck.c
  • lines changed 8, context: html, text, full: html, text
    compare chrom names case dependent refs #11907
• src/hg/hgTables/gffOut.c
  • lines changed 72, context: html, text, full: html, text
    fixes #12107. This fixes the hgTables gtf-output frame column, at least for tables that have exonFrames column available like non-ancient refGene and other genePredExt tables usually do.
• src/hg/hgTracks/hgTracks.c
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    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/hgTracks/snakeTrack.c
  • lines changed 18, context: html, text, full: html, text
    target sequence is no in the blocks that come from HAL
  • lines changed 18, context: html, text, full: html, text
    HAL now has the target sequence in the blocks it gives us.
  • lines changed 2, context: html, text, full: html, text
    fix bug when the sequence is null from HAL snakes
• src/hg/hgc/lowelab.c
  • lines changed 5, context: html, text, full: html, text
    add code to create detail page for tracks with name ended as PgSnp
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 12, context: html, text, full: html, text
    Added bigWigAverageOverBed to the list of utilities and added a section explaining differences between bigWigSummary and bigWigAverageOverBed (redmine #9945)
  • lines changed 33, context: html, text, full: html, text
    Made changes as discussed by Tim and I pertaining to wig/bigWig documentation (redmine #6866)
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 2905, context: html, text, full: html, text
    Updated content of this spec and replaced the Word-generated html version with a version that's consistent with other GB static pages.
• src/hg/htdocs/goldenPath/help/liftOver.html
  • lines changed 2, context: html, text, full: html, text
    Changing awkward wording on a liftOver help page
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Adding missing type line to Aggregate example, refs #12075
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 28, context: html, text, full: html, text
    Made changes as discussed by Tim and I pertaining to wig/bigWig documentation (redmine #6866)
• src/hg/inc/versionInfo.h
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    New version number v292
• src/hg/lib/hdb.c
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    fixes #11651. Accidentally failover was looking for backupcentral.database instead of backupcentral.db which is what all of our configurations have been using. Wow! Busted since 2009.
• src/hg/lib/loweutils.c
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    change code to use all_central db for getting genome info
• src/hg/makeDb/doc/falPer1.txt
  • lines changed 70, context: html, text, full: html, text
    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 180, context: html, text, full: html, text
    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 106, context: html, text, full: html, text
    running up refGene and knownCanonical alignments files for 100-way refs #11808
  • lines changed 114, context: html, text, full: html, text
    cleaning up keys in the oreganno track to clean up joiner checks
  • lines changed 41, context: html, text, full: html, text
    done with refGene and knownCanonical alignment files for 100-way refs #11808
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 125, context: html, text, full: html, text
    running up Ostrich and Falcon lastz to Turkey refs #10272
  • lines changed 7, context: html, text, full: html, text
    finish off falPer1 melGal1 strCam0 galGal4 lastz runs refs #10272
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Adjusted a minCheck value to fix an hg19 joinerCheck error
  • lines changed 1, context: html, text, full: html, text
    Added macEug1 to notEnsemblTranscriptId2 group to fix joinerCheck error
  • lines changed 9, context: html, text, full: html, text
    adding phastBias to tablesIgnored
• src/hg/makeDb/trackDb/human/hg16/blastzBestMm3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzBestPt0.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzBestRn3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzMm3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzRn3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzTightMm3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/blastzTightMm4.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/chainSelf.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/chimpDels.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/cnp.html
  • lines changed 6, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/ecoresFr1.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/ecoresTetraodon.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeAffyRnaSignal.html
  • lines changed 2, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeAffyRnaTransfrags.html
  • lines changed 2, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeGisRnaPet.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeAmplicon.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeBase.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeHs.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeProb.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeQuality.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeSangerChipH3H4.html
  • lines changed 4, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeTbaAlign.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeYaleAffyRNATars.html
  • lines changed 3, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/encodeYaleAffyRNATransMap.html
  • lines changed 3, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/fosmidDiscordant.html
  • lines changed 2, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/humorMm3Rn3.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/multizMm3Rn3GalGal2_phyloHMM.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/multizMm3Rn3Pt0.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/mzPt1Mm3Rn3Gg2_pHMM.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg16/rBestChainPanTro1.html
  • lines changed 1, context: html, text, full: html, text
    working with Matt. changed a bunch of urls to pubmed so they don't redirect
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 1, context: html, text, full: html, text
    Replaced broken link to MHC Haplotype Project for hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 2, context: html, text, full: html, text
    Swapped Aves label for Birds - refs #11808 note 34
  • lines changed 2, context: html, text, full: html, text
    Updating 100way to be listed as main Conservation track refs #11808
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 52, context: html, text, full: html, text
    Added RetroFinder Retroposed Genes track version 6.
  • lines changed 1, context: html, text, full: html, text
    add blank line between stanzas to fix brokeness
  • lines changed 1, context: html, text, full: html, text
    Updating 100way to be listed as main Conservation track refs #11808
• src/hg/makeDb/trackDb/human/phastBias.html
  • lines changed 22, context: html, text, full: html, text
    For phastBias track, added PMIDs & PMCIDS to references, as well as links to journal articles, refs #11697
• src/hg/orthoMap/orthoEvaluate.c
  • lines changed 1, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX identifies non-void function not returning a value refs #12106
• src/hg/utils/automation/ensGene/anaPla1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/cioSav2.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/echTel1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/eriEur1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/ficAlb1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/gadMor1.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/galGal4.ensGene.ra
  • lines changed 7, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/gorGor3.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    correct chrom names case translation refs #11907
• src/hg/utils/automation/ensGene/musFur1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/ochPri2.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/pelSin1.ensGene.ra
  • lines changed 5, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/automation/ensGene/petMar2.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/proCap1.ensGene.ra
  • lines changed 4, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/tarSyr1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/tupBel1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/turTru1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/vicPac1.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/xenTro3.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    update to current copies refs #11675
• src/hg/utils/automation/ensGene/xipMac1.ensGene.ra
  • lines changed 6, context: html, text, full: html, text
    up to date with new files refs #11675
• src/hg/utils/gffToBed/gffToBed.c
  • lines changed 73, context: html, text, full: html, text
    Making this tolerate groups that are reused across chromosomes.
• src/hg/utils/makefile
  • lines changed 11, context: html, text, full: html, text
    do not build refreshNamedSessionCustomTracks on Mac OSX will not work refs #12106
• src/hg/utils/mysqlSecurityCheck/makefile
  • lines changed 14, context: html, text, full: html, text
    update makefile to userApps specifications refs #12106
• src/hg/utils/oligoMatch/oligoMatch.c
  • lines changed 29, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/expected/basicTest.bed
  • lines changed 16, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/input/oligos.fa
  • lines changed 6, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/input/sequence.fa
  • lines changed 4, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 7, context: html, text, full: html, text
    update OMIM otto scripts to a new host
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 1, context: html, text, full: html, text
    update OMIM otto scripts to a new host
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    correct path names to libcrypto and libssl refs #12005
  • lines changed 4, context: html, text, full: html, text
    trying different order for crypto ssl mysql static libs refs @12005
  • lines changed 3, context: html, text, full: html, text
    need duplicate entries for ssl and crypto static libs refs #12005
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    can use static libstdc++.a and librt.a when on hgwdev refs #12005
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    eliminate useless -L/lib directive on Mac OSX refs #12106
• src/lib/cirTree.c
  • lines changed 1, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/elmTree.c
  • lines changed 2, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
• src/utils/bigWigCorrelate/bigWigCorrelate.c
  • lines changed 4, context: html, text, full: html, text
    new 5.0 gcc compiler on mac OSX has the word restrict as a reserved word can not use as a variable refs #12106
• src/utils/qa/weeklybld/buildEnv.csh
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    v292 final build

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• files changed: 108