All File Changes

v293_preview to v293_preview2 (2013-11-18 to 2013-12-02) v293

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 1, context: html, text, full: html, text
    Fixed finding of original paper link - PubMed changed their page format slightly, refs #12196
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/edwFixCshlSpikeins.c
  • lines changed 77, context: html, text, full: html, text
    Program to rename submitFileName of spikins is done.
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/makefile
  • lines changed 4, context: html, text, full: html, text
    Program to rename submitFileName of spikins is done.
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/edwFixGbb2.c
  • lines changed 60, context: html, text, full: html, text
    Program to rerun conversion of gtf files to bigBed seems to work.
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/makefile
  • lines changed 4, context: html, text, full: html, text
    Program to rerun conversion of gtf files to bigBed seems to work.
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/edwFixRenamed.c
  • lines changed 101, context: html, text, full: html, text
    Program to cope with files renamed in ENCODE2 is functional.
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/makefile
  • lines changed 4, context: html, text, full: html, text
    Program to cope with files renamed in ENCODE2 is functional.
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/edwFixReplaced.c
  • lines changed 284, context: html, text, full: html, text
    Program that depricates replaced files in ENCODE2 and tries to connect them to their replacement seems to work. Was run at any rate.
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/makefile
  • lines changed 4, context: html, text, full: html, text
    Program that depricates replaced files in ENCODE2 and tries to connect them to their replacement seems to work. Was run at any rate.
• src/hg/encode3/encodeDataWarehouse/edwFixRevoked/edwFixRevoked.c
  • lines changed 90, context: html, text, full: html, text
    Program to help revoke files mistakenly imported into ENCODE3 seems to work.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Make a new view "vf" in encodeDataWarehouse that joins the edwFile and edwValidFile table,and convert endUploadTime and updateTime to more readable date (YYYY-MM-DD) format.
    
  • lines changed 1, context: html, text, full: html, text
    The vf was changed to display xxxxxTime column in "DATETIME" format:
    endUploadTime: 2013-11-06 14:30:16
    updateTime: 2013-08-12 11:59:27
    
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUser/makefile
  • lines changed 2, context: html, text, full: html, text
    Move the rsyncEdwUser source one more level down the source tree.
• src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c
  • lines changed 42, context: html, text, full: html, text
    Fixed doctor to add in dummy gene_id if not present since gffToBed requires this tag.
• src/hg/encode3/validateManifest/VERSION.TXT
  • lines changed 1, context: html, text, full: html, text
    releasing vm v1.7
• src/hg/hgTables/hal.c
  • lines changed 7, context: html, text, full: html, text
    temporary disable USE_HAL check to verify refs #12119
  • lines changed 7, context: html, text, full: html, text
    remove temporary disable USE_HAL check to verify refs #12119
• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    Adding the option for hyperlinks output in a couple places whereit was missing, for bedGraph and microarray tracks.
    Hyperlinks output also works for database wiggle tracks, but not
    for bigWig. refs #12198
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    deactivate UI for bing.com pubs track
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Adding back-button suppoirt through jquery.history.js API. At this time back-button support is only for position. At all times the image should agree with the cart. This means that moving forward, the image must be stacked in window.History.state and moving back, the image must be refreshed using the old location. Note that full page refreshes complicate the picure. Back-button will recall a client side cached page which may be greatly out of sync with cart. Stretegy is to use image only update, but if all else fails, a full page reload is used. This means, that image only update is preferred going forward. To that end, several previous places that required full page refresh can now be done with image only rtefresh. At this time, anytime the chrom changes, the page will be fully refreshed. Redmine #7473.
• src/hg/hgTracks/pubsTracks.c
  • lines changed 3, context: html, text, full: html, text
    changes for a bing.com pubs track
• src/hg/hgVai/hgVai.c
  • lines changed 40, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 4, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
  • lines changed 6, context: html, text, full: html, text
    Include gene track in trash file name for hgVai's Artificial ExampleVariants, because example variants built with one gene track might
    not have any hits in another.
    
  • lines changed 2, context: html, text, full: html, text
    Fix segfault in databases with no snpNNN tables.
  • lines changed 2, context: html, text, full: html, text
    Updating reference for dbNSFP.
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 90, context: html, text, full: html, text
    Updating ENCODE analysisTools page per Mike Pazin request, reshuffle order, add new tool
  • lines changed 1, context: html, text, full: html, text
    Updating date on bottom of page for analysisTools.html update
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 1, context: html, text, full: html, text
    Added link to mirror requirements section to top of page, refs #12185
  • lines changed 4, context: html, text, full: html, text
    Changing the FAQ to now point to the README from the source tree, instead of the wiki page, refs #11941
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 12, context: html, text, full: html, text
    Adding suggest CT limit to help docs, refs #9134
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 7, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 89, context: html, text, full: html, text
    Adding entry for 100way. refs #11808
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Added PMID to Braney track hub paper. Will update citation again when official print version comes out in the journal.
• src/hg/htdocs/indexNews.html
  • lines changed 77, context: html, text, full: html, text
    Adding entry for 100way. refs #11808
• src/hg/inc/annoGratorGpVar.h
  • lines changed 1, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/js/hgTracks.js
  • lines changed 357, context: html, text, full: html, text
    Adding back-button suppoirt through jquery.history.js API. At this time back-button support is only for position. At all times the image should agree with the cart. This means that moving forward, the image must be stacked in window.History.state and moving back, the image must be refreshed using the old location. Note that full page refreshes complicate the picure. Back-button will recall a client side cached page which may be greatly out of sync with cart. Stretegy is to use image only update, but if all else fails, a full page reload is used. This means, that image only update is preferred going forward. To that end, several previous places that required full page refresh can now be done with image only rtefresh. At this time, anytime the chrom changes, the page will be fully refreshed. Redmine #7473.
• src/hg/js/jquery.history.js
  • lines changed 1, context: html, text, full: html, text
    Checking in jquery.history.js which is a plug-in that enables back-button support. This is a 3rd party file and is untouched by UCSC.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding back-button suppoirt through jquery.history.js API. At this time back-button support is only for position. At all times the image should agree with the cart. This means that moving forward, the image must be stacked in window.History.state and moving back, the image must be refreshed using the old location. Note that full page refreshes complicate the picure. Back-button will recall a client side cached page which may be greatly out of sync with cart. Stretegy is to use image only update, but if all else fails, a full page reload is used. This means, that image only update is preferred going forward. To that end, several previous places that required full page refresh can now be done with image only rtefresh. At this time, anytime the chrom changes, the page will be fully refreshed. Redmine #7473.
• src/hg/lib/annoFormatVep.c
  • lines changed 1, context: html, text, full: html, text
    User request from Case: don't truncate alt allele column so readily.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 3, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    vintage 2005 bug -- genePredNmdTarget was practically guaranteed toreturn FALSE for genes on the - strand because it was comparing a
    relative coord to an absolute coord.
    
• src/hg/lib/gpFx.c
  • lines changed 3, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 71, context: html, text, full: html, text
    I misunderstood the SO term NMD_transcript_variant to mean 'a variantthat induces nonsense-mediate decay', i.e. worse than just a stop-gain.
    However, the term actually means 'variant in a transcript that is
    *already* subject to NMD', i.e. less serious than a variant in an
    intron of a gene that gets translated. gpFx.c now has different
    logic for assigning that term, and hgVai has a new filtering option.
    fixes #12205
    
• src/hg/lib/hgMaf.c
  • lines changed 1, context: html, text, full: html, text
    fix broken if statement refs #12209
• src/hg/lib/imageClone.c
  • lines changed 1, context: html, text, full: html, text
    correctly initialize sizeOne before use refs @12209
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    make sure numChanged and numMatched are initialzed properly before use refs #12209
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    remove redundant semi-colon refs #12209
• src/hg/lib/liftOver.c
  • lines changed 2, context: html, text, full: html, text
    fixing compiler warnings
• src/hg/lib/rmskBed6+10.as
  • lines changed 20, context: html, text, full: html, text
    construct bigBed files for repeat masker result refs #11681
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 2, context: html, text, full: html, text
    Updating test file to match new understanding of NMD_transcript_variant(should have been part of 4c4eb6b4f0) refs #12205
    
• src/hg/lib/variant.c
  • lines changed 1, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
• src/hg/liftOver/tests/makefile
  • lines changed 16, context: html, text, full: html, text
    make sure diff output gets to stderr so we will see the error in email from cron jobs refs #12189
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 24, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 113, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 20, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 20, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 21, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/falPer1.txt
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/gasAcu1.txt
  • lines changed 13, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 32, context: html, text, full: html, text
    Adding entry for UCSF Brain Methyl update. refs #2540
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 13, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 21, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/mm10.txt
  • lines changed 35, context: html, text, full: html, text
    Adding entry for liftover of jaxQtl from mm9 to mm10 refs #7040
  • lines changed 13, context: html, text, full: html, text
    Reloaded table after doing some troubleshooting with Hiram. refs #7040.
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
  • lines changed 15, context: html, text, full: html, text
    mm10.txt
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 26, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 79, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 42, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 23, context: html, text, full: html, text
    complete ensGene lift from taeGut1 with all ens tables refs #10272
• src/hg/makeDb/doc/tetNig2.txt
  • lines changed 22, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 6, context: html, text, full: html, text
    Convert CCDS to select the current CCDS build based on the CCDS build uidrather than the NCBI build id. This was necessitated by two CCDS builds
    being done on top of the same NCBI build.
    
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • lines changed 31, context: html, text, full: html, text
    Convert CCDS to select the current CCDS build based on the CCDS build uidrather than the NCBI build id. This was necessitated by two CCDS builds
    being done on top of the same NCBI build.
    
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 7, context: html, text, full: html, text
    Convert CCDS to select the current CCDS build based on the CCDS build uidrather than the NCBI build id. This was necessitated by two CCDS builds
    being done on top of the same NCBI build.
    
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 1, context: html, text, full: html, text
    fixing compiler warnings
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    Oops, neglected to add a new identifier rule for lrgTranscriptAliand associated tables. Thanks Jonathan! refs #11863
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Updating description pg reference to call group Fish refs #11808
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 3, context: html, text, full: html, text
    Changing Vertebrate spp group name to Fish, and updating spp on by default - see note 77 refs #11808
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Updated 46way vis per bob. refs #11808
  • lines changed 29, context: html, text, full: html, text
    Adding overrides for updated UCSF Brain Methyl track. refs #2540.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    Changing tags to wgEncodeRegTfbsClusteredV3 to stage motif feature on beta, refs #9092
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    Added penant icon designation to trackDb for jaxQtl refs #7040.
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
  • lines changed 1, context: html, text, full: html, text
    Correcting some links on oreNil track description pages
• src/hg/makeDb/trackDb/oreNil/oreNil2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Correcting some links on oreNil track description pages
• src/hg/makeDb/trackDb/oreNil/oreNil2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Correcting some links on oreNil track description pages
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Changing Vertebrate spp group name to Fish, and updating spp on by default - see note 77 refs #11808
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    changes for a bing.com pubs track
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Program to help revoke files mistakenly imported into ENCODE3 seems to work.
• src/hg/oneShot/freen/freen.c
  • lines changed 15, context: html, text, full: html, text
    Program to help revoke files mistakenly imported into ENCODE3 seems to work.
• src/hg/utils/automation/HgRemoteScript.pm
  • lines changed 39, context: html, text, full: html, text
    now allow bash scripts in auto jobs and construct bigBed files for repeat masker result refs #11681
• src/hg/utils/automation/configFiles/allMis1.config.ra
  • lines changed 23, context: html, text, full: html, text
    catching up config files refs #10272
• src/hg/utils/automation/configFiles/papHam1.config.ra
  • lines changed 24, context: html, text, full: html, text
    catching up config files refs #10272
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 2, context: html, text, full: html, text
    also create the bigBed file for use in an assembly hub refs #11770
• src/hg/utils/automation/doGenscan.pl
  • lines changed 8, context: html, text, full: html, text
    prepare bigBed files for assembly hub refs #11681
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 55, context: html, text, full: html, text
    now allow bash scripts in auto jobs and construct bigBed files for repeat masker result refs #11681
• src/hg/utils/automation/rmskBed6+10.pl
  • lines changed 34, context: html, text, full: html, text
    construct bigBed files for repeat masker result refs #11681
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed duplicate entry for refreshNamedSessionCustomTracks (see ${buildRefresh}).
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 5, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding apiMel4 Honey bee for assembly hub build refs #11681
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 9, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 3, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
• src/inc/hmac.h
  • lines changed 12, context: html, text, full: html, text
    created to have hmacSha1() and hmacMd5() functions in kent/src/lib tocalculate openssl keyed-hash message authentication code (HMAC)
    
• src/inc/net.h
  • lines changed 2, context: html, text, full: html, text
    fixing compiler warnings
• src/lib/annoOption.c
  • lines changed 2, context: html, text, full: html, text
    Fixing ridiculous uninitialized use error found by Hiram and new Mac gcc.refs #12209
    
• src/lib/cirTree.c
  • lines changed 2, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    remove redundant set of parens refs #12209
  • lines changed 2, context: html, text, full: html, text
    correctly size 8 byte array for swapping routines refs @12209
• src/lib/elmTree.c
  • lines changed 2, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/gff.c
  • lines changed 1, context: html, text, full: html, text
    Program to help revoke files mistakenly imported into ENCODE3 seems to work.
• src/lib/hmac.c
  • lines changed 58, context: html, text, full: html, text
    created to have hmacSha1() and hmacMd5() functions in kent/src/lib tocalculate openssl keyed-hash message authentication code (HMAC)
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    created to have hmacSha1() and hmacMd5() functions in kent/src/lib tocalculate openssl keyed-hash message authentication code (HMAC)
    
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/net.c
  • lines changed 4, context: html, text, full: html, text
    fixing compiler warnings
• src/lib/twoBit.c
  • lines changed 6, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/udc.c
  • lines changed 4, context: html, text, full: html, text
    fixing compiler warnings
• src/lib/vcf.c
  • lines changed 82, context: html, text, full: html, text
    Fixed vcfGetSlashSepAllelesFromWords to use same logic asvcfRecordTrimIndelLeftBase to detect the VCF left padding base.
    Made improvements to the display of symbolic alleles from dbSNP.
    Fixed strand bug in parseDbSnpAltAlleles. Thanks Jonathan!
    refs #11460 (hgVai: paste/upload variant input options)
    
  • lines changed 3, context: html, text, full: html, text
    Suppress a vcfFileErr about something that occurs in 1000 Genomes Phase 1VCF and is not really a big deal: if there's a keyword for which we're
    not expecting any particular number of values ("Number=." in header,
    def->fieldCount=-1), and the '=' is omitted when there are no values
    to report, just carry on and pretend we saw an '=' with no values
    after it.
    
  • lines changed 3, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/makefile
  • lines changed 4, context: html, text, full: html, text
    allow alpha target to work with make -j N parallel make refs #9149
• src/product/README.requirements
  • lines changed 29, context: html, text, full: html, text
    Adding README document about the minimum hardware and software requirements for a mirror, refs #11941
  • lines changed 20, context: html, text, full: html, text
    Adding commands to find the size of directories on hgdownload, refs #11941
• src/product/scripts/README.trashCleaning
  • lines changed 65, context: html, text, full: html, text
    describe the history of trash cleaning refs #11957
  • lines changed 6, context: html, text, full: html, text
    describe the history of trash cleaning refs #11957
  • lines changed 57, context: html, text, full: html, text
    additional material refs #11957
  • lines changed 22, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
  • lines changed 5, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
  • lines changed 1, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/browserEnvironment.txt
  • lines changed 8, context: html, text, full: html, text
    better defaults for a generic installation refs #11957
• src/product/scripts/cleanLostTables.sh
  • lines changed 54, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/dirStatsFromFind.pl
  • lines changed 228, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/fileStatsFromFind.pl
  • lines changed 61, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/lostTables.pl
  • lines changed 196, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/measureTrash.sh
  • lines changed 70, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/trashCleanMonitor.sh
  • lines changed 97, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
  • lines changed 6, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashCleaner.bash
  • lines changed 381, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashCleaner.csh
  • lines changed 87, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
  • lines changed 294, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashSizeMonitor.sh
  • lines changed 116, context: html, text, full: html, text
    addition to generic trash cleaner system refs #11957
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    avoid the bedToBigBed/tests/input/itemRgb.as duplicate
• src/userApps/fetchKentSource.sh
  • lines changed 6, context: html, text, full: html, text
    improve note about HEAD vs beta branch refs #9149
• src/utils/bedToBigBed/chrom.sizes
  • lines changed 49, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/itemRgb.as
  • lines changed 13, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/itemRgb.bed
  • lines changed 22, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/makefile
  • lines changed 9, context: html, text, full: html, text
    fixing up make test for bedToBigBed
  • lines changed 4, context: html, text, full: html, text
    do not need the redundant test target refs #9104
• src/utils/bedToBigBed/test.bed
  • lines changed 12, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/tests/input/chrom.sizes
  • lines changed 49, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/tests/input/itemRgb.as
  • lines changed 13, context: html, text, full: html, text
    fixing up make test for bedToBigBed
  • lines changed 1, context: html, text, full: html, text
    avoid duplicate definition of this structure from src/hg/lib/fullBed.as
  • lines changed 1, context: html, text, full: html, text
    avoid duplicate definition of this structure from src/hg/lib/fullBed.as
• src/utils/bedToBigBed/tests/input/itemRgb.bed
  • lines changed 22, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/bedToBigBed/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    fixing up make test for bedToBigBed
• src/utils/faRandomize/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    make sure diff output gets to stderr so we will see the error in email from cron jobs refs #12189
• src/utils/qa/copyHgcentral
  • lines changed 440, context: html, text, full: html, text
    Added new copyHgcentral script and added to makefile (redmine #6508)
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Added new copyHgcentral script and added to makefile (redmine #6508)
  • lines changed 1, context: html, text, full: html, text
    Removed '.csh' from copyHgcentral filename in makefile
• src/utils/qa/qaConfig.csh
  • lines changed 1, context: html, text, full: html, text
    Table status files now back on hgnfs1
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v293 preview2
• src/utils/qa/weeklybld/buildOneUseCase
  • lines changed 31, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090
• src/utils/qa/weeklybld/buildWithUseCases
  • lines changed 109, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090
• src/utils/qa/weeklybld/runBuildWithUseCases.sh
  • lines changed 2, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090

• lines changed: 5198
• files changed: 165