All File Changes

v342_preview to v342_preview2 (2016-11-14 to 2016-11-28) v342

• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    570869c7eb24e48b2fa781a7bcc3d4368d3fc15d Sun Nov 27 01:11:38 2016 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 2, context: html, text, full: html, text
    c556a384887c1957f99800e526e041eac6b3b9d7 Tue Nov 15 14:18:43 2016 -0800
    Adding PNG file support.
  • lines changed 55, context: html, text, full: html, text
    f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
    CIRM: libifying the CDW menubar so cdwGetFile can replace <!--menuBar--> with the current menubar in html files it is serving.
  • lines changed 23, context: html, text, full: html, text
    3bb73cec9a7c6d0fa8ce9d919f6877e422dc13d7 Tue Nov 22 13:26:10 2016 -0800
    CIRM: redoing the support for tbi/bai index files in the CDW after having learned more about how index files are handled in the CDW.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 5, context: html, text, full: html, text
    c556a384887c1957f99800e526e041eac6b3b9d7 Tue Nov 15 14:18:43 2016 -0800
    Adding PNG file support.
• src/hg/cirm/cdw/cdwManiFastqToKallisto/cdwManiFastqToKallisto
  • lines changed 3, context: html, text, full: html, text
    39ec684cf810dd9a2520c23443c39fa022fa5615 Mon Nov 14 11:37:18 2016 -0800
    Changing the transcriptome link and fixing a bug Jim caught, reps #17630
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 1, context: html, text, full: html, text
    c556a384887c1957f99800e526e041eac6b3b9d7 Tue Nov 15 14:18:43 2016 -0800
    Adding PNG file support.
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 91, context: html, text, full: html, text
    f5edba37a5064a01966411e3e01629d67e4983cc Tue Nov 15 00:10:59 2016 -0800
    CIRM: first go at VCF summary
  • lines changed 7, context: html, text, full: html, text
    907bc39d3d6aaf523023a576113f79cf24ab9e58 Tue Nov 15 00:13:58 2016 -0800
    CIRM: trying to work around missing kallisto log file data for Chris
  • lines changed 22, context: html, text, full: html, text
    a0d5aafda3f5ac8cff678675c715f33b9618c732 Tue Nov 15 11:33:05 2016 -0800
    CIRM: some more summary fixes, potentially related to MISCE
  • lines changed 3, context: html, text, full: html, text
    c292622618eeb59d87b5d32c7b8d4a9d95aef541 Fri Nov 18 11:43:58 2016 -0800
    CIRM: cdw summary, allowing meta file to end with .tsv instead of .tab and making sure other extensions lead to abort
  • lines changed 17, context: html, text, full: html, text
    f2784612ffb81605574914f99fd62becab52e07b Mon Nov 21 10:52:46 2016 -0800
    CIRM: allowing a manually generated summary section
  • lines changed 1, context: html, text, full: html, text
    bf7071731ecf6b4b61e79786d6782326251f69c0 Mon Nov 21 16:52:55 2016 -0800
    CIRM: fixing cdwSummary bug
  • lines changed 16, context: html, text, full: html, text
    60c5a57c325d324fce6072bc30b8ae859fee1030 Wed Nov 23 14:03:16 2016 -0800
    CIRM: allowing summaries without data
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.h
  • lines changed 47, context: html, text, full: html, text
    e3d3e22fd4592d4f6772efa594651ff8de791724 Mon Nov 21 15:21:29 2016 -0800
    CIRM: fixing build problem
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    afa442d6ca0f9efec5230763fb5efc7e8b5fcf98 Mon Nov 14 11:43:50 2016 -0800
    Fixing some small bugs before pushing out, switched ra and tsv order. Refs #17870
  • lines changed 3, context: html, text, full: html, text
    abedc8513b43b8f8779a11d9b18b9ad62c6248fa Mon Nov 14 14:28:44 2016 -0800
    fixing up a couple small bugs Jim pointed out during the Monday meeting, refs #17870
  • lines changed 1, context: html, text, full: html, text
    f400b02b0e3250d3269123f6c89bf35375ecfafd Tue Nov 15 14:20:53 2016 -0800
    Adding PNG file support.
  • lines changed 48, context: html, text, full: html, text
    f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
    CIRM: libifying the CDW menubar so cdwGetFile can replace <!--menuBar--> with the current menubar in html files it is serving.
  • lines changed 3, context: html, text, full: html, text
    9ee67f1cd4bc5cd0fa4c0cd6a03bf13d02765986 Wed Nov 16 18:30:59 2016 -0800
    Adding an image which links to a joint data set page, no redmine
  • lines changed 4, context: html, text, full: html, text
    e40775ea4202615e8d65554bc0aa9510a8c3423e Fri Nov 18 11:00:28 2016 -0800
    adding a border to the image and left aligning it, refs #17870
  • lines changed 2, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
  • lines changed 49, context: html, text, full: html, text
    66425c3d8163cb5d85e09866f165ebed0dd1a326 Mon Nov 21 14:47:21 2016 -0800
    CIRM: fix the custom track links to the genome browser to use the new "bigDataIndex" tags
  • lines changed 47, context: html, text, full: html, text
    3bb73cec9a7c6d0fa8ce9d919f6877e422dc13d7 Tue Nov 22 13:26:10 2016 -0800
    CIRM: redoing the support for tbi/bai index files in the CDW after having learned more about how index files are handled in the CDW.
  • lines changed 3, context: html, text, full: html, text
    7574ad5f746a28f97151740c3feaa009c18cc7da Tue Nov 22 15:46:46 2016 -0800
    Adding csv output to query page.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 1, context: html, text, full: html, text
    20a8a5268bb932b7aba9b71ba8b2bb9364db6645 Tue Nov 8 12:23:07 2016 -0800
    Documenting some more version changes.
  • lines changed 2, context: html, text, full: html, text
    74714f1017bb47242286c4b04ce772c901003bf1 Tue Nov 15 14:19:36 2016 -0800
    Adding PNG file support.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
    CIRM: libifying the CDW menubar so cdwGetFile can replace <!--menuBar--> with the current menubar in html files it is serving.
  • lines changed 2, context: html, text, full: html, text
    59172abe9a5474b3978a897ad69d419436235984 Mon Nov 21 15:17:54 2016 -0800
    CIRM: fixing header problem
  • lines changed 2, context: html, text, full: html, text
    3bb73cec9a7c6d0fa8ce9d919f6877e422dc13d7 Tue Nov 22 13:26:10 2016 -0800
    CIRM: redoing the support for tbi/bai index files in the CDW after having learned more about how index files are handled in the CDW.
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 3, context: html, text, full: html, text
    c556a384887c1957f99800e526e041eac6b3b9d7 Tue Nov 15 14:18:43 2016 -0800
    Adding PNG file support.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 15, context: html, text, full: html, text
    7c6869c09250c3428900ffe87aacaced2512ba31 Mon Nov 14 11:44:36 2016 -0800
    Fixing up the global variable names as pointed out by Jonathan, changing the null tag to a a n/a tag, refs #17870
  • lines changed 1, context: html, text, full: html, text
    abedc8513b43b8f8779a11d9b18b9ad62c6248fa Mon Nov 14 14:28:44 2016 -0800
    fixing up a couple small bugs Jim pointed out during the Monday meeting, refs #17870
  • lines changed 56, context: html, text, full: html, text
    f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
    CIRM: libifying the CDW menubar so cdwGetFile can replace <!--menuBar--> with the current menubar in html files it is serving.
  • lines changed 14, context: html, text, full: html, text
    3bb73cec9a7c6d0fa8ce9d919f6877e422dc13d7 Tue Nov 22 13:26:10 2016 -0800
    CIRM: redoing the support for tbi/bai index files in the CDW after having learned more about how index files are handled in the CDW.
  • lines changed 66, context: html, text, full: html, text
    7574ad5f746a28f97151740c3feaa009c18cc7da Tue Nov 22 15:46:46 2016 -0800
    Adding csv output to query page.
• src/hg/cirm/cdw/lib/cdwNavBar.h
  • lines changed 47, context: html, text, full: html, text
    e3d3e22fd4592d4f6772efa594651ff8de791724 Mon Nov 21 15:21:29 2016 -0800
    CIRM: fixing build problem
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 11, context: html, text, full: html, text
    c556a384887c1957f99800e526e041eac6b3b9d7 Tue Nov 15 14:18:43 2016 -0800
    Adding PNG file support.
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    134d8af99fcff59e59aa0d8d807050808a11132f Wed Nov 23 14:06:07 2016 -0800
    CIRM: adding cdwSummary to main CDW makefile
• src/hg/hgBlat/hgBlat.c
  • lines changed 89, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/hg/hgGtexTrackSettings/README.txt
  • lines changed 6, context: html, text, full: html, text
    e328ec6cb3ebca54bec6c782ffff9f14aed6ebda Mon Nov 14 17:17:45 2016 -0800
    Edits to final art SVG as described in hg/hgGtexSettings/README.txt. refs #17369
  • lines changed 2, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 21, context: html, text, full: html, text
    b694541552528887abb34b563336a17e0628e197 Thu Nov 17 15:00:40 2016 -0800
    Response to QA. 1. Align GO button. 2. Abandon bolding of tissue labels to preserve alignment with leader lines. 3. Draw leader line on top when highlighted. refs #17369
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 2, context: html, text, full: html, text
    c74646cfe6256554338b95939bb5540812c059bd Mon Nov 14 17:19:06 2016 -0800
    Rename SVG to be more accurate. refs #17369
  • lines changed 32, context: html, text, full: html, text
    747eae7a2f3f12196fe59f6b2340f2c61eedac45 Tue Nov 15 14:44:59 2016 -0800
    Add last updated and schema link. refs #17369
  • lines changed 35, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 2, context: html, text, full: html, text
    60b4b2383869d11fba48ea5dfe616d9b90ebaecf Thu Nov 17 09:43:58 2016 -0800
    Fix GO button (broken by CSS refactor). refs #17369
  • lines changed 10, context: html, text, full: html, text
    185dae5a5dd7912b1f08e0f0c19b756687a3c6db Thu Nov 17 09:53:38 2016 -0800
    Cleanup overlong lines. refs #17369
  • lines changed 46, context: html, text, full: html, text
    637185cb51ee2ce0651a4defe22862d735dfb3ff Thu Nov 17 15:01:34 2016 -0800
    Remove globals in response to code review. refs #17369
  • lines changed 1, context: html, text, full: html, text
    20fb3ee25697137ab4c9fff427f59249e906e109 Thu Nov 17 15:09:18 2016 -0800
    Add default track name if 'g' cart variable missing. To make this demo-friendly (run CGI directly). refs #17369
  • lines changed 2, context: html, text, full: html, text
    9a7fb2974573b7e57ddac45f2b35c80c66deca53 Mon Nov 21 11:31:32 2016 -0800
    1. Fix Firefox initialization -- it apparently loads SVG faster than Chrome, so need to check before setting event handler. 2. Fix HOME link image (UCSC browser logo), lost during CSS refactoring. refs #17369
  • lines changed 6, context: html, text, full: html, text
    f24a065a92a0545e812439a036867b9bc8f3c212 Mon Nov 21 12:19:19 2016 -0800
    Swap bodymap and config panels. More intuitive we think. refs #17369
  • lines changed 2, context: html, text, full: html, text
    7ea79bbbda7357606cc73423f790e1459492d9dd Mon Nov 21 17:07:18 2016 -0800
    Add pointer cursor to track description navigation arrows. Responding to Chris Lee comments. refs #17369
  • lines changed 1, context: html, text, full: html, text
    4696818cfc16fbc325297013a9a7a1966b1a665d Wed Nov 23 11:23:34 2016 -0800
    Move credit off illustration, to just below it. Request of QA. refs #17369
  • lines changed 4, context: html, text, full: html, text
    ca9e008e9edbcf048e0c4cd747c15a9c07ed9a26 Wed Nov 23 11:34:24 2016 -0800
    Minor layout repair. In response to QA. refs #17369
  • lines changed 1, context: html, text, full: html, text
    490dd90fc4afdee56311b607e3cfc2a7a69345de Wed Nov 23 11:36:51 2016 -0800
    Tweak credit, AnnZ request. refs #17369
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html
  • lines changed 108, context: html, text, full: html, text
    29caec4eeb0bbd158ec6935c4d0bc4780d49c1e8 Thu Nov 17 10:15:35 2016 -0800
    Removing vestigial file. refs #17369
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 3, context: html, text, full: html, text
    7a5ae9c2c1d5519793a4bdd99cca3a911c14b68e Fri Nov 18 16:36:51 2016 -0800
    Added support for split tables to annoStreamDb since ChrisV found it was missing which broke some hgIntegrator queries in hg18 and older dbs. refs #18397
• src/hg/hgTables/bam.c
  • lines changed 4, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
  • lines changed 2, context: html, text, full: html, text
    8610c522f28515c16aed778408997136448f3c45 Wed Nov 23 05:15:16 2016 -0800
    fixing summary button for bigDataIndex support in table browser, refs #18420
• src/hg/hgTables/bigWig.c
  • lines changed 22, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/hg/hgTables/vcf.c
  • lines changed 13, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/hg/hgTracks/bamTrack.c
  • lines changed 4, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 15, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/hg/hgTracks/cds.c
  • lines changed 3, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    e4ba9d262524dcb90690e480a3fa5ebe2e12fb13 Mon Nov 21 10:34:57 2016 -0800
    Suppress bodyMap UI under IE. (Additional work needed to make it functional). refs #17369
  • lines changed 4, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
• src/hg/hgTracks/snakeTrack.c
  • lines changed 14, context: html, text, full: html, text
    142948ffb4e89b89443006817bb49990dd1a7924 Tue Nov 15 10:32:50 2016 -0800
    allow a halSnake track to declare database alias names refs #13553
  • lines changed 2, context: html, text, full: html, text
    6fe08e419d9eaf9c40eac041dc9d8d2ba42f3061 Wed Nov 16 17:12:00 2016 -0800
    fix problem with snake track height when there's an error message or no items in track.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 4, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/hgVai/hgVai.c
  • lines changed 6, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 2, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/hgc/gtexClick.c
  • lines changed 8, context: html, text, full: html, text
    8e01434bfdc7b343d768e46efe31441e9a1e5229 Mon Nov 21 10:59:31 2016 -0800
    Fix gene search with alternative item naming. refs #18412
• src/hg/hgc/hgc.c
  • lines changed 28, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
  • lines changed 30, context: html, text, full: html, text
    eb572b9de60c49871e84bf8b6bd548210b69d44f Thu Nov 17 15:21:02 2016 -0800
    attempting to make the hal links prettier refs #13553
  • lines changed 2, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
  • lines changed 30, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/hg/hgc/vcfClick.c
  • lines changed 4, context: html, text, full: html, text
    e4267cc044021c629d0b80d4ad50ec077634c3cd Tue Nov 22 16:10:57 2016 -0800
    fixing up bigDataIndex support for VCF and hgc clicks, refs #18420
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 45, context: html, text, full: html, text
    515fcbf5970f71ff9d3adf549472d206f3b4c098 Tue Nov 22 08:58:49 2016 -0800
    modified FAQcustom ref #17433
  • lines changed 3, context: html, text, full: html, text
    dbb3e5345bb35c868ac8970c32c7934c35bce316 Tue Nov 22 09:25:35 2016 -0800
    changed FAQcustom ref #17433
  • lines changed 16, context: html, text, full: html, text
    8e9badf8e84a51bbb6c9af7d05311c9d328ca4cc Wed Nov 23 13:46:54 2016 -0800
    add more changes to FAQ refs #17433
  • lines changed 1, context: html, text, full: html, text
    c101b3830cf3ed023ee78668d247caedb4d84590 Wed Nov 23 14:18:21 2016 -0800
    add more changes to FAQ refs #17433
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    98467d14485b5b1ec11ca45a75839068dc2b9e86 Tue Nov 22 09:00:31 2016 -0800
    added link to FAQformat ref #17433
  • lines changed 6, context: html, text, full: html, text
    8e9badf8e84a51bbb6c9af7d05311c9d328ca4cc Wed Nov 23 13:46:54 2016 -0800
    add more changes to FAQ refs #17433
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    4299aebf0fcb2ecca685bdf1efa2c41851f2ef17 Mon Nov 14 14:44:53 2016 -0800
    editing credits.html refs #18382
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 9, context: html, text, full: html, text
    7a2c9f322efcc286fb999cc1439de7f37b92fc29 Mon Nov 14 13:34:23 2016 -0800
    Adding a note about validateFiles and bedGraph per request from ENCODE from long ago on bedgraph.html refs #15586
  • lines changed 1, context: html, text, full: html, text
    a583eaa4afe284cfc18fab55f7855817fe178cd7 Mon Nov 14 13:37:53 2016 -0800
    Small typo fix for bedgraph.html refs #15586
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 14, context: html, text, full: html, text
    fe6363ffc75a664439c261befff24b2981e960cd Fri Nov 18 15:15:18 2016 -0800
    Documenting new addTools command to gbic script, refs #14399
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    ac9849c213f0b7b73eb7cacc7c0382437e228c1c Tue Nov 22 13:15:31 2016 -0800
    Fixing broken VisiGene description links, refs #17323
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 2, context: html, text, full: html, text
    e585df1a1af3538bd2e41bb2fb3e2e1157ca9b16 Tue Nov 15 15:41:19 2016 -0800
    mention CRAM in section about BAM in trackDb doc
  • lines changed 6, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 2, context: html, text, full: html, text
    e585df1a1af3538bd2e41bb2fb3e2e1157ca9b16 Tue Nov 15 15:41:19 2016 -0800
    mention CRAM in section about BAM in trackDb doc
  • lines changed 6, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    e585df1a1af3538bd2e41bb2fb3e2e1157ca9b16 Tue Nov 15 15:41:19 2016 -0800
    mention CRAM in section about BAM in trackDb doc
  • lines changed 18, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
  • lines changed 11, context: html, text, full: html, text
    7ab7bca1baa845258f88a43349483f1195b5c562 Tue Nov 22 15:16:06 2016 -0800
    Removing extraneously copied dataVersion stanza
• src/hg/htdocs/images/bodyMap.svg
  • lines changed 960, context: html, text, full: html, text
    f3d78bbabb983d1179f2028a015651a6b3bf79a3 Mon Nov 14 17:16:14 2016 -0800
    Final art from Jeff West. With some corrections, and a credit line on the rock. refs #17369
  • lines changed 146, context: html, text, full: html, text
    e328ec6cb3ebca54bec6c782ffff9f14aed6ebda Mon Nov 14 17:17:45 2016 -0800
    Edits to final art SVG as described in hg/hgGtexSettings/README.txt. refs #17369
  • lines changed 1996, context: html, text, full: html, text
    c74646cfe6256554338b95939bb5540812c059bd Mon Nov 14 17:19:06 2016 -0800
    Rename SVG to be more accurate. refs #17369
• src/hg/htdocs/images/cdwImages/qbg_krgSeurat.png
  • lines changed 0, context: html, text, full: html, text
    b4c166bf5ccebd05462ad2bb6f2a977d643463ea Wed Nov 16 18:07:36 2016 -0800
    Adding an image that will link from the home page to a data set page, no redmine
  • lines changed 0, context: html, text, full: html, text
    5fec9444a7322ec038d168b78e388349bfca990f Wed Nov 16 18:27:32 2016 -0800
    Updating the image to have some text over it, still no redmine
• src/hg/htdocs/images/gtexBodyMap.svg
  • lines changed 1996, context: html, text, full: html, text
    c74646cfe6256554338b95939bb5540812c059bd Mon Nov 14 17:19:06 2016 -0800
    Rename SVG to be more accurate. refs #17369
  • lines changed 1, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 1, context: html, text, full: html, text
    cfb2a129645c68bc7e0edb6f8a89e6fed5f8b879 Thu Nov 17 10:14:44 2016 -0800
    Fixed id on Brain Cerebellum; thanks to Angie for suggested area to dig at, from code review. refs #17369
  • lines changed 6, context: html, text, full: html, text
    f56f671c81a2560ffe62843863af4c80aeaf7f1e Thu Nov 17 13:09:20 2016 -0800
    Change easily changeable text labels to match GTEx labels (largely casification differences). Response to QA. refs #17369
  • lines changed 2, context: html, text, full: html, text
    d5af99c46e3bbdfe7a09a62cffab7d1c8c73861f Thu Nov 17 14:01:44 2016 -0800
    Illustration display fine tuning, in response to QA. 1. Change Skin suprapubic outline to black to match other tissues. Make breast visible when not highlighted. refs #17369
  • lines changed 1, context: html, text, full: html, text
    fd839b13a655839366a8cc231f5c9e4709c34042 Mon Nov 21 11:53:02 2016 -0800
    Tweak label position, in response to QA. refs #17369
  • lines changed 1, context: html, text, full: html, text
    132b97a008048228aa8658f8dcf358c518a6bb34 Mon Nov 21 12:40:31 2016 -0800
    Restore previous width, to preserve font size similarity to tissue table. refs #7136
  • lines changed 87, context: html, text, full: html, text
    4696818cfc16fbc325297013a9a7a1966b1a665d Wed Nov 23 11:23:34 2016 -0800
    Move credit off illustration, to just below it. Request of QA. refs #17369
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 53, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
• src/hg/htdocs/style/bootstrap.min.css
  • lines changed 14, context: html, text, full: html, text
    d1862cafdb2f1e6527548d15c6ee24fcbe2077e9 Sat Nov 19 14:09:06 2016 -0800
    Using minimal bootstrap CSS for grid layout. refs #17369
• src/hg/htdocs/style/gb.css
  • lines changed 264, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 6, context: html, text, full: html, text
    60b4b2383869d11fba48ea5dfe616d9b90ebaecf Thu Nov 17 09:43:58 2016 -0800
    Fix GO button (broken by CSS refactor). refs #17369
  • lines changed 4, context: html, text, full: html, text
    b694541552528887abb34b563336a17e0628e197 Thu Nov 17 15:00:40 2016 -0800
    Response to QA. 1. Align GO button. 2. Abandon bolding of tissue labels to preserve alignment with leader lines. 3. Draw leader line on top when highlighted. refs #17369
  • lines changed 3, context: html, text, full: html, text
    10882ae780149f4978bd4bb1233d914429a7adf5 Sat Nov 19 13:53:27 2016 -0800
    Fix alignment issue on Firefox. refs #17369
  • lines changed 1, context: html, text, full: html, text
    7eff837e8e696cc677550bcb184c81b0a8b87ed6 Mon Nov 21 12:11:05 2016 -0800
    Add margin to track description images, as per QA request. refs #17369
  • lines changed 1, context: html, text, full: html, text
    a51822e6fb60ef8640bce44bab2b22ebb7616d64 Mon Nov 21 12:12:03 2016 -0800
    Add margin around image on track description, as pwer QA request.
  • lines changed 4, context: html, text, full: html, text
    7ea79bbbda7357606cc73423f790e1459492d9dd Mon Nov 21 17:07:18 2016 -0800
    Add pointer cursor to track description navigation arrows. Responding to Chris Lee comments. refs #17369
  • lines changed 2, context: html, text, full: html, text
    d5c18df19333bae9bd4ccc0e1acc5819d083e0a8 Sun Nov 27 19:17:12 2016 -0800
    Layout tweak. refs #17369
• src/hg/htdocs/style/gbAfterMenu.css
  • lines changed 19, context: html, text, full: html, text
    bfa6b385b094aaae229a39dde91ff62df919b8ff Wed Nov 16 16:30:09 2016 -0800
    Cleanup CSS. refs #17369
• src/hg/htdocs/style/hgGtexTrackSettings.css
  • lines changed 6, context: html, text, full: html, text
    a8936307e2c298da14b8eef67b9607c2a6db7e47 Tue Nov 15 14:46:59 2016 -0800
    Add last updated and schema link. refs #17369
  • lines changed 285, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 5, context: html, text, full: html, text
    b694541552528887abb34b563336a17e0628e197 Thu Nov 17 15:00:40 2016 -0800
    Response to QA. 1. Align GO button. 2. Abandon bolding of tissue labels to preserve alignment with leader lines. 3. Draw leader line on top when highlighted. refs #17369
  • lines changed 2, context: html, text, full: html, text
    8324f2b60ec7e0e7532d1ef5bc48a0eff31b7052 Thu Nov 17 15:25:02 2016 -0800
    Tweak font size to get closer to body map labels. refs #17369
  • lines changed 6, context: html, text, full: html, text
    1f86f70f8eec5861fce8294a718210258b1d739f Sat Nov 19 14:49:10 2016 -0800
    Add SVG sizing (needed by IE). refs #17369
  • lines changed 2, context: html, text, full: html, text
    0c923b0c57feb5bb2c8d857f7b101c52052ee918 Mon Nov 21 10:30:23 2016 -0800
    Syntax errs. refs #17369
  • lines changed 1, context: html, text, full: html, text
    0a7c44ba2677b94f2770c82bd38e78cc8db754ad Mon Nov 21 12:37:25 2016 -0800
    Add left margin so tissue table labels are closer to body map. refs #17369
  • lines changed 8, context: html, text, full: html, text
    4696818cfc16fbc325297013a9a7a1966b1a665d Wed Nov 23 11:23:34 2016 -0800
    Move credit off illustration, to just below it. Request of QA. refs #17369
  • lines changed 4, context: html, text, full: html, text
    ca9e008e9edbcf048e0c4cd747c15a9c07ed9a26 Wed Nov 23 11:34:24 2016 -0800
    Minor layout repair. In response to QA. refs #17369
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 1, context: html, text, full: html, text
    3a7394d66eb8ba2d1777b1c304cd68e355d9a7bb Wed Nov 16 16:31:40 2016 -0800
    Cleanup CSS. refs #17369
• src/hg/inc/bigPsl.h
  • lines changed 6, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/hg/inc/gtexUi.h
  • lines changed 12, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
• src/hg/inc/hAnno.h
  • lines changed 5, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/hg/inc/hgBam.h
  • lines changed 4, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
• src/hg/inc/tagRepo.h
  • lines changed 10, context: html, text, full: html, text
    40fc79826f7de636f623e2c6dbe2c49e3d191e78 Fri Nov 18 16:10:12 2016 -0800
    oops, left this out
• src/hg/inc/web.h
  • lines changed 9, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
• src/hg/js/hgGtexTrackSettings.js
  • lines changed 24, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 2, context: html, text, full: html, text
    60b4b2383869d11fba48ea5dfe616d9b90ebaecf Thu Nov 17 09:43:58 2016 -0800
    Fix GO button (broken by CSS refactor). refs #17369
  • lines changed 7, context: html, text, full: html, text
    b694541552528887abb34b563336a17e0628e197 Thu Nov 17 15:00:40 2016 -0800
    Response to QA. 1. Align GO button. 2. Abandon bolding of tissue labels to preserve alignment with leader lines. 3. Draw leader line on top when highlighted. refs #17369
  • lines changed 16, context: html, text, full: html, text
    936eb3cbf8b163d420be36aa98beccd665ded1b3 Thu Nov 17 15:55:06 2016 -0800
    Add event handlers to color patches in tissue table (friendlier). refs #17369
  • lines changed 19, context: html, text, full: html, text
    9a7fb2974573b7e57ddac45f2b35c80c66deca53 Mon Nov 21 11:31:32 2016 -0800
    1. Fix Firefox initialization -- it apparently loads SVG faster than Chrome, so need to check before setting event handler. 2. Fix HOME link image (UCSC browser logo), lost during CSS refactoring. refs #17369
• src/hg/js/jquery.plugins.js
  • lines changed 40, context: html, text, full: html, text
    8d4d24be22066c27b2faa03b7e5ead3f303ddf93 Wed Nov 16 00:31:50 2016 -0800
    CIRM: making our menubar work with newer jquery versions needed for D3
• src/hg/lib/annoStreamDb.c
  • lines changed 90, context: html, text, full: html, text
    7a5ae9c2c1d5519793a4bdd99cca3a911c14b68e Fri Nov 18 16:36:51 2016 -0800
    Added support for split tables to annoStreamDb since ChrisV found it was missing which broke some hgIntegrator queries in hg18 and older dbs. refs #18397
• src/hg/lib/bigChain.as
  • lines changed 1, context: html, text, full: html, text
    c4c419da6f898053370b2b8b31a165c7cda9b5a0 Mon Nov 14 12:58:24 2016 -0800
    score in chains is double, not unsigned
• src/hg/lib/bigPsl.as
  • lines changed 1, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/hg/lib/bigPsl.c
  • lines changed 20, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
  • lines changed 1, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/hg/lib/customFactory.c
  • lines changed 13, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
  • lines changed 1, context: html, text, full: html, text
    02177c0c71b2dd943ca6a68b5fa714c7fd9e6832 Mon Nov 21 17:02:56 2016 -0800
    CIRM: Fixing first bug in bigDataIndex handling.
• src/hg/lib/gbHeader.h
  • lines changed 18, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
  • lines changed 1, context: html, text, full: html, text
    9a7fb2974573b7e57ddac45f2b35c80c66deca53 Mon Nov 21 11:31:32 2016 -0800
    1. Fix Firefox initialization -- it apparently loads SVG faster than Chrome, so need to check before setting event handler. 2. Fix HOME link image (UCSC browser logo), lost during CSS refactoring. refs #17369
• src/hg/lib/gtexUi.c
  • lines changed 1, context: html, text, full: html, text
    aa0cfbb0615ef43df732be87847a759a72d532b5 Mon Nov 21 14:29:22 2016 -0800
    Layout sanitization. refs #17369
  • lines changed 1, context: html, text, full: html, text
    446d4dd6202954c076bb107023ae2677b6901b7f Mon Nov 21 14:37:53 2016 -0800
    Micro consistency tweak.
  • lines changed 28, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
  • lines changed 5, context: html, text, full: html, text
    791bce382259ecb38e5781d2c11f1f0d23ce4ddc Wed Nov 23 12:40:23 2016 -0800
    Remove temp config option. refs #17369
• src/hg/lib/hAnno.c
  • lines changed 11, context: html, text, full: html, text
    7a5ae9c2c1d5519793a4bdd99cca3a911c14b68e Fri Nov 18 16:36:51 2016 -0800
    Added support for split tables to annoStreamDb since ChrisV found it was missing which broke some hgIntegrator queries in hg18 and older dbs. refs #18397
  • lines changed 21, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/hg/lib/hgBam.c
  • lines changed 8, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
  • lines changed 10, context: html, text, full: html, text
    a9dd8b9c383927df373d50e5917b20c959c662fc Wed Nov 23 10:49:30 2016 -0800
    Link to new GTEX Body Map configuration page from hgc and config page. From QA review. refs #17369
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    20d55c43d0b08eb53447faad789e9a840a71decf Tue Nov 15 11:09:28 2016 -0800
    Fixing dependency so web.o is rebuilt when jWestBanner.h or jWestHeader.h is rebuilt.
  • lines changed 1, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
• src/hg/lib/tagRepo.c
  • lines changed 130, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 1, context: html, text, full: html, text
    cd635a44aa56aaa0ee3df7dbb3d099c6a7acb18f Fri Nov 25 08:51:01 2016 -0800
    fixing compile error related to bigDataIndex support
• src/hg/lib/web.c
  • lines changed 34, context: html, text, full: html, text
    f16abb2f99276fcf1811ef04f4f767ce1631c4c7 Wed Nov 16 16:27:45 2016 -0800
    Cleanup CSS. refs #17369
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.cactus.trackDb.txt
  • lines changed 36, context: html, text, full: html, text
    af11f081301ae8b83914773504013e9dccba62d6 Thu Nov 17 14:47:33 2016 -0800
    better long labels refs #13553
  • lines changed 17, context: html, text, full: html, text
    d9c0dfab390f345628526c839ca68651947a2236 Thu Nov 17 15:16:16 2016 -0800
    better long labels refs #13553
• src/hg/makeDb/hgLoadBed/makefile
  • lines changed 1, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/hg/makeDb/trackDb/cow/bosTau8/description.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 25, context: html, text, full: html, text
    212a8086c5717831e89537239a48f81273b0c059 Tue Nov 15 12:01:17 2016 -0800
    Adding coloring info and reference to ClinVar description page. Some other minor wording edits. refs #18377
  • lines changed 7, context: html, text, full: html, text
    ab87f4460ab9b564470285cde7f93f43d4ee9e10 Mon Nov 21 14:46:12 2016 -0800
    Adding note about ClinVar vs ExAC reprocessed variants and how we display the variant info from ClinVar FTP site, refs #16292
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 1, context: html, text, full: html, text
    c9d994962c2238b3d8b34a6067ac3337e828b62b Sat Nov 19 14:40:41 2016 -0800
    Fix minor HTML err.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 2, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 4, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/mouse/mm10/mouseStrains.cactus.trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    5eb9120e25320a9643c2cba7e331682d6b4d6047 Tue Nov 15 11:41:38 2016 -0800
    adding mouse strain halSnake track refs #13553
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    79cfbc46d6507b99aa722b1193deb85dfd89ecc8 Thu Nov 17 22:17:16 2016 -0800
    mouse hubs arrive with the attached hub refs #13553
• src/hg/makeDb/trackDb/mouse/mm7/description.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/mouse/mm8/description.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/mouse/mm9/description.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/mouseStrains.html
  • lines changed 98, context: html, text, full: html, text
    5eb9120e25320a9643c2cba7e331682d6b4d6047 Tue Nov 15 11:41:38 2016 -0800
    adding mouse strain halSnake track refs #13553
• src/hg/makeDb/trackDb/orangutan/ponAbe2/gap.html
  • lines changed 1, context: html, text, full: html, text
    cccce387b01e558b4917ef53f773e5233ef849d5 Tue Nov 22 12:39:36 2016 -0800
    Correcting usages of unlocalized vs unplaced in our description pages and docs, refs #16466
• src/hg/makeDb/trackDb/rat/rn6/mouseStrains.cactus.trackDb.ra
  • lines changed 163, context: html, text, full: html, text
    5eb9120e25320a9643c2cba7e331682d6b4d6047 Tue Nov 15 11:41:38 2016 -0800
    adding mouse strain halSnake track refs #13553
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5eb9120e25320a9643c2cba7e331682d6b4d6047 Tue Nov 15 11:41:38 2016 -0800
    adding mouse strain halSnake track refs #13553
  • lines changed 1, context: html, text, full: html, text
    79cfbc46d6507b99aa722b1193deb85dfd89ecc8 Thu Nov 17 22:17:16 2016 -0800
    mouse hubs arrive with the attached hub refs #13553
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    5eb9120e25320a9643c2cba7e331682d6b4d6047 Tue Nov 15 11:41:38 2016 -0800
    adding mouse strain halSnake track refs #13553
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d949fff04e610f14ff4a2d962ab1849f3ccc590c Fri Nov 18 12:45:58 2016 -0800
    Adjust Augustus short and longLabels, refs #18381
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/hg/utils/bigPslToPsl/bigPslToPsl.c
  • lines changed 2, context: html, text, full: html, text
    2b3b809dcbcd3f3827965f1cae071c6e470db6fe Wed Nov 16 19:31:11 2016 -0800
    fix up bigPslToPsl to use the new API.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 6, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 2, context: html, text, full: html, text
    8382b726e33752590567c6dcbf834070ae51ae14 Fri Nov 11 10:15:16 2016 -0800
    making sure the clinvar otherId row can get wrapped by firefox
  • lines changed 11, context: html, text, full: html, text
    3711849a2a11ee46b13609e7f2a322da52a14c68 Wed Nov 16 00:22:07 2016 -0800
    fixing clinvar color problem, refs #18377
  • lines changed 42, context: html, text, full: html, text
    b0174a409ff0f509cbdc9c26694826045083cf77 Wed Nov 16 12:59:26 2016 -0800
    adding clinvar outlinks and fixing the gene outlink bug, refs #18377
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 6, context: html, text, full: html, text
    b0174a409ff0f509cbdc9c26694826045083cf77 Wed Nov 16 12:59:26 2016 -0800
    adding clinvar outlinks and fixing the gene outlink bug, refs #18377
• src/hg/utils/pslToBigPsl/makefile
  • lines changed 14, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
  • lines changed 48, context: html, text, full: html, text
    464490ebad9e39144ad981f86d859219cc5c658d Thu Nov 24 06:57:31 2016 -0800
    add alpha,beta targets to pslToBigPsl and bedToBigBed makefiles
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
  • lines changed 11, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 2, context: html, text, full: html, text
    ac9849c213f0b7b73eb7cacc7c0382437e228c1c Tue Nov 22 13:15:31 2016 -0800
    Fixing broken VisiGene description links, refs #17323
• src/inc/annoStreamVcf.h
  • lines changed 1, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/inc/bamFile.h
  • lines changed 13, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/inc/common.mk
  • lines changed 2, context: html, text, full: html, text
    9c6ff1359fac6e8ba96d9a4b6b5613b88ffce412 Wed Nov 16 09:46:53 2016 -0800
    add -lz and -lm to everything refs #18336
• src/inc/linefile.h
  • lines changed 7, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/inc/tagStorm.h
  • lines changed 3, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
• src/inc/userApp.mk
  • lines changed 3, context: html, text, full: html, text
    9c6ff1359fac6e8ba96d9a4b6b5613b88ffce412 Wed Nov 16 09:46:53 2016 -0800
    add -lz and -lm to everything refs #18336
• src/inc/vcf.h
  • lines changed 9, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
    Adding VAI/DAI support for bigDataIndex, refs #18420
• src/lib/bamFile.c
  • lines changed 25, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
  • lines changed 6, context: html, text, full: html, text
    a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
    adding bigDataIndex support to the table browser, refs #18420
• src/lib/linefile.c
  • lines changed 19, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/lib/psl.c
  • lines changed 2, context: html, text, full: html, text
    dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800
    add support for protein psls in bigPsl
• src/lib/tagStorm.c
  • lines changed 8, context: html, text, full: html, text
    a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800
    tagStorm file support for track hubs. NEEEDS DOC!!!
• src/lib/vcf.c
  • lines changed 13, context: html, text, full: html, text
    0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800
    CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
• src/product/installer/README.md
  • lines changed 12, context: html, text, full: html, text
    fe6363ffc75a664439c261befff24b2981e960cd Fri Nov 18 15:15:18 2016 -0800
    Documenting new addTools command to gbic script, refs #14399
• src/product/installer/browserSetup.sh
  • lines changed 3, context: html, text, full: html, text
    07e8efc180a7d715a0a0f6d836d35ea778d4af7b Fri Nov 18 12:50:26 2016 -0800
    GBIC, adding note about missing pkgs
  • lines changed 8, context: html, text, full: html, text
    72e5b12d3507134b50d4b802358c8ced5f4e63a3 Fri Nov 18 15:57:34 2016 -0800
    making sure that GBIC works with Mysql 5.7 which is the default for Ubuntu 16.04
• src/product/installer/docker/Dockerfile
  • lines changed 18, context: html, text, full: html, text
    86ecaa82d903eccdfb6323a9baab7f60e761ba1c Fri Nov 18 15:54:43 2016 -0800
    adding a first version of a dockerfile for the GBIC, refs #14399
• src/product/installer/docker/apache.service
  • lines changed 21, context: html, text, full: html, text
    86ecaa82d903eccdfb6323a9baab7f60e761ba1c Fri Nov 18 15:54:43 2016 -0800
    adding a first version of a dockerfile for the GBIC, refs #14399
• src/product/installer/docker/mysql.service
  • lines changed 2, context: html, text, full: html, text
    86ecaa82d903eccdfb6323a9baab7f60e761ba1c Fri Nov 18 15:54:43 2016 -0800
    adding a first version of a dockerfile for the GBIC, refs #14399
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 37, context: html, text, full: html, text
    172629f518d8fe9e99314d8f2baed030eaa9bdba Wed Nov 9 11:03:22 2016 -0800
    Expanding -counts option to display number of distinct values.
• src/utils/bedToBigBed/makefile
  • lines changed 14, context: html, text, full: html, text
    3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800
    implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
  • lines changed 48, context: html, text, full: html, text
    464490ebad9e39144ad981f86d859219cc5c658d Thu Nov 24 06:57:31 2016 -0800
    add alpha,beta targets to pslToBigPsl and bedToBigBed makefiles
• src/utils/qa/getPubHubContact.sh
  • lines changed 52, context: html, text, full: html, text
    997f530b3abf1e33b636be6255a30243205796d1 Tue Nov 22 13:22:59 2016 -0800
    Adding new script that scrapes public hubs on the RR for contact emails and places them on a genecats webpage, refs #18316
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    337d1c77df23fb3ea3f35b24400e9b5d731bd4c4 Mon Nov 28 09:55:33 2016 -0800
    v342 preview2 refs #18399

• lines changed: 9525
• files changed: 261