All File Changes

v369_preview to v369_preview2 (2018-07-16 to 2018-07-23) v369

• confs/hgwbeta-public.hg.conf
  • lines changed 16, context: html, text, full: html, text
    a418bdda66692d67fe8406c90bc06d78fff553e2 Sun Jul 22 01:11:40 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 187, context: html, text, full: html, text
    a418bdda66692d67fe8406c90bc06d78fff553e2 Sun Jul 22 01:11:40 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/ameme/ameme.c
  • lines changed 1, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    0df12ec107fde773b7b1b6bcb78932051c5b5ed4 Tue Jul 17 17:42:53 2018 -0700
    oops need to also allow rows with allAccess > 0. fixes #21710.
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 20, context: html, text, full: html, text
    70df03b1c8cf41f219c9d14393dd939c52e280f3 Tue Jul 17 06:59:24 2018 -0700
    fixing cdwWebBrowse makefile, somehow this is a huge change for a small file. As per email from Galt/Hiram.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 1, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 12, context: html, text, full: html, text
    83b80a4c0e63a6f006c4b82d2c06702a5ed64793 Wed Jul 18 13:33:52 2018 -0700
    Adding 12 new tags.
• src/hg/hgCert/hgCert.c
  • lines changed 2, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/hgGene/hgGene.c
  • lines changed 13, context: html, text, full: html, text
    a2d849d0acd9e8921d1ff131d907ca867c858d11 Thu Jul 19 10:47:57 2018 -0700
    changes to support new new Gencode models in hgGene
• src/hg/hgGene/hgGene.h
  • lines changed 3, context: html, text, full: html, text
    a2d849d0acd9e8921d1ff131d907ca867c858d11 Thu Jul 19 10:47:57 2018 -0700
    changes to support new new Gencode models in hgGene
• src/hg/hgGene/synonym.c
  • lines changed 1, context: html, text, full: html, text
    a2d849d0acd9e8921d1ff131d907ca867c858d11 Thu Jul 19 10:47:57 2018 -0700
    changes to support new new Gencode models in hgGene
• src/hg/hgGenome/browseRegions.c
  • lines changed 2, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • lines changed 2, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 11, context: html, text, full: html, text
    045e182a27b1059a13c90c5a1ed9fdc8a31b18f2 Thu Jul 19 14:45:08 2018 -0700
    more changes to enable using Ensembl id as primary id in knownGene.
  • lines changed 1, context: html, text, full: html, text
    d9ed1a589b8ab2d03412919fc2e8461cb18d7765 Fri Jul 20 12:56:28 2018 -0700
    a few more Gencode2 changes
• src/hg/hgTracks/bigBedFilter.h
  • lines changed 23, context: html, text, full: html, text
    6791876ba30394c3aad18702708feb4bfb6ec761 Thu Jul 19 17:04:44 2018 -0700
    add bigBed numeric and filterBy filters
  • lines changed 1, context: html, text, full: html, text
    6e842bcc421f0c27a6d13ab23615102963c8010d Fri Jul 20 10:14:43 2018 -0700
    change the name of a bigBed filter function
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 164, context: html, text, full: html, text
    6791876ba30394c3aad18702708feb4bfb6ec761 Thu Jul 19 17:04:44 2018 -0700
    add bigBed numeric and filterBy filters
• src/hg/hgTracks/encode.c
  • lines changed 115, context: html, text, full: html, text
    6791876ba30394c3aad18702708feb4bfb6ec761 Thu Jul 19 17:04:44 2018 -0700
    add bigBed numeric and filterBy filters
  • lines changed 3, context: html, text, full: html, text
    fab970524dae1a360fed5951f1b69c8491cdc352 Fri Jul 20 10:01:47 2018 -0700
    make bigNarrowPeak support signalFilter on signalValue field. This means that arbitrary number filtering doesn't work on bigNarrowPeak
  • lines changed 4, context: html, text, full: html, text
    6e842bcc421f0c27a6d13ab23615102963c8010d Fri Jul 20 10:14:43 2018 -0700
    change the name of a bigBed filter function
• src/hg/hgTracks/simpleTracks.c
  • lines changed 39, context: html, text, full: html, text
    d9ed1a589b8ab2d03412919fc2e8461cb18d7765 Fri Jul 20 12:56:28 2018 -0700
    a few more Gencode2 changes
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    9693f2410fbc02d1db1c3294b6ae2896db4ef761 Tue Jul 17 09:02:47 2018 -0700
    Announcing DECIPHER SNVs track for hg19, refs #21104
  • lines changed 1, context: html, text, full: html, text
    f8a55d8cc723f0364c44dd1092342cac5713dbed Tue Jul 17 09:38:06 2018 -0700
    Updating announcment date for DECIPHER track, refs #21104
  • lines changed 1, context: html, text, full: html, text
    99f6d16a7ee7d998c4af9f8ed1002003f61de2a3 Tue Jul 17 11:08:45 2018 -0700
    Changing the last incorrect date for the DECIPHER announcment, refs #21104
  • lines changed 6, context: html, text, full: html, text
    675797890df1dad8e77216e89f0434079d20b014 Tue Jul 17 11:17:57 2018 -0700
    Adding bullet points to the DECIPHER announcement, refs #21104
• src/hg/htdocs/indexNews.html
  • lines changed 8, context: html, text, full: html, text
    9693f2410fbc02d1db1c3294b6ae2896db4ef761 Tue Jul 17 09:02:47 2018 -0700
    Announcing DECIPHER SNVs track for hg19, refs #21104
  • lines changed 2, context: html, text, full: html, text
    f8a55d8cc723f0364c44dd1092342cac5713dbed Tue Jul 17 09:38:06 2018 -0700
    Updating announcment date for DECIPHER track, refs #21104
• src/hg/lib/customFactory.c
  • lines changed 75, context: html, text, full: html, text
    0cbb3c5bec7a5745148e2e997f7882951232d330 Tue Jul 17 08:59:00 2018 -0700
    Improve error messages when a custom track chrom is not valid, and when a specified type expects some BED fields but there's a problem with one of them. refs #18853 notes 24-26
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    6791876ba30394c3aad18702708feb4bfb6ec761 Thu Jul 19 17:04:44 2018 -0700
    add bigBed numeric and filterBy filters
• src/hg/lib/kgColor.sql
  • lines changed 1, context: html, text, full: html, text
    02b0a3f5b948147bfa8781fc7366f4668bae5845 Wed Jul 18 10:50:31 2018 -0700
    changes to SQL files to support new ucsc genes with ENST identifiers. Changes are backwards compatible.
• src/hg/lib/knownIsoforms.sql
  • lines changed 2, context: html, text, full: html, text
    02b0a3f5b948147bfa8781fc7366f4668bae5845 Wed Jul 18 10:50:31 2018 -0700
    changes to SQL files to support new ucsc genes with ENST identifiers. Changes are backwards compatible.
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh
  • lines changed 951, context: html, text, full: html, text
    a2bcc20474a994fa100474209bebd017255d10c7 Wed Jul 18 10:41:49 2018 -0700
    changes to makeGencodeKnownGene to use the Ensembl id as the primary id instead of the uc id. Doc for building the proof of concept on grcHhh38
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh
  • lines changed 1, context: html, text, full: html, text
    7aa2c736ad6d5be50449b4765527e15a091812ee Wed Jul 18 10:46:26 2018 -0700
    needed to load fish blastTabs
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 34, context: html, text, full: html, text
    a2bcc20474a994fa100474209bebd017255d10c7 Wed Jul 18 10:41:49 2018 -0700
    changes to makeGencodeKnownGene to use the Ensembl id as the primary id instead of the uc id. Doc for building the proof of concept on grcHhh38
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 20, context: html, text, full: html, text
    440661ca4a47efb4eea5d186d03e121ba933e106 Tue Jul 17 00:51:54 2018 -0700
    improving crispr track docs, as per email from Bob to browser-staff
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 2, context: html, text, full: html, text
    26c00663e50d90fc5f6d8b75e9566055f09ab240 Fri Jul 20 07:58:59 2018 -0700
    Updating a broken link for vicPac2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/crispr.html
  • lines changed 61, context: html, text, full: html, text
    440661ca4a47efb4eea5d186d03e121ba933e106 Tue Jul 17 00:51:54 2018 -0700
    improving crispr track docs, as per email from Bob to browser-staff
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 1, context: html, text, full: html, text
    02ba35d091ad3d013197e7e9fdae3a1563e2d1af Fri Jul 20 08:07:31 2018 -0700
    Changing patch tracks to default on visibility after feedback from Jim, refs #21778
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.ra
  • lines changed 1, context: html, text, full: html, text
    02ba35d091ad3d013197e7e9fdae3a1563e2d1af Fri Jul 20 08:07:31 2018 -0700
    Changing patch tracks to default on visibility after feedback from Jim, refs #21778
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    58dd1fcbcbc42068e4a2501c662fb69aad68d4a8 Mon Jul 16 15:55:19 2018 -0700
    Removing alpha,beta release tags to release the DECIPHER SNVs to the RR, refs #21104
  • lines changed 1, context: html, text, full: html, text
    50ad79caf669a566f169085444bd69bed26736b7 Tue Jul 17 12:19:10 2018 -0700
    Adding pennantIcon for the new decipher track for hg19, refs #21104
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
  • lines changed 1, context: html, text, full: html, text
    02ba35d091ad3d013197e7e9fdae3a1563e2d1af Fri Jul 20 08:07:31 2018 -0700
    Changing patch tracks to default on visibility after feedback from Jim, refs #21778
• src/hg/mouseStuff/makefile
  • lines changed 2, context: html, text, full: html, text
    d7e32f57cdacaaffa1c5d807b779cc5e41313c77 Tue Jul 17 14:07:52 2018 -0700
    Moving chainBridge into the userApps build, because it is used by doSameSpeciesLiftOver.pl. Thanks Jonathan.
• src/hg/phyloPng/phyloPng.c
  • lines changed 3, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/sageVisCGI/sageVisCGI.c
  • lines changed 1, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/useCount/useCount.c
  • lines changed 2, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 1, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/tabFile/tabToHtml/tabToHtml.c
  • lines changed 4, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/tagStorm/tagStormToHtml/tagStormToHtml.c
  • lines changed 4, context: html, text, full: html, text
    b04a39a028980ea32b2ac62950bdff0a67de16d0 Wed Jul 18 14:48:19 2018 -0700
    Add missing CSP header to pages not handled automatically by library functions. refs #21729.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    d71fe609d0d7e701cee3bdda9735fa5674688931 Mon Jul 23 10:04:05 2018 -0700
    v369 preview2, refs #21768

• lines changed: 1822
• files changed: 51