All File Changes

v364_preview to v364_preview2 (2018-04-02 to 2018-04-09) v364

• src/hg/hgTables/vcf.c
  • lines changed 15, context: html, text, full: html, text
    5780fed8b94b69b4b22e2d389112e4d34d51368f Fri Apr 6 09:31:50 2018 -0700
    Fixing lack of NULL checks on result of vcfFileName. Symptom was crash on tgpPhase3 which has no file for chrM when doing genome-wide query. refs #21218
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 34, context: html, text, full: html, text
    28a3595deb73b7dfab305a37512b413786b3289a Tue Apr 3 08:50:50 2018 -0700
    Staging ncbi refseq announcement, leaving commented out just in case I can't get everything finished today
  • lines changed 14, context: html, text, full: html, text
    133f242044d8db326365c9f45cc7b9caacc6bb15 Tue Apr 3 10:12:49 2018 -0700
    Removing a redundant 'below' and replacing a > with the HTML entity for the hgCollection announcement. refs #21066
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    0f710dfdb9681e83583bc4282ff20a4eb88aff2e Tue Apr 3 15:43:28 2018 -0700
    Final draft of ncbi refseq for model orgs announcement
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    4c848d50d0299646c5bc1b2335afe88c936af3e1 Wed Apr 4 08:39:53 2018 -0700
    Getting the right dates on the ncbi refseq announcement, refs #20215
• src/hg/htdocs/indexNews.html
  • lines changed 22, context: html, text, full: html, text
    133f242044d8db326365c9f45cc7b9caacc6bb15 Tue Apr 3 10:12:49 2018 -0700
    Removing a redundant 'below' and replacing a > with the HTML entity for the hgCollection announcement. refs #21066
  • lines changed 6, context: html, text, full: html, text
    4c848d50d0299646c5bc1b2335afe88c936af3e1 Wed Apr 4 08:39:53 2018 -0700
    Getting the right dates on the ncbi refseq announcement, refs #20215
• src/hg/lib/annoGratorGpVar.c
  • lines changed 3, context: html, text, full: html, text
    74bbd952e4cb5fef80030a534ec6b714bc561adb Wed Apr 4 14:38:30 2018 -0700
    Use hasAltAllele to determine what soTerm to use in aggvGenelessRow. Thanks Jonathan! refs #21204
• src/hg/lib/hui.c
  • lines changed 11, context: html, text, full: html, text
    7cdc9f476f19a65d36e015aadf41be9634e15920 Wed Apr 4 11:45:43 2018 -0700
    For genePred tracks, limit baseColorDrawOpt to genomicCodons if it's set to a fancy PSL option because the setting comes from a view that includes a PSL track. refs #21194
• src/hg/makeDb/trackDb/blastHg17KG.html
  • lines changed 2, context: html, text, full: html, text
    ac8f2dfe1d663602daa41a0f63453501bf527f72 Fri Apr 6 09:46:47 2018 -0700
    Updating redirected links for monDom1. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/chainDroAna2.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/chainDroEre1.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/chainDroYak2.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevSignal.html
  • lines changed 6, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevTransfrags.html
  • lines changed 6, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/bacEndPairs.html
  • lines changed 7, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseNoncoding.html
  • lines changed 2, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 6, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/nscanPasaGene.html
  • lines changed 4, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm3/phastConsElements15way.html
  • lines changed 5, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/drosophila/netDroAna2.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/netDroEre1.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/drosophila/netDroYak2.html
  • lines changed 3, context: html, text, full: html, text
    adffb86dcfc7e995d7f41593c67c9b0be3812a93 Thu Apr 5 09:11:02 2018 -0700
    Updating links for dm3. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 6, context: html, text, full: html, text
    3d66f7b123f12681fb75b661cb0656fd2000317e Wed Apr 4 10:50:17 2018 -0700
    turning on some net tracks for default on refs #21123
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 4, context: html, text, full: html, text
    3d66f7b123f12681fb75b661cb0656fd2000317e Wed Apr 4 10:50:17 2018 -0700
    turning on some net tracks for default on refs #21123
  • lines changed 1, context: html, text, full: html, text
    6d75732b70497a6968cc7c5e54a8910ba95c0220 Wed Apr 4 15:12:30 2018 -0700
    Turning panTro4 and danRer7 nets on by default for hg19
  • lines changed 2, context: html, text, full: html, text
    7e87fd20ab547350579d7385a775bb182665eb17 Mon Apr 9 09:47:02 2018 -0700
    display o_Organism instead of o_db for otoGar3 refs #21123
  • lines changed 6, context: html, text, full: html, text
    60b44477fff98ab5c70ca8c3f8435e253f4c57fd Mon Apr 9 09:48:28 2018 -0700
    display o_Organism instead of o_db for otoGar3 and panPan2 refs #21123
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 7, context: html, text, full: html, text
    3d66f7b123f12681fb75b661cb0656fd2000317e Wed Apr 4 10:50:17 2018 -0700
    turning on some net tracks for default on refs #21123
  • lines changed 1, context: html, text, full: html, text
    6d75732b70497a6968cc7c5e54a8910ba95c0220 Wed Apr 4 15:12:30 2018 -0700
    Turning panTro4 and danRer7 nets on by default for hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8207339c76fee70f8c6e819637af7c446c26897a Tue Apr 3 15:08:59 2018 -0700
    Staging ncbi refseq track on hg19, refs #20215
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    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 6, context: html, text, full: html, text
    52b80499f34651203ec470248bb73e0cfa0ba754 Fri Apr 6 11:00:54 2018 -0700
    add links to genomewiki info pages refs #21236
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    703475e4ef944947cd13512c1e98585c76e2d0e3 Tue Apr 3 10:24:58 2018 -0700
    Fixing broken links for oryLat2, no Redmine.
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
  • lines changed 5, context: html, text, full: html, text
    703475e4ef944947cd13512c1e98585c76e2d0e3 Tue Apr 3 10:24:58 2018 -0700
    Fixing broken links for oryLat2, no Redmine.
• src/hg/makeDb/trackDb/mostConserved.html
  • lines changed 5, context: html, text, full: html, text
    ac8f2dfe1d663602daa41a0f63453501bf527f72 Fri Apr 6 09:46:47 2018 -0700
    Updating redirected links for monDom1. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/opossum/multiz5way.html
  • lines changed 7, context: html, text, full: html, text
    ac8f2dfe1d663602daa41a0f63453501bf527f72 Fri Apr 6 09:46:47 2018 -0700
    Updating redirected links for monDom1. uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/blastHg18KG.html
  • lines changed 2, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/mrna.html
  • lines changed 1, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
  • lines changed 2, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 9, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/sgdGene.html
  • lines changed 2, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/sgdOther.html
  • lines changed 2, context: html, text, full: html, text
    0c3ab18eb0ec4dc55343cb219c061cfef77e9ccc Tue Apr 3 10:40:30 2018 -0700
    Fixing broken links for sacCer3, no Redmine.
• src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/worm/blastCe4SG.html
  • lines changed 1, context: html, text, full: html, text
    4d4de0e3576d9a8da1c5c5f3b2e3ca5232d0f995 Wed Apr 4 08:31:57 2018 -0700
    Updating redirected links for caePb1, no Redmine.
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/worm/chainCb3.html
  • lines changed 1, context: html, text, full: html, text
    4d4de0e3576d9a8da1c5c5f3b2e3ca5232d0f995 Wed Apr 4 08:31:57 2018 -0700
    Updating redirected links for caePb1, no Redmine.
• src/hg/makeDb/trackDb/worm/chainCe4.html
  • lines changed 2, context: html, text, full: html, text
    4d4de0e3576d9a8da1c5c5f3b2e3ca5232d0f995 Wed Apr 4 08:31:57 2018 -0700
    Updating redirected links for caePb1, no Redmine.
• src/hg/makeDb/trackDb/worm/netCb3.html
  • lines changed 1, context: html, text, full: html, text
    4d4de0e3576d9a8da1c5c5f3b2e3ca5232d0f995 Wed Apr 4 08:31:57 2018 -0700
    Updating redirected links for caePb1, no Redmine.
• src/hg/makeDb/trackDb/worm/netCe4.html
  • lines changed 2, context: html, text, full: html, text
    4d4de0e3576d9a8da1c5c5f3b2e3ca5232d0f995 Wed Apr 4 08:31:57 2018 -0700
    Updating redirected links for caePb1, no Redmine.
• src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
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    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    f8f12927758a952128b720b58ab47d83c964b5fe Tue Apr 3 15:24:03 2018 -0700
    Staging ncbi refseq genes track on public, refs #20215
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 67, context: html, text, full: html, text
    cd941de60fc40d88860897421f4fe4b80a395e6d Thu Apr 5 13:52:33 2018 -0700
    adding trackHub option to construct big* files for trackHub use refs #18874
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 45, context: html, text, full: html, text
    cd941de60fc40d88860897421f4fe4b80a395e6d Thu Apr 5 13:52:33 2018 -0700
    adding trackHub option to construct big* files for trackHub use refs #18874
  • lines changed 20, context: html, text, full: html, text
    1654fa4ef72989a830f722119ceff5be180ea8e9 Thu Apr 5 14:08:51 2018 -0700
    add cleanup step refs #18874
• src/hg/utils/automation/ucscAltAgp
  • lines changed 40, context: html, text, full: html, text
    1bf3b778f91427db8eee4c35397ada236a9a2b35 Fri Apr 6 13:35:22 2018 -0700
    Remove zebrafish-specific pattern so this can be used on other species; use python instead of shell commands to extract information from inputFile, find alt AGP files, and build altChrmList.
• src/userApps/fetchKentSource.sh
  • lines changed 5, context: html, text, full: html, text
    0548004ba6d14450ed2431a2e134c5c3fa882fd3 Thu Apr 5 16:31:59 2018 -0700
    change cse address to soe address refs #18874
• src/utils/qa/weeklybld/buildEnv.csh
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    592108b57d0f4a843640a4de30f80f353258065f Mon Apr 9 10:23:18 2018 -0700
    v364 preview2 refs #21221

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• files changed: 64