All File Changes

v369_preview2 to v369_base (2018-07-23 to 2018-07-30) v369

• confs/hgwbeta-public.hg.conf
  • lines changed 16, context: html, text, full: html, text
    dc3ed2a6e75dbf6e78411ebd971e292d7eb5c54d Sun Jul 29 01:11:36 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 187, context: html, text, full: html, text
    dc3ed2a6e75dbf6e78411ebd971e292d7eb5c54d Sun Jul 29 01:11:36 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 4, context: html, text, full: html, text
    5aeeb074c99503d22fbc6360c35c9614432f02e8 Tue Jul 24 19:53:25 2018 -0700
    refs# #21511. fixes problem with null==n/a and also an difference in handling groupId=0 between new code and old code.
• src/hg/hgTracks/bedTrack.c
  • lines changed 8, context: html, text, full: html, text
    5847cd8496ad3bc5783f9f6eb03f97c7ff3699a1 Tue Jul 24 15:30:33 2018 -0700
    fix problems with filtering on beds with less than 9 fields, and work around brain damaged cart variables that different based on the storage class of a bigBed field ... argh!
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 30, context: html, text, full: html, text
    5847cd8496ad3bc5783f9f6eb03f97c7ff3699a1 Tue Jul 24 15:30:33 2018 -0700
    fix problems with filtering on beds with less than 9 fields, and work around brain damaged cart variables that different based on the storage class of a bigBed field ... argh!
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    e4f5f425fdbe2461959a971726cdd0d40fc1495a Tue Jul 24 07:59:17 2018 -0700
    Adding View sequences keyboard shortcut, refs #21777
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    c63d99f6d729517271a0813a8e52f32b18812943 Mon Jul 23 14:56:17 2018 -0700
    Fixes #21801 a bug reported by a user, caused by not freeing the results set early enough.
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 14, context: html, text, full: html, text
    bdf3d9eabb14427335916b677dbf2bb2f145af9a Mon Jul 23 16:43:14 2018 -0700
    Adding settings gbdbLoc1 and forceTwoBit to suggested .hg.conf contents in mysql.html for utilities that need to access /gbdb and retrieve genomic sequence.
• src/hg/htdocs/training/index.html
  • lines changed 52, context: html, text, full: html, text
    362ed5df06cd7bb621f76ca129a29560b9774b28 Fri Jul 27 10:55:58 2018 -0700
    remove NHGRI, Novartis, Jax Lab workshops. add UNC, Duke, NIEHS
• src/hg/inc/hui.h
  • lines changed 9, context: html, text, full: html, text
    5847cd8496ad3bc5783f9f6eb03f97c7ff3699a1 Tue Jul 24 15:30:33 2018 -0700
    fix problems with filtering on beds with less than 9 fields, and work around brain damaged cart variables that different based on the storage class of a bigBed field ... argh!
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    2e6c47ae43ce4a804b3e3b6934036635a8e776cc Mon Jul 30 10:10:54 2018 -0700
    New version number v369
• src/hg/lib/annoStreamDb.c
  • lines changed 25, context: html, text, full: html, text
    c60ed6e679740c931f15ad7c7f86fa542dcf9b2c Wed Jul 25 16:26:56 2018 -0700
    Revert "Added new config parameters rightJoinDtf and rightJoinMainField to give the option of limiting rows to those that join with some other table. The motivation for this is wanting to get only the rows of ncbiRefSeqPsl that join with ncbiRefSeqCurated." This reverts commit 869708731727a455813ab88e67d46be978ab77b0.
• src/hg/lib/annoStreamDbPslPlus.c
  • lines changed 3, context: html, text, full: html, text
    13dddf36dc0f43a27a792519213d87939b51d99c Wed Jul 25 16:23:50 2018 -0700
    Revert "Use the new annoStreamDb params rightJoinDtf and rightJoinMainField to restrict ncbiRefSeqPsl rows to only those that appear in the selected genePred table (e.g. ncbiRefSeqCurated)." This reverts commit dd285f81141e45dabf1caf0f90723810f2c6f8a1.
  • lines changed 17, context: html, text, full: html, text
    61cf5e21f11e752e855b40094d72c0348687c27b Wed Jul 25 16:58:53 2018 -0700
    Instead of a SQL join to restrict ncbiRefSeqPsl rows to ncbiRefSeqCurated or Predicted subset, use an ID hash because when a transcript has multiple placements on main and _alt chroms, the join was producing redundant results. refs #21770
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    5847cd8496ad3bc5783f9f6eb03f97c7ff3699a1 Tue Jul 24 15:30:33 2018 -0700
    fix problems with filtering on beds with less than 9 fields, and work around brain damaged cart variables that different based on the storage class of a bigBed field ... argh!
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 9, context: html, text, full: html, text
    523c3bcbf230bbebe25528e3ed1229288d8a8c61 Fri Jul 27 14:07:41 2018 -0700
    Fixing up track usage script to account for new apache log format, refs #21785
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 3, context: html, text, full: html, text
    518868bf6330092429609ef7d57aa53619ed9fe1 Wed Jul 25 11:22:06 2018 -0700
    more stuff to ignore
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    8e07d64c21aff216b7b30038224bc4b361a2dec3 Tue Jul 24 12:36:31 2018 -0700
    all.joiner fixes for ensGene v92, refs #21421
• src/hg/makeDb/trackDb/mouse/igtc.html
  • lines changed 1, context: html, text, full: html, text
    39f54ed9477eaa81418fb3ee18590f1f8ba9aa62 Fri Jul 27 08:19:14 2018 -0700
    Updating redirected links for mm8, uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm8/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    39f54ed9477eaa81418fb3ee18590f1f8ba9aa62 Fri Jul 27 08:19:14 2018 -0700
    Updating redirected links for mm8, uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 1, context: html, text, full: html, text
    39f54ed9477eaa81418fb3ee18590f1f8ba9aa62 Fri Jul 27 08:19:14 2018 -0700
    Updating redirected links for mm8, uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/pig/susScr2/gold.html
  • lines changed 1, context: html, text, full: html, text
    ed7b43c69e4777fdc0a46b54c958f04cdd90f985 Thu Jul 26 08:20:08 2018 -0700
    Updating a redirected link for susScr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/gap.html
  • lines changed 1, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/gold.html
  • lines changed 1, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
  • lines changed 3, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/sangerGene.html
  • lines changed 1, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/sangerPseudoGene.html
  • lines changed 1, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/sangerRnaGene.html
  • lines changed 1, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
  • lines changed 2, context: html, text, full: html, text
    234ee39b543a2e3cfe5fbbf304aade947dd1135c Wed Jul 25 08:52:43 2018 -0700
    Updating redirected links found for ce4, uiLinks cronjob.
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 20, context: html, text, full: html, text
    01aa1907832f74960290312092d1d5ab3fbf24f0 Mon Jul 30 09:34:50 2018 -0700
    updating clinvar colors refs #21810
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    2e6c47ae43ce4a804b3e3b6934036635a8e776cc Mon Jul 30 10:10:54 2018 -0700
    New version number v369
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    886394b3c47b10e0edf10af545eb1240e1401cb0 Mon Jul 30 10:10:07 2018 -0700
    v369 final build, refs #21768

• lines changed: 431
• files changed: 33