All File Changes

v366_preview to v366_preview2 (2018-05-14 to 2018-05-21) v366

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 117, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 140, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
  • lines changed 1, context: html, text, full: html, text
    b149298b6c13f49e0c240d7ae624f7c63fa6e4c8 Mon May 14 15:39:17 2018 -0700
    oops sql typo
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
  • lines changed 1, context: html, text, full: html, text
    b06b83258db575bfc151c50e794e4e40ee801c6d Thu May 17 17:35:12 2018 -0700
    oops cdwGetMetadataAsFile needs to be in for cgi support
• src/hg/cirm/cdw/oneShot/facetFieldTest/facetFieldTest.c
  • lines changed 13, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    b21eddfdc8de1a35c2b42382d4068ac35aca5e62 Fri May 18 10:39:25 2018 -0700
    Adding button for CESCG publications page, refs #21475
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    ec3e0ff0e32f2ed7dcbb88bd1b59019569cc9fa3 Mon May 14 19:45:45 2018 -0700
    special case rmskJoined tracks when in full mode for height calculation and clean up spaces at the end of lines refs #21454
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    c6103b8638b54e6e2698dc041647464b7294b838 Wed May 16 10:45:03 2018 -0700
    Fixing a potential long/endless loop issue, refs #21462
  • lines changed 116, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/hgc/hgc.c
  • lines changed 126, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 2, context: html, text, full: html, text
    92488162ded9601a1e38aac9ace866bee53b127e Wed May 16 11:34:15 2018 -0700
    take out NOTE that searchIndex doesn't work in composites.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    92488162ded9601a1e38aac9ace866bee53b127e Wed May 16 11:34:15 2018 -0700
    take out NOTE that searchIndex doesn't work in composites.
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 1, context: html, text, full: html, text
    c8cb107bb02a1d7ef445afc09a56880bf9973352 Tue May 15 14:23:00 2018 -0700
    change instance of "New Collection" to "Add Collection"
• src/hg/htdocs/training/index.html
  • lines changed 41, context: html, text, full: html, text
    89ec0d5f011c156f15b93b12c6e431b27f21f646 Tue May 15 11:28:35 2018 -0700
    dropped rotterdam workshop. added JAX course. added some links for later
• src/hg/inc/facetField.h
  • lines changed 26, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/inc/tablesTables.h
  • lines changed 4, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/lib/bigBedFind.c
  • lines changed 3, context: html, text, full: html, text
    d7e3a288583acdcba9bc31168a2eca854f7450c7 Wed May 16 11:04:02 2018 -0700
    fix RM#21101 (searchIndex in composite)
• src/hg/lib/decipherRaw.sql
  • lines changed 3, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/lib/decipherSnvsRaw.sql
  • lines changed 17, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/lib/facetField.c
  • lines changed 257, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    025bb848de51cd3dc938c0b691909401aac4022f Wed May 16 11:49:11 2018 -0700
    fix RM#21172 (show schema on custom tracks on assembly hubs)
• src/hg/lib/tablesTables.c
  • lines changed 228, context: html, text, full: html, text
    a20e4c95a5fde014130e2d04d61ce814cbe5413b Mon May 14 15:25:47 2018 -0700
    CIRM facetedSearch
• src/hg/makeDb/doc/mm10.txt
  • lines changed 61, context: html, text, full: html, text
    cef07350b5c47b0d02898bcbf789e47b8422b971 Tue May 15 10:03:45 2018 -0700
    Starting rmskJoined for mm10, refs #18273
  • lines changed 40, context: html, text, full: html, text
    1694c14eccabda8f635965265a61264edfc60a36 Wed May 16 09:01:08 2018 -0700
    fixing the broken crispr 10K track refs #19874
  • lines changed 8, context: html, text, full: html, text
    3cf410cd9bf140ee71d0a17b5fb6de8ecbf2eff8 Wed May 16 12:12:53 2018 -0700
    starting rmskJoined steps, refs #18273
  • lines changed 23, context: html, text, full: html, text
    5fbefb8182c60c214256795b118e01ab81b44081 Wed May 16 16:47:06 2018 -0700
    Finished rmskJoined update for mm10, refs #18273
• src/hg/makeDb/doc/ucscGenes/qa.mm10.ucscGenes17.sh
  • lines changed 134, context: html, text, full: html, text
    e42d776a3c3194647fb6044bb015be341fe66906 Tue May 15 11:12:59 2018 -0700
    add script of commands used to qa the ucsc gene models for mm10 version 17
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • lines changed 26, context: html, text, full: html, text
    19c33f8d93cdc9f07a8a82fe9edbc21e3aa07954 Thu May 17 18:18:22 2018 -0700
    fixed problem with sqlSafef no long working for ccds queries
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/makeDb/trackDb/apis/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    f45d1de9dacef7dc80b3b3d6d96b42e69656aed0 Thu May 17 10:14:36 2018 -0700
    Updating redirected links for apiMel1, uiLinks cronjob.
• src/hg/makeDb/trackDb/apis/rmsk.html
  • lines changed 3, context: html, text, full: html, text
    f45d1de9dacef7dc80b3b3d6d96b42e69656aed0 Thu May 17 10:14:36 2018 -0700
    Updating redirected links for apiMel1, uiLinks cronjob.
• src/hg/makeDb/trackDb/blastDm1FB.html
  • lines changed 1, context: html, text, full: html, text
    f45d1de9dacef7dc80b3b3d6d96b42e69656aed0 Thu May 17 10:14:36 2018 -0700
    Updating redirected links for apiMel1, uiLinks cronjob.
• src/hg/makeDb/trackDb/chainDm2.html
  • lines changed 2, context: html, text, full: html, text
    f45d1de9dacef7dc80b3b3d6d96b42e69656aed0 Thu May 17 10:14:36 2018 -0700
    Updating redirected links for apiMel1, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/est.html
  • lines changed 1, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 5, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/mrna.html
  • lines changed 1, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    e304108241cf461199448acbf6c98eaa4230a60f Wed May 16 09:11:51 2018 -0700
    Updating redirected and broken links for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 14, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 68, context: html, text, full: html, text
    409da45333fce7a2c26687a5663e0d69a16a9283 Wed May 16 19:54:59 2018 -0700
    Nearly forgot the html page, refs #18951
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    e5fb8ac0129286c4fa8985ef09e75e3c869a9fa8 Mon May 14 11:07:27 2018 -0700
    Adding the rest of the release tags to gnomad, refs #18951
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 8, context: html, text, full: html, text
    017f25a497b45c01989d56c4466e43954d4edc5f Tue May 15 08:47:52 2018 -0700
    Updating redirected links for anoCar2, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    6c51a5fe508bb2626d012c0bd2dfc1734ac09081 Mon May 14 13:31:38 2018 -0700
    Adding alpha and beta release tags to stage UCSC Genes v17 for mm10 on hgwbeta, refs #19786
  • lines changed 1, context: html, text, full: html, text
    91029f6760f1660c6e124bbe37048d2c6bed19d0 Fri May 18 14:59:21 2018 -0700
    Staging mm10's new UCSC Genes track for release, refs #19786
• src/hg/phyloPng/phyloPng.c
  • lines changed 2, context: html, text, full: html, text
    a31817fef0383e08ab35bea6004568fd8de1ab50 Thu May 17 10:51:13 2018 -0700
    Some typo fixes request by Ann, refs #17322
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    e94544af212fcdc8feaa80eba76f700fd2522f60 Wed May 16 15:20:25 2018 -0700
    Adding helpful utility for calculating maximum rowsize of mysql tables
• src/hg/utils/mysqlRowSizes.pl
  • lines changed 108, context: html, text, full: html, text
    e94544af212fcdc8feaa80eba76f700fd2522f60 Wed May 16 15:20:25 2018 -0700
    Adding helpful utility for calculating maximum rowsize of mysql tables
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 14, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
  • lines changed 1, context: html, text, full: html, text
    76755fa4e8f110f1641a1832d171ff7005b436d6 Thu May 17 10:00:44 2018 -0700
    Fixing chrM name clash in decipher build scripts, refs #21104
  • lines changed 1, context: html, text, full: html, text
    c5abf36107541af763593e3bc8c99298414c0767 Thu May 17 11:01:39 2018 -0700
    Using tawk instead of awk, refs #21104
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 10, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/utils/otto/decipher/decipher.tables
  • lines changed 2, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/utils/otto/decipher/login.perl
  • lines changed 5, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/hg/utils/otto/decipher/makefile
  • lines changed 1, context: html, text, full: html, text
    89ab8ae5fb747465c8f9c218c8556750033e2061 Wed May 16 20:02:03 2018 -0700
    DECIPHER CNVs track handles new format, also release of SNVs track, refs #21104
• src/parasol/makefile
  • lines changed 10, context: html, text, full: html, text
    33c8e4dcd12b3522f6584a43787d93a256341caf Sun May 20 19:16:46 2018 -0700
    correctly set DESTDIR MACHTYPE and BINDIR when they are set to nothing no redmine
• src/product/installer/browserSetup.sh
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    e3650e4385148e2d96e3e272925dfe2e094c9d84 Wed May 16 09:25:07 2018 -0700
    Fixing typos in mysql root password generation for gbic, found by Martin Marcher
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    3a2957d7f8098bdc5057ead99443c9ff156919b2 Mon May 21 10:00:38 2018 -0700
    v366 preview2 refs #21332

• lines changed: 1721
• files changed: 61