All File Changes

v375_base to v376_preview (2018-12-10 to 2018-12-17) v376

• confs/hgwbeta.hg.conf
  • lines changed 2, context: html, text, full: html, text
    78056116458d6016e206292717273b1adc318570 Sun Dec 16 01:11:34 2018 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    78056116458d6016e206292717273b1adc318570 Sun Dec 16 01:11:34 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/altSplice/altSplice/orthoSplice.c
  • lines changed 2, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/cartReset/cartReset.c
  • lines changed 3, context: html, text, full: html, text
    cf7bc66b112f6a96139222a17b1ae2211f8031f3 Fri Dec 7 19:52:20 2018 -0800
    cartReset as too permissive allowing Open Redirect problems. Reported by Anthony. refs #22596
• src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
  • lines changed 4, context: html, text, full: html, text
    7b3995bc4b3b79eedd919332f0955fc16fe6354f Wed Dec 12 10:30:09 2018 -0800
    Creating a cdwCurrentUser function that is used by multiple applications rather than them each having their own method for getting current user. This fixes some problems with some of the applications not authenticating right.
• src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
  • lines changed 15, context: html, text, full: html, text
    7b3995bc4b3b79eedd919332f0955fc16fe6354f Wed Dec 12 10:30:09 2018 -0800
    Creating a cdwCurrentUser function that is used by multiple applications rather than them each having their own method for getting current user. This fixes some problems with some of the applications not authenticating right.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 15, context: html, text, full: html, text
    7b3995bc4b3b79eedd919332f0955fc16fe6354f Wed Dec 12 10:30:09 2018 -0800
    Creating a cdwCurrentUser function that is used by multiple applications rather than them each having their own method for getting current user. This fixes some problems with some of the applications not authenticating right.
  • lines changed 2, context: html, text, full: html, text
    df8e4bfad00a077691523131219c2d2aa90fbfaf Wed Dec 12 10:48:00 2018 -0800
    Oops, missed one conversion to library routine, and in the most visible place. setCdwUser changed to a library function now in cdwWebBrowse.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 1, context: html, text, full: html, text
    df8e4bfad00a077691523131219c2d2aa90fbfaf Wed Dec 12 10:48:00 2018 -0800
    Oops, missed one conversion to library routine, and in the most visible place. setCdwUser changed to a library function now in cdwWebBrowse.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    7b3995bc4b3b79eedd919332f0955fc16fe6354f Wed Dec 12 10:30:09 2018 -0800
    Creating a cdwCurrentUser function that is used by multiple applications rather than them each having their own method for getting current user. This fixes some problems with some of the applications not authenticating right.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 17, context: html, text, full: html, text
    7b3995bc4b3b79eedd919332f0955fc16fe6354f Wed Dec 12 10:30:09 2018 -0800
    Creating a cdwCurrentUser function that is used by multiple applications rather than them each having their own method for getting current user. This fixes some problems with some of the applications not authenticating right.
• src/hg/das/das.c
  • lines changed 2, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/featureBits/featureBits.c
  • lines changed 8, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgGene/altSplice.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgGene/hgGene.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgGenome/wiggle.c
  • lines changed 9, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgTables/wiggle.c
  • lines changed 11, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 2, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgTracks/rmskTrack.c
  • lines changed 2, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/dbRIP.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/hgc.c
  • lines changed 153, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
  • lines changed 4, context: html, text, full: html, text
    09d617c6c75f512a0952d6fde7f39793815377f2 Thu Dec 13 13:18:00 2018 -0800
    Add support for encode3/4 TFBS clusters. refs #21139
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    09d617c6c75f512a0952d6fde7f39793815377f2 Thu Dec 13 13:18:00 2018 -0800
    Add support for encode3/4 TFBS clusters. refs #21139
• src/hg/hgc/interactClick.c
  • lines changed 1, context: html, text, full: html, text
    a0ad0a9802dd731ab2ec778cfae5eff8ef2edc55 Wed Dec 12 15:45:33 2018 -0800
    Fix url generation issue, found by Simon Fishelivich (Weizmann Institute).
• src/hg/hgc/lowelab.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/peakClusters.c
  • lines changed 35, context: html, text, full: html, text
    09d617c6c75f512a0952d6fde7f39793815377f2 Thu Dec 13 13:18:00 2018 -0800
    Add support for encode3/4 TFBS clusters. refs #21139
• src/hg/hgc/regMotif.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/retroClick.c
  • lines changed 6, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/rmskJoinedClick.c
  • lines changed 8, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/hgc/wiggleClick.c
  • lines changed 4, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 7, context: html, text, full: html, text
    1e172503150781b450a389abbb3a3526bb492f11 Fri Dec 14 16:59:10 2018 -0800
    Adding additional info to 2bit format description ref #20843
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 7, context: html, text, full: html, text
    76c89d63104f23191054ee1ba970ec361316ae91 Fri Dec 14 18:07:16 2018 +0100
    trying to direct users away from gbibs if they have no human data, refs #22645
  • lines changed 3, context: html, text, full: html, text
    3c3a7d8052fdc29e6c9590ef2d712a554b25f2e0 Fri Dec 14 09:56:22 2018 -0800
    Making sure users are aware of all options on GBiB page ref#22646
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    4bf875ab60f4143147f093a9a7a680774405abed Wed Dec 12 13:15:55 2018 -0800
    Improving visibility when searching for help with trix file ref#21506
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 1, context: html, text, full: html, text
    4bf875ab60f4143147f093a9a7a680774405abed Wed Dec 12 13:15:55 2018 -0800
    Improving visibility when searching for help with trix file ref#21506
• src/hg/htdocs/images/phylo/ce11_135way.png
  • lines changed 0, context: html, text, full: html, text
    3cd24da966ff1bd7b2056dc22d8e49546b85a554 Mon Dec 10 10:07:07 2018 -0800
    phylo tree for ce11 135-way refs #22599
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    971b0c6c08b7b5cb584c6341c706bdf1a6eaa953 Mon Dec 10 10:35:23 2018 -0800
    adding link to gladstone. adding singapore to long-range schedule
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/lib/annoStreamDb.c
  • lines changed 1, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/lib/chainNetDbLoad.c
  • lines changed 2, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/lib/hAnno.c
  • lines changed 3, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/lib/hdb.c
  • lines changed 12, context: html, text, full: html, text
    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    ff6bb807522a2d8d7976f1f272fe246cec83293b Wed Dec 12 14:00:01 2018 -0800
    take out ill considered code to turn off bigBed score filtering by default
• src/hg/lib/jksql.c
  • lines changed 4, context: html, text, full: html, text
    3247510dde097fab841ab57d3a1fb34fbff8d69e Fri Dec 7 19:51:05 2018 -0800
    Blank identifiers should not be allowed as parameters in SQL statements in unquoted %s format strings. refs #22596
  • lines changed 5, context: html, text, full: html, text
    83fcfc003aad68c20e56e546e75f79c63c7332d6 Fri Dec 14 12:36:43 2018 -0800
    Simple testing shows that this gets an error when just switching from one db to another. Although it is a nice idea, it could be a lot of work to be sure nowhere in the code is using the blank identifier. So it stays in for now.
• src/hg/makeDb/doc/ce11/ce11.135way.scientificName.nh
  • lines changed 135, context: html, text, full: html, text
    c4bc784cebbf4074de507ec3bf32154bcaedafc6 Sat Dec 15 16:07:23 2018 -0800
    record the 4d distance adjusted phylo trees refs #22599
• src/hg/makeDb/doc/ce11/ce11.135way.sequenceName.nh
  • lines changed 135, context: html, text, full: html, text
    c4bc784cebbf4074de507ec3bf32154bcaedafc6 Sat Dec 15 16:07:23 2018 -0800
    record the 4d distance adjusted phylo trees refs #22599
• src/hg/makeDb/doc/ce11/ce11.135way.taxId.nh
  • lines changed 135, context: html, text, full: html, text
    c4bc784cebbf4074de507ec3bf32154bcaedafc6 Sat Dec 15 16:07:23 2018 -0800
    record the 4d distance adjusted phylo trees refs #22599
• src/hg/makeDb/doc/ce11/multiz135way.txt
  • lines changed 2623, context: html, text, full: html, text
    8a1174e0a3b81f1538d200c80b8c2d50b90c0aeb Mon Dec 10 14:09:12 2018 -0800
    done through iRow annotation refs #22599
  • lines changed 476, context: html, text, full: html, text
    43cd1b612fb01fc85888df9c16a618a1b725699a Fri Dec 14 15:49:03 2018 -0800
    running phyloP refs #22599
  • lines changed 162, context: html, text, full: html, text
    192feaea8c95a262f46aad739936cdb4da1e012e Sat Dec 15 16:24:35 2018 -0800
    add the taxonomy procedures and finishing up with download construction refs #22599
• src/hg/makeDb/genbank/etc/copyDbDev.sh
  • lines changed 108, context: html, text, full: html, text
    6a28a72a46a9d6a05a0790e6190308935e39062e Thu Dec 13 11:16:10 2018 -0800
    tweak rn3 in genbank.conf, check in some new scripts that copy stuff from genbank-101 to hgwdev
• src/hg/makeDb/genbank/etc/copyMetaDev.sh
  • lines changed 1, context: html, text, full: html, text
    6a28a72a46a9d6a05a0790e6190308935e39062e Thu Dec 13 11:16:10 2018 -0800
    tweak rn3 in genbank.conf, check in some new scripts that copy stuff from genbank-101 to hgwdev
• src/hg/makeDb/genbank/etc/gbMetadataTablesReg.txt
  • lines changed 24, context: html, text, full: html, text
    6a28a72a46a9d6a05a0790e6190308935e39062e Thu Dec 13 11:16:10 2018 -0800
    tweak rn3 in genbank.conf, check in some new scripts that copy stuff from genbank-101 to hgwdev
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    6a28a72a46a9d6a05a0790e6190308935e39062e Thu Dec 13 11:16:10 2018 -0800
    tweak rn3 in genbank.conf, check in some new scripts that copy stuff from genbank-101 to hgwdev
• src/hg/makeDb/trackDb/bacteria/staAur2/description.html
  • lines changed 64, context: html, text, full: html, text
    16e228a41bf8b7506cee7a2fa155a54a6c17db9b Thu Dec 13 14:43:03 2018 -0800
    initial files from makeGenomeDb.pl refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/gap.html
  • lines changed 28, context: html, text, full: html, text
    16e228a41bf8b7506cee7a2fa155a54a6c17db9b Thu Dec 13 14:43:03 2018 -0800
    initial files from makeGenomeDb.pl refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/gold.html
  • lines changed 33, context: html, text, full: html, text
    16e228a41bf8b7506cee7a2fa155a54a6c17db9b Thu Dec 13 14:43:03 2018 -0800
    initial files from makeGenomeDb.pl refs #19937
• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    16e228a41bf8b7506cee7a2fa155a54a6c17db9b Thu Dec 13 14:43:03 2018 -0800
    initial files from makeGenomeDb.pl refs #19937
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    25d438880923505ec11c1a8ea5f3b67293a1f21b Thu Dec 13 14:50:53 2018 -0800
    add gold/assembly search rule refs #19937
• src/hg/makeDb/trackDb/marmoset/calJac1/gap.html
  • lines changed 3, context: html, text, full: html, text
    e972c8760f42ba84788c88d882581ceffeb54e0e Fri Dec 14 11:09:42 2018 -0800
    Updating redirected links for calJac1. Also removing a broken link to WUSTL, uiLinks cronjob.
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 4, context: html, text, full: html, text
    e972c8760f42ba84788c88d882581ceffeb54e0e Fri Dec 14 11:09:42 2018 -0800
    Updating redirected links for calJac1. Also removing a broken link to WUSTL, uiLinks cronjob.
• src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html
  • lines changed 2, context: html, text, full: html, text
    e972c8760f42ba84788c88d882581ceffeb54e0e Fri Dec 14 11:09:42 2018 -0800
    Updating redirected links for calJac1. Also removing a broken link to WUSTL, uiLinks cronjob.
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 5, context: html, text, full: html, text
    8c47c5b3c78c946e522188693eeb974b9c67612b Wed Dec 12 09:46:03 2018 -0800
    Updating redirected links for rn6, uiLinks cronjob.
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
  • lines changed 2, context: html, text, full: html, text
    8c47c5b3c78c946e522188693eeb974b9c67612b Wed Dec 12 09:46:03 2018 -0800
    Updating redirected links for rn6, uiLinks cronjob.
• src/hg/makeDb/trackDb/rat/sgpGene.html
  • lines changed 1, context: html, text, full: html, text
    8c47c5b3c78c946e522188693eeb974b9c67612b Wed Dec 12 09:46:03 2018 -0800
    Updating redirected links for rn6, uiLinks cronjob.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 8, context: html, text, full: html, text
    b6898620988fedd37c5f627c4570002d2580c2f8 Sat Dec 15 17:28:49 2018 -0800
    adding the sGroups for the ce11 135-way refs #22599
• src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.html
  • lines changed 172, context: html, text, full: html, text
    5bc6c34e4bcaaafc8a5113734658659ad3af88eb Fri Dec 14 12:53:52 2018 -0800
    adding html page for this composite refs #22599
• src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.ra
  • lines changed 1330, context: html, text, full: html, text
    d74188df6210bb2cf73bfb6bff3af47ee5b2bfa5 Fri Dec 14 12:41:05 2018 -0800
    composite track for all chain net tracks refs #22599
  • lines changed 1, context: html, text, full: html, text
    fcdd3425e1062d3808a1ccf85e24609591460b38 Fri Dec 14 12:46:05 2018 -0800
    remove the .ordered from the labels refs #22599
  • lines changed 1, context: html, text, full: html, text
    5bc6c34e4bcaaafc8a5113734658659ad3af88eb Fri Dec 14 12:53:52 2018 -0800
    adding html page for this composite refs #22599
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
  • lines changed 1106, context: html, text, full: html, text
    544ac417e26ac22f657752566cea925f54f70a2b Sat Dec 15 17:26:06 2018 -0800
    now correctly 119 nematodes, flatworms and ci3 with description page table refs #22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra
  • lines changed 113, context: html, text, full: html, text
    51506aea54e26f8a2837e35f91b4656b6d8601fd Fri Dec 14 13:40:52 2018 -0800
    first look at 135-way multiz refs #22599
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    544ac417e26ac22f657752566cea925f54f70a2b Sat Dec 15 17:26:06 2018 -0800
    now correctly 119 nematodes, flatworms and ci3 with description page table refs #22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    d74188df6210bb2cf73bfb6bff3af47ee5b2bfa5 Fri Dec 14 12:41:05 2018 -0800
    composite track for all chain net tracks refs #22599
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    51506aea54e26f8a2837e35f91b4656b6d8601fd Fri Dec 14 13:40:52 2018 -0800
    first look at 135-way multiz refs #22599
• src/hg/makeDb/trackDb/zebrafish/danRer5/affyConsensusAndTargetZonWildType.html
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    d5cb0580b6fedec15d9e20ae756c8f2f643e5631 Mon Dec 10 10:11:23 2018 -0800
    Updating redirected links found by the uiLinks cronjob for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/ctgPos2.html
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    d5cb0580b6fedec15d9e20ae756c8f2f643e5631 Mon Dec 10 10:11:23 2018 -0800
    Updating redirected links found by the uiLinks cronjob for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/rmsk.html
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    d5cb0580b6fedec15d9e20ae756c8f2f643e5631 Mon Dec 10 10:11:23 2018 -0800
    Updating redirected links found by the uiLinks cronjob for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/vegaGene.html
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    d5cb0580b6fedec15d9e20ae756c8f2f643e5631 Mon Dec 10 10:11:23 2018 -0800
    Updating redirected links found by the uiLinks cronjob for danRer5, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer5/vegaPseudoGene.html
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    d5cb0580b6fedec15d9e20ae756c8f2f643e5631 Mon Dec 10 10:11:23 2018 -0800
    Updating redirected links found by the uiLinks cronjob for danRer5, no Redmine.
• src/hg/mouseStuff/knownVsBlat/knownVsBlat.c
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    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/orthoMap/orthoMap.c
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    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/ratStuff/mafGene/mafGene.c
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    e81403a315a24af601884b8a19e89bcecc92f267 Sat Dec 8 20:04:28 2018 -0800
    Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596.
• src/hg/utils/otto/omim/checkOmim.sh
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    9a9a800bf90c566a12770234f72caa1603b0997c Fri Dec 14 10:01:47 2018 -0800
    New omim otto script for backing up omimGene2 records that change chromosomes in a new build, no refs
• src/hg/utils/otto/omim/flagOmimGene.py
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    9a9a800bf90c566a12770234f72caa1603b0997c Fri Dec 14 10:01:47 2018 -0800
    New omim otto script for backing up omimGene2 records that change chromosomes in a new build, no refs
• src/hg/utils/otto/omim/makefile
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    9a9a800bf90c566a12770234f72caa1603b0997c Fri Dec 14 10:01:47 2018 -0800
    New omim otto script for backing up omimGene2 records that change chromosomes in a new build, no refs
• src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl
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    831c1e4a0ef39cfa4b16bd712558821797e0ef70 Fri Dec 14 11:36:34 2018 -0800
    now working with database lists that may not actually be databases refs #18874
• src/lib/udc.c
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    9df27d2ca511fbb3f2ab62154e3290d70758c957 Tue Dec 11 02:40:52 2018 -0800
    added comments based on discoveries made while looking at the code
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    5553caa35ac431614c6dbde7242f0495152c3058 Tue Dec 11 07:11:25 2018 -0800
    opps, checked in debugging test with comments. SORRY
• src/utils/qa/weeklybld/buildEnv.csh
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    ccb8cb2787ef3ff16d882267f11b27f726278798 Mon Dec 17 09:56:10 2018 -0800
    v376 preview1, refs #22531

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