All File Changes

v428_preview to v428_preview2 (2022-02-28 to 2022-03-07) v428

• src/hg/cartReset/cartReset.c
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    d95aae72e5192d7f7172522f042c373868f55ec3 Thu Mar 3 09:21:05 2022 -0800
    Fixing cartReset destination redirect which should not allow quote marks, spaces, or empty strings which make the page go into an infinite loop. Reported by NetSparker scan.
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
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    b8fd0b0fa23324dcb600302cc2ce42e6a88d46e9 Wed Mar 2 18:33:03 2022 -0800
    Fixing sql injection bug with sqlSafeFrag. Reported by NetSparker scan.
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 2, context: html, text, full: html, text
    a8fe8b8abb36f00fab1e4b11c1c008990df4965c Sat Mar 5 17:23:16 2022 -0800
    add chromAliasSetup to hgIntegrator`
• src/hg/hgTables/usage.c
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    679ac7af00f7a9437fef0ebf1c93ed63861ba589 Wed Mar 2 06:03:28 2022 -0800
    changes after code review, refs #28975
• src/hg/hgTracks/barChartTrack.c
  • lines changed 28, context: html, text, full: html, text
    a981318c28445664c4fb9c6ef2b6918e2094da98 Fri Mar 4 14:38:29 2022 -0800
    Changes from code review. Also restore original bar width calculation as it makes barChartStretchToItem work better, refs #29021
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    a3f0ccd5b293748d18d565669907d1827a46c3be Wed Mar 2 16:00:07 2022 -0800
    take bigMaf out of the list of types we parallel load.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    8a31e0f33a6ae49ebd897a2df38b54ae4dbf62b7 Sat Mar 5 17:25:29 2022 -0800
    fix valgrind discovered bug in density coverage calculation
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    54256f85f370573466cad8249e55e6505eded45a Tue Mar 1 10:10:44 2022 -0800
    Fix missing chromAliasSetup in hgVai, refs #28956
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 6, context: html, text, full: html, text
    24c983f5d9b1a0f4792eae2e4c1c9725efee919d Tue Mar 1 16:56:08 2022 -0800
    Adding note about ref genome requirement refs #29017
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    547d66239f70b9636b33694ec29a8042e66e95aa Thu Mar 3 08:19:38 2022 -0800
    adding cdsStartStat docs, refs #29030
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    f3463c39dcd4e6f8aaff1f4142cf0101b567b435 Fri Mar 4 02:01:44 2022 -0800
    updating cdsStartStat docs, refs #29030
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 58, context: html, text, full: html, text
    5980d946ead37a1db3066b34ce972ba78ca62d0f Thu Mar 3 16:36:08 2022 -0800
    Adding a gene FAQ entry about non-coding and coding gene selection refs #29030
  • lines changed 4, context: html, text, full: html, text
    fc450d4031fd9494b3a5bd8ee0fbeba83905a61a Thu Mar 3 16:48:59 2022 -0800
    Edits to new coding/non-coding gene FAQ refs #29030
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    9861b0b8447a0433000fb3e35cf652b01d1672d1 Fri Mar 4 12:13:36 2022 -0800
    Incorporating MarkDs input on non-coding GENCODE, noting how lncRNA miRNA pseudogenes are not an unambiguous topic refs #29030
  • lines changed 39, context: html, text, full: html, text
    60ecb412e9bba9ed0a0665a45051fa63952c1035 Fri Mar 4 15:37:56 2022 -0800
    More MarkD input on non-coding GENCODE FAQ (just show lncRNAs) refs #29030
• src/hg/htdocs/covid19.html
  • lines changed 2, context: html, text, full: html, text
    b94971d0e99a26cf605713a3cfedde810bec62c0 Wed Mar 2 12:45:30 2022 -0800
    Adding acknowledgement of funding for refs #28949
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 3, context: html, text, full: html, text
    547d66239f70b9636b33694ec29a8042e66e95aa Thu Mar 3 08:19:38 2022 -0800
    adding cdsStartStat docs, refs #29030
  • lines changed 2, context: html, text, full: html, text
    f3463c39dcd4e6f8aaff1f4142cf0101b567b435 Fri Mar 4 02:01:44 2022 -0800
    updating cdsStartStat docs, refs #29030
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    b1f2a82f8e47c64bdd201907419e1761a77aea50 Thu Mar 3 15:24:13 2022 -0800
    Adding a small note to mouseOver about more than 8 fields (in mouseOverField already)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    c72fe34696163a8421925b26fd55e6829e098ec4 Mon Feb 28 16:03:58 2022 -0800
    Removing comma for CR refs #29022
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    a381e294a9b7c94c78b8aa00ac36f2acb4d75704 Fri Mar 4 14:21:44 2022 -0800
    Making edits to variantMuts track and adding predResist track #29035
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a381e294a9b7c94c78b8aa00ac36f2acb4d75704 Fri Mar 4 14:21:44 2022 -0800
    Making edits to variantMuts track and adding predResist track #29035
• src/hg/inc/barChartUi.h
  • lines changed 2, context: html, text, full: html, text
    a981318c28445664c4fb9c6ef2b6918e2094da98 Fri Mar 4 14:38:29 2022 -0800
    Changes from code review. Also restore original bar width calculation as it makes barChartStretchToItem work better, refs #29021
• src/hg/inc/bigRmskAlignBed.h
  • lines changed 79, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/inc/bigRmskBed.h
  • lines changed 76, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    0a355b48d73c07ba33a04bf1dfd7266f12d0cafe Sat Mar 5 17:24:04 2022 -0800
    scale up the size of a trackDb we'll accept
• src/hg/lib/bigRmskAlignBed.as
  • lines changed 21, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/bigRmskAlignBed.c
  • lines changed 212, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/bigRmskAlignBed.sql
  • lines changed 27, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/bigRmskBed.as
  • lines changed 18, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/bigRmskBed.c
  • lines changed 197, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/bigRmskBed.sql
  • lines changed 24, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/lib/evaSnp.as
  • lines changed 15, context: html, text, full: html, text
    c12ecb21298a3c6d19b6381ede7bd1477cabefab Mon Feb 28 17:20:04 2022 -0800
    changes per BriLee code review, incl conforming to makedoc conventions, adding filters on dogSnp track. added evaSnp.as file, which was forgotten. refs #29025
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    42ccdd815277a3dc7d78b48fa0ac36d469ab628a Mon Feb 28 19:07:04 2022 -0800
    added bigRmsk autoSql files from Robert Hubley
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    e27fd8c7e843c93ef395c2065f0c72530a13dbba Mon Feb 28 12:11:00 2022 -0800
    adding a rat assembly GCA_021556685.1_UTH_Rnor_SHRSP_BbbUtx_1.0 per user request refs #28841
• src/hg/makeDb/doc/bosTau9/lastzRuns.txt
  • lines changed 95, context: html, text, full: html, text
    efd88f6acfb7fc2bfcf6b15583aa8bc35a8540c9 Mon Feb 28 12:12:48 2022 -0800
    bosTau9 vs. bosTau5 lastz/chain/net run for user, refs #28943
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 73, context: html, text, full: html, text
    c12ecb21298a3c6d19b6381ede7bd1477cabefab Mon Feb 28 17:20:04 2022 -0800
    changes per BriLee code review, incl conforming to makedoc conventions, adding filters on dogSnp track. added evaSnp.as file, which was forgotten. refs #29025
  • lines changed 1, context: html, text, full: html, text
    cd5b2b3bcde639cf2242c96fb0afcc016bdf77b1 Wed Mar 2 16:33:34 2022 -0800
    adapting a line to proper format
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    08c6032c3b09c6275f152e4cd07166b1ecf983d5 Mon Mar 7 02:54:23 2022 -0800
    adding Agilent hg19 arrays downloaded by Dan, refs #23591
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    bff7103f9b04262250a790222c23f05ed298ed10 Mon Mar 7 03:08:56 2022 -0800
    adding docs page and colors for agilent track, refs #23591
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e27fd8c7e843c93ef395c2065f0c72530a13dbba Mon Feb 28 12:11:00 2022 -0800
    adding a rat assembly GCA_021556685.1_UTH_Rnor_SHRSP_BbbUtx_1.0 per user request refs #28841
• src/hg/makeDb/doc/mm10.txt
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    daaa7326c7534ffa3834fc99efcc8adf823ae66a Sat Mar 5 17:28:11 2022 -0800
    add a bigBed version of the TOGA gene track
• src/hg/makeDb/doc/wuhCor1/resistPred.doc
  • lines changed 5, context: html, text, full: html, text
    5864de93205bac95ba8441e2ef8a8fbbfe893e15 Wed Mar 2 05:27:13 2022 -0800
    adding predicted resistance mutations track on wuhCor1, refs #29035
• src/hg/makeDb/scripts/resistPred/resistPred.as
  • lines changed 20, context: html, text, full: html, text
    5864de93205bac95ba8441e2ef8a8fbbfe893e15 Wed Mar 2 05:27:13 2022 -0800
    adding predicted resistance mutations track on wuhCor1, refs #29035
• src/hg/makeDb/trackDb/dog/canFam3/evaSnp.html
  • lines changed 2, context: html, text, full: html, text
    f5a8348facb65899baa73f0aa6fd69501d37210f Mon Feb 28 15:56:49 2022 -0800
    improved the wording a little on a variant class description
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    c12ecb21298a3c6d19b6381ede7bd1477cabefab Mon Feb 28 17:20:04 2022 -0800
    changes per BriLee code review, incl conforming to makedoc conventions, adding filters on dogSnp track. added evaSnp.as file, which was forgotten. refs #29025
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    c12ecb21298a3c6d19b6381ede7bd1477cabefab Mon Feb 28 17:20:04 2022 -0800
    changes per BriLee code review, incl conforming to makedoc conventions, adding filters on dogSnp track. added evaSnp.as file, which was forgotten. refs #29025
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 27, context: html, text, full: html, text
    bff7103f9b04262250a790222c23f05ed298ed10 Mon Mar 7 03:08:56 2022 -0800
    adding docs page and colors for agilent track, refs #23591
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 27, context: html, text, full: html, text
    08c6032c3b09c6275f152e4cd07166b1ecf983d5 Mon Mar 7 02:54:23 2022 -0800
    adding Agilent hg19 arrays downloaded by Dan, refs #23591
  • lines changed 27, context: html, text, full: html, text
    bff7103f9b04262250a790222c23f05ed298ed10 Mon Mar 7 03:08:56 2022 -0800
    adding docs page and colors for agilent track, refs #23591
• src/hg/makeDb/trackDb/human/hg38/cancerExpr.ra
  • lines changed 24, context: html, text, full: html, text
    f461afbf427a340a2018f2ecf11708568031172c Tue Mar 1 10:41:19 2022 -0800
    Fixing the trackDb order of labels for both tcgaGeneExpr and tcgaTranscExpr, refs #28933
• src/hg/makeDb/trackDb/virus/wuhCor1/resistPred.html
  • lines changed 37, context: html, text, full: html, text
    5864de93205bac95ba8441e2ef8a8fbbfe893e15 Wed Mar 2 05:27:13 2022 -0800
    adding predicted resistance mutations track on wuhCor1, refs #29035
  • lines changed 18, context: html, text, full: html, text
    a381e294a9b7c94c78b8aa00ac36f2acb4d75704 Fri Mar 4 14:21:44 2022 -0800
    Making edits to variantMuts track and adding predResist track #29035
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    5864de93205bac95ba8441e2ef8a8fbbfe893e15 Wed Mar 2 05:27:13 2022 -0800
    adding predicted resistance mutations track on wuhCor1, refs #29035
  • lines changed 3, context: html, text, full: html, text
    a381e294a9b7c94c78b8aa00ac36f2acb4d75704 Fri Mar 4 14:21:44 2022 -0800
    Making edits to variantMuts track and adding predResist track #29035
  • lines changed 1, context: html, text, full: html, text
    4b1abc5275734acc94c89b71e4e0b93b4841a94a Mon Mar 7 02:16:41 2022 -0800
    small title tweak to credit database more in wuhCor1 resistance track, refs #29035
  • lines changed 4, context: html, text, full: html, text
    3633702881de2c1287243e393350d2c718226d69 Mon Mar 7 02:18:58 2022 -0800
    fixing merge problem, refs #29035
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 3, context: html, text, full: html, text
    a381e294a9b7c94c78b8aa00ac36f2acb4d75704 Fri Mar 4 14:21:44 2022 -0800
    Making edits to variantMuts track and adding predResist track #29035
• src/hg/utils/automation/asmHubCrisprAll.pl
  • lines changed 278, context: html, text, full: html, text
    da977cb10ba717d64216de2cbeeb9948c9c78714 Wed Mar 2 16:33:41 2022 -0800
    adding crisprAll as an asmHub track no redmine
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 35, context: html, text, full: html, text
    da977cb10ba717d64216de2cbeeb9948c9c78714 Wed Mar 2 16:33:41 2022 -0800
    adding crisprAll as an asmHub track no redmine
• src/hg/utils/automation/asmHubXenoRefGene.pl
  • lines changed 7, context: html, text, full: html, text
    da977cb10ba717d64216de2cbeeb9948c9c78714 Wed Mar 2 16:33:41 2022 -0800
    adding crisprAll as an asmHub track no redmine
• src/hg/utils/automation/doCrispr.pl
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    be6de36d134aa80ccf9c34cf4d14a2adf36f1e24 Wed Mar 2 16:32:11 2022 -0800
    link the constructed indexes in an assembly hub build into the public crispor data directory for other parts of the procedure no redmine
• src/hg/utils/otto/omim/checkOmimUpload.sh
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    a20b9bd3b6167ed987592a293297e4b5cd459765 Tue Mar 1 16:35:59 2022 -0800
    Revert "Adding change between otto running script in hive vs tree, refs Jonathan" This reverts commit 490598d3b0bd8599908253ece43d519d5772b5e9.
• src/hg/utils/otto/omim/omimUploadWrapper.sh
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    8f7fe3985d51a8575fd383de0bc4edeb60d215ed Tue Mar 1 10:18:47 2022 -0800
    Removing subject mail so as not to get output emails when nothing happens, no RM
• src/lib/udc.c
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    eff2b7558e9806b284bfd562e7ae52c1426f0c78 Sat Mar 5 17:27:05 2022 -0800
    increase the maxSize of the buffer in udc
• src/oneShot/sqlToAs/makefile
  • lines changed 8, context: html, text, full: html, text
    2c9615338fe3f7c620421e2a265a63cf30cf98f1 Sat Mar 5 17:33:06 2022 -0800
    move sqlToAs out of oneShot an into utils
• src/oneShot/sqlToAs/sqlToAs
  • lines changed 98, context: html, text, full: html, text
    2c9615338fe3f7c620421e2a265a63cf30cf98f1 Sat Mar 5 17:33:06 2022 -0800
    move sqlToAs out of oneShot an into utils
• src/product/installer/browserSetup.sh
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    522acfa3342235ba4fc6292c6d282fff85d22b13 Tue Mar 1 05:21:31 2022 -0800
    hopefully last bugfix for mysql strict mode issue in gbic, refs #28733
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    5ab1a92dcc44639ade2b91bcf06e75fc291d5e05 Tue Mar 1 06:12:19 2022 -0800
    another mariadb fix in gbic, refs #28348
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    b81739df02e5268cc9dc3d9be1de89d4d455f3fb Thu Mar 3 07:35:28 2022 -0800
    supporting mysql 5.5 on centos7 for gbic, refs #28348
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    e9b1c817c2560280e0374fa46debde4de2f7ebea Fri Mar 4 05:52:10 2022 -0800
    the neverending bug fix series of gbic continues, refs #28348
• src/utils/qa/weeklybld/buildEnv.csh
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    9e241344833bfb0ea109fa77cb4f759108099b86 Mon Mar 7 10:03:41 2022 -0800
    v428 preview2, refs #29014
• src/utils/sqlToAs/makefile
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    2c9615338fe3f7c620421e2a265a63cf30cf98f1 Sat Mar 5 17:33:06 2022 -0800
    move sqlToAs out of oneShot an into utils
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    ca0629197b6dba6cb3637d28ef36a27dc9eb895d Sat Mar 5 17:34:14 2022 -0800
    fix makefile to have correct name for util
• src/utils/sqlToAs/sqlToAs
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    2c9615338fe3f7c620421e2a265a63cf30cf98f1 Sat Mar 5 17:33:06 2022 -0800
    move sqlToAs out of oneShot an into utils

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• files changed: 75