All File Changes

v392_base to v393_preview (2020-01-06 to 2020-01-13) v393

• src/hg/cartReset/cartReset.c
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    3f71cd4547c5afb1a52d80d9290fb76fc826e0a0 Fri Jan 10 15:18:12 2020 -0800
    expanding filtering to take in just "//" since it is equivalent to "://" and we want to forbid both. This url pattern is a protocol-agnostic form which uses the context of the page. Reported to us as XSS violation. refs#24750.
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    38d05d1d1259c64a71c7d46444a9e9bb91e21676 Fri Jan 10 23:46:22 2020 -0800
    Changing cartReset to use CSP meta head to suppress XSS javascript in the destination CGI parameter. refs#24750
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    aa893970733f283ded63b3ea8ed1ddd43117be74 Thu Jan 9 21:55:11 2020 -0800
    Fix problem with multi-view composites using hideEmptySubtracks. refs #23665
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    10b43bfe4fdaa293a79ddd639f8c29ad2aa7b8f9 Thu Jan 9 11:30:27 2020 -0800
    Adding a plug for the API in the getDNA page section relating to bulk download refs #355
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    62c9e871dba2a1b400d00422a1fd4b21f7c650f8 Fri Jan 10 18:08:04 2020 -0800
    Fixing htcDnaNearGene to use cartWebStart so that it has a standard header protecting the page with CSP. refs#24750
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 64, context: html, text, full: html, text
    326be23c6ed7fba520c184f77d789cfc483ac693 Thu Jan 9 15:29:22 2020 -0800
    Correcting blat capitalization according to http://genomewiki.soe.ucsc.edu/genecats/index.php/Details_pages_--_conventions#Referring_to_BLAT and making repeat explanation more clear for CR #24719
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 3, context: html, text, full: html, text
    1914160557032a2cdb33aa9fd8cb548af5c19686 Mon Jan 6 15:24:28 2020 -0800
    Adding a note on bedgraph.html about 50,000,000 line limit and bigWig suggestion refs #24729
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 9, context: html, text, full: html, text
    e67a7fb01f99795dce4381516669678731f71a5e Sat Jan 11 11:27:04 2020 -0800
    Adding NIH link on Hosting refs #24744
  • lines changed 63, context: html, text, full: html, text
    fc861d161025576103b92f11ff76a6ea84c28e0f Sun Jan 12 21:06:11 2020 -0800
    extending track hub hosting section, refs #24744
• src/hg/inc/partitionSort.h
  • lines changed 46, context: html, text, full: html, text
    7cc9ee442be0bb8ab7a90e77566f5df30bdb7277 Thu Jan 9 08:29:12 2020 -0800
    add option to use parallel sort for pslPartition and bedPartition
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    aaf0240947b1065aff097758ab30bab780007f4c Wed Jan 8 14:56:22 2020 -0800
    Even more subgroups (needed by ENCODE megahub). refs #24652
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    aa893970733f283ded63b3ea8ed1ddd43117be74 Thu Jan 9 21:55:11 2020 -0800
    Fix problem with multi-view composites using hideEmptySubtracks. refs #23665
• src/hg/lib/trackDbCache.c
  • lines changed 3, context: html, text, full: html, text
    d19aa81bb03ee6934c53511b7332b5646d66ac20 Thu Jan 9 12:37:07 2020 -0800
    make trackDb cache directory if it doesnt exist.
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 2, context: html, text, full: html, text
    008447b8fbe04a4fa16c3236f542dd17f4ea0b80 Wed Jan 8 14:45:06 2020 -0800
    Updating redirected links for felCat4 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/cgapSage.html
  • lines changed 1, context: html, text, full: html, text
    0c02de0fb27eb0d6e6a53f99058e631a3ba165f5 Wed Jan 8 15:00:06 2020 -0800
    Updating redirected links for mm8 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/gorilla/gorGor5/gap.html
  • lines changed 1, context: html, text, full: html, text
    800df2fc2f73b030c96b684a7fb7d8816adb5dc7 Wed Jan 8 13:11:15 2020 -0800
    Updating http to https for gorGor5, uiLinks cronjob
• src/hg/makeDb/trackDb/gorilla/gorGor5/gold.html
  • lines changed 1, context: html, text, full: html, text
    800df2fc2f73b030c96b684a7fb7d8816adb5dc7 Wed Jan 8 13:11:15 2020 -0800
    Updating http to https for gorGor5, uiLinks cronjob
• src/hg/makeDb/trackDb/human/avada.html
  • lines changed 1, context: html, text, full: html, text
    fc360268b7f7102a5012bf5e0e813692de7ae305 Fri Jan 10 10:58:47 2020 -0800
    Switching the API link to be relative refs #24156
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    7de961c9f9118e190f6e6967e2b6fb962bbbcb06 Thu Jan 9 14:23:18 2020 -0800
    corrected acronym LOEUF to match Broad's
• src/hg/makeDb/trackDb/human/hg19/platinumGenomes.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 13, context: html, text, full: html, text
    cf3ed41429a20232c8b71badda508c2657b5606f Fri Jan 10 12:30:09 2020 -0800
    Staging gnomad missense constraint track on dev, refs #24751
  • lines changed 40, context: html, text, full: html, text
    6492d15c380c58b5291ae24ee17d77678c848409 Fri Jan 10 16:23:43 2020 -0800
    Organizing all the gnomad tracks on hg19 into a super track to prevent proliferation of the variation track group, refs #24751
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 3, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 3, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 3, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 3, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
  • lines changed 3, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/hicAndMicroC.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/omimLocation.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/platinumGenomes.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/human/hg38/primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/ucscRetroAli9.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.html
  • lines changed 2, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    c092ec93e74dbc86b50167c304661528aa89b7ce Wed Jan 8 15:18:14 2020 -0800
    Updating redirected links for hg38 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 2, context: html, text, full: html, text
    111af33461ddecbdc01107656c60cef12170534a Wed Jan 8 15:11:57 2020 -0800
    Updating redirected links for mm9 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra
  • lines changed 4, context: html, text, full: html, text
    aa893970733f283ded63b3ea8ed1ddd43117be74 Thu Jan 9 21:55:11 2020 -0800
    Fix problem with multi-view composites using hideEmptySubtracks. refs #23665
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/makeDb/trackDb/mouse/mm8/NIAGene.html
  • lines changed 1, context: html, text, full: html, text
    0c02de0fb27eb0d6e6a53f99058e631a3ba165f5 Wed Jan 8 15:00:06 2020 -0800
    Updating redirected links for mm8 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 1, context: html, text, full: html, text
    0c02de0fb27eb0d6e6a53f99058e631a3ba165f5 Wed Jan 8 15:00:06 2020 -0800
    Updating redirected links for mm8 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 3, context: html, text, full: html, text
    0c02de0fb27eb0d6e6a53f99058e631a3ba165f5 Wed Jan 8 15:00:06 2020 -0800
    Updating redirected links for mm8 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm8/wssdCoverage.html
  • lines changed 1, context: html, text, full: html, text
    0c02de0fb27eb0d6e6a53f99058e631a3ba165f5 Wed Jan 8 15:00:06 2020 -0800
    Updating redirected links for mm8 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 2, context: html, text, full: html, text
    111af33461ddecbdc01107656c60cef12170534a Wed Jan 8 15:11:57 2020 -0800
    Updating redirected links for mm9 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
  • lines changed 1, context: html, text, full: html, text
    111af33461ddecbdc01107656c60cef12170534a Wed Jan 8 15:11:57 2020 -0800
    Updating redirected links for mm9 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 2, context: html, text, full: html, text
    111af33461ddecbdc01107656c60cef12170534a Wed Jan 8 15:11:57 2020 -0800
    Updating redirected links for mm9 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/oreganno.html
  • lines changed 1, context: html, text, full: html, text
    111af33461ddecbdc01107656c60cef12170534a Wed Jan 8 15:11:57 2020 -0800
    Updating redirected links for mm9 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 16, context: html, text, full: html, text
    562929f81d9d89531be4f778e221fe3a350a5f68 Fri Jan 10 12:33:44 2020 -0800
    temporarily disable MGC track
• src/hg/makeDb/trackDb/trackDb.transMap.ra
  • lines changed 1, context: html, text, full: html, text
    4a08b4785143306d5388ab61c4eed13ee4212cd7 Fri Jan 10 15:37:05 2020 -0800
    Cleaning up stale pennantIcons, starting the new year Fresh. No rm.
• src/hg/pslDropOverlap/pslDropOverlap.c
  • lines changed 185, context: html, text, full: html, text
    e11b77d06719918edef238edac8d9b9e320b3076 Fri Jan 10 15:21:15 2020 -0800
    Cleaning up old experimental util to drop trivial self-aligning blocks from PSL like lavToAxt -dropSelf does. refs #24694
• src/hg/pslPartition/pslPartition.c
  • lines changed 25, context: html, text, full: html, text
    7cc9ee442be0bb8ab7a90e77566f5df30bdb7277 Thu Jan 9 08:29:12 2020 -0800
    add option to use parallel sort for pslPartition and bedPartition
• src/hg/pslPartition/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    7cc9ee442be0bb8ab7a90e77566f5df30bdb7277 Thu Jan 9 08:29:12 2020 -0800
    add option to use parallel sort for pslPartition and bedPartition
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 49, context: html, text, full: html, text
    06d156f363b5dc4c4aa59b90084724822ee7781a Mon Jan 6 15:22:09 2020 -0800
    correctly handle duplicates and faster refs #23891
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 169, context: html, text, full: html, text
    e87ffcb94edd42fabe93f3057a0719aa92d77381 Wed Jan 8 15:36:13 2020 -0800
    now constructing files in assembly hub build environment refs #23891
• src/hg/utils/bedPartition/bedPartition.c
  • lines changed 26, context: html, text, full: html, text
    7cc9ee442be0bb8ab7a90e77566f5df30bdb7277 Thu Jan 9 08:29:12 2020 -0800
    add option to use parallel sort for pslPartition and bedPartition
• src/hg/utils/bedPartition/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    7cc9ee442be0bb8ab7a90e77566f5df30bdb7277 Thu Jan 9 08:29:12 2020 -0800
    add option to use parallel sort for pslPartition and bedPartition
• src/lib/net.c
  • lines changed 90, context: html, text, full: html, text
    86351e141ea3ce1d6465d0293a5247164b0494eb Mon Jan 6 11:13:33 2020 -0800
    If ipv6 is disabled, retry with ipv4-only listening socket. Tweak packet ip address filtering routine to tolerate the ipv4 address format. fixes #24730.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    07a3eaa5813cf7968d0def551473bcfe730a6c69 Mon Jan 13 10:19:15 2020 -0800
    v393 preview1

• lines changed: 901
• files changed: 64