All File Changes

v378_preview to v378_preview2 (2019-02-11 to 2019-02-18) v378

• src/hg/cirm/cdw/cdwWebBrowse/version.doc
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    034978a0431e1e2268d71c41ff6fc4a078d6ecb7 Thu Feb 14 17:31:21 2019 -0800
    Documenting latest changes.
• src/hg/cirm/cdw/oneShot/cdwMissingAnalysis/cdwMissingAnalysis.c
  • lines changed 278, context: html, text, full: html, text
    c864d822349bb49a947189d426ec9108241e5f80 Thu Feb 14 17:25:46 2019 -0800
    Adding a utility to help find data sets that still need analysis.
• src/hg/cirm/cdw/oneShot/cdwMissingAnalysis/makefile
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    c864d822349bb49a947189d426ec9108241e5f80 Thu Feb 14 17:25:46 2019 -0800
    Adding a utility to help find data sets that still need analysis.
• src/hg/cirm/gateway/htdocs/inc/header.html
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    10cefe46dda5af56846d8d1d180d7bb4c9e60ad2 Tue Feb 12 08:59:16 2019 -0800
    Fixing link tags to make public site link in secure site banner show up white, refs #22934
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    26884c8b40c83d121f23cc635596fb0f75528a05 Wed Feb 13 14:19:54 2019 -0800
    Fixing CIRM static page login/logout javascript, refs #22878, #22831
• src/hg/cirm/gateway/htdocs/js/cirmStuff.js
  • lines changed 11, context: html, text, full: html, text
    26884c8b40c83d121f23cc635596fb0f75528a05 Wed Feb 13 14:19:54 2019 -0800
    Fixing CIRM static page login/logout javascript, refs #22878, #22831
• src/hg/hgCollection/hgCollection.c
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    80a3eefccdc921047ee4265ee46b552ea1e64074 Wed Feb 13 14:31:02 2019 -0800
    add hgsid to the call to hgTracks when you press 'Go'
• src/hg/hgSession/backup.c
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    770ed6ada89bdaaac49ba96963510af0a9338b89 Thu Feb 14 11:44:29 2019 -0800
    hgSession custom track backup archive creation for downloading. Changing approach from backupAndRestore to backupOnly. Uses just plain real ascii .ct custom tracks.
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    1758abf67337a0da83715097a7ace1f3e8f7bfd6 Thu Feb 14 23:42:40 2019 -0800
    changing it to clear out the name-to-use for the downloaded archive.
• src/hg/hgSession/backupRestore.c
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    3b5084ded7ac5f510cb166ead434d75f11a2fc7c Mon Feb 11 15:31:19 2019 -0800
    oops missing wibFile setting. I thought the library was doing this already. oh well.
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    e12773a8da047136e017623cfed61ea802e2f676 Mon Feb 11 15:47:42 2019 -0800
    oops, wib also needs path to trash patch
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    3d07d037db54a3b7aa2dd10fc4b6db33041e49f7 Thu Feb 14 11:51:32 2019 -0800
    git was supposed to handle the git mv somefilename otherfilename better than this. it gave a merge conflict where tthere was none. and instead of using git add to resolve the merge conflict, as I have done for every other case I have ever heard of, this one apparently wanted me to use git rm somefilename to remove the thing from the system. yuck. Nobody on master branch had done any further work on the file being renamed, so this conflict makes little sense. sounds like using git to mv files and then squashing may ALWAYS lead to this unfortunate hassle.
• src/hg/hgSession/hgSession.c
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    770ed6ada89bdaaac49ba96963510af0a9338b89 Thu Feb 14 11:44:29 2019 -0800
    hgSession custom track backup archive creation for downloading. Changing approach from backupAndRestore to backupOnly. Uses just plain real ascii .ct custom tracks.
  • lines changed 4, context: html, text, full: html, text
    1758abf67337a0da83715097a7ace1f3e8f7bfd6 Thu Feb 14 23:42:40 2019 -0800
    changing it to clear out the name-to-use for the downloaded archive.
• src/hg/hgSession/hgSession.h
  • lines changed 13, context: html, text, full: html, text
    770ed6ada89bdaaac49ba96963510af0a9338b89 Thu Feb 14 11:44:29 2019 -0800
    hgSession custom track backup archive creation for downloading. Changing approach from backupAndRestore to backupOnly. Uses just plain real ascii .ct custom tracks.
• src/hg/hgSession/makefile
  • lines changed 1, context: html, text, full: html, text
    770ed6ada89bdaaac49ba96963510af0a9338b89 Thu Feb 14 11:44:29 2019 -0800
    hgSession custom track backup archive creation for downloading. Changing approach from backupAndRestore to backupOnly. Uses just plain real ascii .ct custom tracks.
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    d6cb1cc5d720f53812bf6bd34ca529a8c109d3f6 Thu Feb 14 12:54:13 2019 -0800
    hgTables was calling too many things that called popWarnHandler after hgPositionsHtml. refs #22945
• src/hg/hgTracks/interactTrack.c
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    15c582a98aceed3f49165b6c0105fa481059307f Wed Feb 13 11:59:59 2019 -0800
    distinguish between zero items and maxItems #21988
• src/hg/htdocs/FAQ/FAQgenes.html
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    c0ce4f1d992ebf0fda293dc504774d93aeb66d5d Thu Feb 14 11:25:24 2019 -0800
    Working on unreleased FAQ genes page ref#22696
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    786b8887a8dca6df2efdb312b8a00018df7d0cbe Thu Feb 14 15:45:54 2019 -0800
    Working on unreleased FAQ genes page ref#22696
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 5, context: html, text, full: html, text
    ca3424b322fe30c0e353abe69f9b25622faba9ef Fri Feb 15 16:00:42 2019 -0800
    added some hyphens
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 22, context: html, text, full: html, text
    770ed6ada89bdaaac49ba96963510af0a9338b89 Thu Feb 14 11:44:29 2019 -0800
    hgSession custom track backup archive creation for downloading. Changing approach from backupAndRestore to backupOnly. Uses just plain real ascii .ct custom tracks.
  • lines changed 48, context: html, text, full: html, text
    664836533e0c385d9c0066f3394348ebd26796ff Fri Feb 15 17:18:30 2019 -0800
    adding directions for restoring cts from the backup archive using hgCustom
• src/hg/htdocs/gtex.html
  • lines changed 7, context: html, text, full: html, text
    bfff6a7a7ee93a2fbf2d19ffbc1fc294cef93cf4 Wed Feb 13 10:34:39 2019 -0800
    reducing lines to <100 chars, adding short link for session, refs #22678
• src/hg/htdocs/history.html
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    579389443d168282e02d17ea47c058556ab91509 Mon Feb 11 17:04:40 2019 -0800
    Adding information to the history.html page from the Google Doc. No edits to the text other than changing 'UCSC Genome Bioinformatics Group' and 'UC Santa Cruz Group' to UCSC Genome Browser Group, refs #20314
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    6bf7c9c88c87ba1df563e87f3df35ce568685610 Tue Feb 12 10:05:31 2019 -0800
    Changing 'UCSC Genome Browser Group' back to 'UC Santa Cruz group' after Ann's input, refs #20314
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 1, context: html, text, full: html, text
    80a3eefccdc921047ee4265ee46b552ea1e64074 Wed Feb 13 14:31:02 2019 -0800
    add hgsid to the call to hgTracks when you press 'Go'
• src/hg/hubApi/apiUtils.c
  • lines changed 33, context: html, text, full: html, text
    2817c6f81dd844b54f6232d688c001e6a12f9ebb Wed Feb 13 11:17:54 2019 -0800
    beginning to partition the code out to files refs #18869
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    81549209efed163c45d074d1ead4e9b30608c0fa Thu Feb 14 09:35:53 2019 -0800
    correct naming of functions refs #18869
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    b5cd41df4b0f7113a4641a82973ddcd331df1c1b Fri Feb 15 10:11:17 2019 -0800
    ready to select table data refs #18869
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    d96cce85869936e100269b1b5859acef8e1fec80 Fri Feb 15 11:22:27 2019 -0800
    now dumping contents of any database table refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 50, context: html, text, full: html, text
    2817c6f81dd844b54f6232d688c001e6a12f9ebb Wed Feb 13 11:17:54 2019 -0800
    beginning to partition the code out to files refs #18869
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    774479fda06428280150d609bdf4052f5f35d571 Wed Feb 13 14:17:16 2019 -0800
    list functions moved to list.c refs #18869
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    81549209efed163c45d074d1ead4e9b30608c0fa Thu Feb 14 09:35:53 2019 -0800
    correct naming of functions refs #18869
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    b5cd41df4b0f7113a4641a82973ddcd331df1c1b Fri Feb 15 10:11:17 2019 -0800
    ready to select table data refs #18869
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    d96cce85869936e100269b1b5859acef8e1fec80 Fri Feb 15 11:22:27 2019 -0800
    now dumping contents of any database table refs #18869
• src/hg/hubApi/getData.c
  • lines changed 55, context: html, text, full: html, text
    2817c6f81dd844b54f6232d688c001e6a12f9ebb Wed Feb 13 11:17:54 2019 -0800
    beginning to partition the code out to files refs #18869
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    774479fda06428280150d609bdf4052f5f35d571 Wed Feb 13 14:17:16 2019 -0800
    list functions moved to list.c refs #18869
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    81549209efed163c45d074d1ead4e9b30608c0fa Thu Feb 14 09:35:53 2019 -0800
    correct naming of functions refs #18869
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    b5cd41df4b0f7113a4641a82973ddcd331df1c1b Fri Feb 15 10:11:17 2019 -0800
    ready to select table data refs #18869
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    d96cce85869936e100269b1b5859acef8e1fec80 Fri Feb 15 11:22:27 2019 -0800
    now dumping contents of any database table refs #18869
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    55b54d043a87a29773ca196c360a0af1346947ec Mon Feb 18 07:05:59 2019 -0800
    the trackDb from hubs appears to be flattened ? refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 54, context: html, text, full: html, text
    0722486013be8ff695612a47d218b52135357d1a Mon Feb 11 14:38:12 2019 -0800
    now with dowload date stamps refs #18869
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    06ce406a7fe0566c6f6984b445c9035088c1bd38 Mon Feb 11 15:17:30 2019 -0800
    now with correct application/json content type header refs #18869
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    fa326179d9bd70fb1fb1d2fe4996c3a5545257aa Tue Feb 12 14:57:50 2019 -0800
    now traversing trackDb recursively to show all composite tracks refs #18869
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    3507479860c1b84b51d6f7faddbcbd49fa94227b Tue Feb 12 18:50:44 2019 -0800
    now returning sequence DNA from specified UCSC db refs #18869
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    8719bd3fc718d52ab67ce568131b5a97638c2fb7 Wed Feb 13 11:03:32 2019 -0800
    minor formatting clean up before restructure refs #18869
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    2817c6f81dd844b54f6232d688c001e6a12f9ebb Wed Feb 13 11:17:54 2019 -0800
    beginning to partition the code out to files refs #18869
  • lines changed 141, context: html, text, full: html, text
    774479fda06428280150d609bdf4052f5f35d571 Wed Feb 13 14:17:16 2019 -0800
    list functions moved to list.c refs #18869
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    9f527929694c8bada3e0f6ab0145aada1a0973e5 Wed Feb 13 14:23:42 2019 -0800
    remove code that moved out refs #18869
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    81549209efed163c45d074d1ead4e9b30608c0fa Thu Feb 14 09:35:53 2019 -0800
    correct naming of functions refs #18869
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    b5cd41df4b0f7113a4641a82973ddcd331df1c1b Fri Feb 15 10:11:17 2019 -0800
    ready to select table data refs #18869
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    d96cce85869936e100269b1b5859acef8e1fec80 Fri Feb 15 11:22:27 2019 -0800
    now dumping contents of any database table refs #18869
  • lines changed 33, context: html, text, full: html, text
    55b54d043a87a29773ca196c360a0af1346947ec Mon Feb 18 07:05:59 2019 -0800
    the trackDb from hubs appears to be flattened ? refs #18869
• src/hg/hubApi/list.c
  • lines changed 346, context: html, text, full: html, text
    774479fda06428280150d609bdf4052f5f35d571 Wed Feb 13 14:17:16 2019 -0800
    list functions moved to list.c refs #18869
  • lines changed 17, context: html, text, full: html, text
    81549209efed163c45d074d1ead4e9b30608c0fa Thu Feb 14 09:35:53 2019 -0800
    correct naming of functions refs #18869
  • lines changed 12, context: html, text, full: html, text
    b5cd41df4b0f7113a4641a82973ddcd331df1c1b Fri Feb 15 10:11:17 2019 -0800
    ready to select table data refs #18869
  • lines changed 29, context: html, text, full: html, text
    d96cce85869936e100269b1b5859acef8e1fec80 Fri Feb 15 11:22:27 2019 -0800
    now dumping contents of any database table refs #18869
  • lines changed 23, context: html, text, full: html, text
    55b54d043a87a29773ca196c360a0af1346947ec Mon Feb 18 07:05:59 2019 -0800
    the trackDb from hubs appears to be flattened ? refs #18869
• src/hg/hubApi/makefile
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    2817c6f81dd844b54f6232d688c001e6a12f9ebb Wed Feb 13 11:17:54 2019 -0800
    beginning to partition the code out to files refs #18869
  • lines changed 1, context: html, text, full: html, text
    774479fda06428280150d609bdf4052f5f35d571 Wed Feb 13 14:17:16 2019 -0800
    list functions moved to list.c refs #18869
• src/hg/hubApi/tests/expected.json.gz
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    4734dfb72de2549a50df10a31f7871c43f822d65 Tue Feb 12 09:25:17 2019 -0800
    beginning to add error verification refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 37, context: html, text, full: html, text
    4734dfb72de2549a50df10a31f7871c43f822d65 Tue Feb 12 09:25:17 2019 -0800
    beginning to add error verification refs #18869
• src/hg/hubApi/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    4734dfb72de2549a50df10a31f7871c43f822d65 Tue Feb 12 09:25:17 2019 -0800
    beginning to add error verification refs #18869
• src/hg/inc/hdb.h
  • lines changed 11, context: html, text, full: html, text
    945197799e507e8fb1d9365b822c9c1a46d3799c Tue Feb 12 11:21:24 2019 -0800
    Undoing overzealous removal of chrNameCmpWithAltRandom from hdb.h, just before it was needed elsewhere.
• src/hg/lib/customFactory.c
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    eee25d4eb77429189279297e6f4098bd726e811f Thu Feb 14 23:41:09 2019 -0800
    make hgCustom custom track loading reset the lazarus time to live back to 20 minutes for every track being loaded, in case somebody loads an enormous concatenated file with hundreds of tracks.
• src/hg/lib/hgFind.c
  • lines changed 5, context: html, text, full: html, text
    45e79d76639fb235b57f43a27ba6ee257aac1fde Mon Feb 11 15:42:43 2019 -0800
    Making the search for known genes prioritize results on the main chromosome over those on alt haplotypes.
• src/hg/lib/tablesTables.c
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    09793009c7ec55f6d44ff76a6d30dc236a0d29f7 Mon Feb 11 15:31:26 2019 -0800
    Fixing an unwanted word-wrap that was making table format off in browse/files.
• src/hg/lib/variantProjector.c
  • lines changed 7, context: html, text, full: html, text
    0b524327ab6d7e471a7944c58349e5b2fd02c8f5 Thu Feb 14 11:55:44 2019 -0800
    Support VCF4.2 ALT value '*' (allele missing due to deletion). refs #22947
• src/hg/makeDb/doc/proteins/170510.txt
  • lines changed 207, context: html, text, full: html, text
    3c1bb3b25f05371f15bf508214ff4e74d85fe5ae Wed Feb 13 16:04:05 2019 -0800
    Finally committing makedocs for old proteins work on dev server - never went live, no ticket
• src/hg/makeDb/doc/uniProt/sp170510.txt
  • lines changed 77, context: html, text, full: html, text
    3c1bb3b25f05371f15bf508214ff4e74d85fe5ae Wed Feb 13 16:04:05 2019 -0800
    Finally committing makedocs for old proteins work on dev server - never went live, no ticket
• src/hg/makeDb/genbank/etc/build-genbank
  • lines changed 13, context: html, text, full: html, text
    7cda3085ade8ba7ba7b19808438b421987bb9635 Thu Feb 14 09:50:22 2019 -0800
    fix up the procedure to follow if there is a validation error
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    442d58d3e1e2ec015b9eba45a3794e7ff28d7c2b Sun Feb 17 08:35:36 2019 -0800
    some instructions to fix copy of hgFixed to dev
• src/hg/makeDb/genbank/etc/genbank.conf
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    a3786113c11a152ffeeaef1e1d3f2bf0f5ae599e Fri Feb 15 11:05:13 2019 -0800
    go back to aligning to the original hg19
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    09066590ca3deae20d09bf085e068938c8282d3d Sat Feb 16 14:38:32 2019 -0800
    load the descriptions for everything (xeno and native) on hg38
• src/hg/makeDb/schema/all.joiner
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    7a626fd45cde618455bc539fa2e70dba7ce56603 Wed Feb 13 17:52:49 2019 -0800
    all.joiner for ncbiRefSeqHgmd, refs #22659
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
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    a30576bb71fb1cf4cc78ecc49ae9bbfd4b02b282 Fri Feb 15 14:04:08 2019 -0800
    removing override statement on fr3 trackDb.ra, refs #22925
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
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    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/chainSelf.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeGencodeGene.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeGencodeIntron.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeSangerChipH3H4.html
  • lines changed 5, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeUcsdNgGif.html
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    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeYaleAffyRNATars.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encodeYaleAffyRNATransMap.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/encode_tba23EvoFold.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/hg17Kg.html
  • lines changed 2, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/mzPt1Mm3Rn3Gg2_pHMM.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/rBestChainPanTro1.html
  • lines changed 1, context: html, text, full: html, text
    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
    Updating redirected links for hg16 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/hg16/rBestNetPanTro1.html
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    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
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    79944079c8c70bb1bf129a2068336580287523b4 Mon Feb 11 10:55:44 2019 -0800
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    cb04f6deaf80f5bc4dc3e37dd48f959aa0a6d410 Wed Feb 13 11:39:09 2019 -0800
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    bf574709f3c53992e14d84b6340d0fd0fe8e0488 Sat Feb 16 09:04:25 2019 -0800
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    bf574709f3c53992e14d84b6340d0fd0fe8e0488 Sat Feb 16 09:04:25 2019 -0800
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    bf574709f3c53992e14d84b6340d0fd0fe8e0488 Sat Feb 16 09:04:25 2019 -0800
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    e415908171485847b1089ce4e71e74b5bc746727 Mon Feb 11 12:40:11 2019 -0800
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    93713cf0b9c19876ee14e41ef2559865b7eaa8ef Mon Feb 11 15:55:21 2019 -0800
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    c939870f6812ab1eed40f2a0631004e0de8d8cc0 Mon Feb 11 16:16:13 2019 -0800
    Turning off auto-scaling for the Coverage tracks by default, refs #21811
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    bf574709f3c53992e14d84b6340d0fd0fe8e0488 Sat Feb 16 09:04:25 2019 -0800
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    cb04f6deaf80f5bc4dc3e37dd48f959aa0a6d410 Wed Feb 13 11:39:09 2019 -0800
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    e35b45b19df0468ae8554920eafa94e0706a72f7 Fri Feb 15 09:27:27 2019 -0800
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