All File Changes

v388_preview2 to v388_base (2019-09-16 to 2019-09-23) v388

• src/hg/cirm/gateway/htdocs/examples/datasetPageTemplate.html
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    9c66b7b454139b6c6764f9b94c4977fe11338570 Wed Sep 18 11:33:01 2019 -0700
    Minor correction to template. Adding necessary setRoot.html. no redmine
• src/hg/cirm/gateway/htdocs/examples/setRoot.html
  • lines changed 5, context: html, text, full: html, text
    9c66b7b454139b6c6764f9b94c4977fe11338570 Wed Sep 18 11:33:01 2019 -0700
    Minor correction to template. Adding necessary setRoot.html. no redmine
• src/hg/hgGene/domains.c
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    de6863ac47223a5971cb506caec79c8e8552e79c Wed Sep 18 14:43:52 2019 -0700
    Removing links to chimerax, refs #22953
• src/hg/hgc/interactClick.c
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    84a498e5605cb332998c9650c2e254ea4993d739 Mon Sep 16 10:15:55 2019 -0700
    Add note about forcing interactions to pack in MR mode. From JK input. refs #24037
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    c3077e2a7da1c10641ac87799738d68e3525670d Mon Sep 16 10:39:04 2019 -0700
    Make setting conform to our flexible convention. refs #24037
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    213a9ed6ded66b132124cce8bc4850b40c37aa5d Wed Sep 18 13:23:02 2019 -0700
    Tweak text on page, responding to QA. refs #24037
• src/hg/htdocs/FAQ/FAQdownloads.html
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    a9c610f57dfd949068316c822d7c5f4a2beb9c48 Wed Sep 18 11:55:33 2019 -0700
    Adding FAQ entry on analysis sets refs #24071
• src/hg/htdocs/goldenPath/gbdDescriptions.html
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    acecde132ebb9310c523d1a204bfbd72836f5c94 Thu Sep 19 13:34:44 2019 -0700
    Adding a note about the API on a retired page that describes how to find schema information.
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 24, context: html, text, full: html, text
    0cee4b190ab4c2ddfa9fafc6e50c16cca5542851 Wed Sep 18 11:04:50 2019 -0700
    Expanding API documentation for mirrors refs #24129
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 13, context: html, text, full: html, text
    dee72cee166208ce54ff7f4c0c5baece0dc33331 Tue Sep 17 10:43:28 2019 -0700
    Adding information about loading bams to gbib.html refs #24137
• src/hg/htdocs/goldenPath/help/interact.html
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    67993730687f98fab64a01c80a33821bb8baaeb4 Mon Sep 16 14:47:18 2019 -0700
    Code review changes added to interact.html changes refs #24147
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    66fd7cc1b66487ccc2864b670c100e244fe3add2 Mon Sep 16 10:50:19 2019 -0700
    Add multiregion setting to trackDb docs. refs #24037
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    79f2015bd4a398a8e9eece9c457cbeba41ca5831 Mon Sep 16 10:54:12 2019 -0700
    Aim for a little consistency. sigh. refs #24037
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 4, context: html, text, full: html, text
    66fd7cc1b66487ccc2864b670c100e244fe3add2 Mon Sep 16 10:50:19 2019 -0700
    Add multiregion setting to trackDb docs. refs #24037
  • lines changed 1, context: html, text, full: html, text
    79f2015bd4a398a8e9eece9c457cbeba41ca5831 Mon Sep 16 10:54:12 2019 -0700
    Aim for a little consistency. sigh. refs #24037
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    66fd7cc1b66487ccc2864b670c100e244fe3add2 Mon Sep 16 10:50:19 2019 -0700
    Add multiregion setting to trackDb docs. refs #24037
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    d97dbc73b0b17df995a94a1dffcab2b02e569910 Tue Sep 17 11:42:13 2019 -0700
    Updating newsarch.html for the grcIncidentDb track for galGal6 and danRer11, refs #24024
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    ea73d04b05c28fa98e2dd13862fc5a2c6b4b3adc Tue Sep 17 15:04:06 2019 -0700
    Editing newsarch.html for grc incident track release, refs #24024
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    2b626d7e2bfd3a9757bae4d62e534c249b09f3ee Tue Sep 17 15:16:49 2019 -0700
    Updating date on newsarch for grc track release, refs #24024
• src/hg/htdocs/images/Jim-Kent-David-Haussler-Scot-Kennedy-Patrick-Gavin-genome-assembly-era-Group-2000.jpg
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    dd22eb530a64205c2ff00dcd2ee10aa829fb9928 Fri Sep 20 16:23:13 2019 -0700
    Adding an image of Jim, David, Scot, and Patrick for the history page, refs #20314
• src/hg/htdocs/images/renMouseDev.png
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    3e17a5dd38b22e37e7c31cb9983272e58900d41b Wed Sep 18 17:32:52 2019 -0700
    Add graphic of mouse developmental stages assayed by ENCODE 3, from Ren lab. refs #23880
• src/hg/htdocs/training/index.html
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    5417ab11cc63a4748ec5b77b91a5601c4f8afe8e Mon Sep 16 13:36:08 2019 -0700
    removed completed kansas city workshop, moved PAG workshop to next-four list, added eshg berlin
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    7e78be73008fb8c9b56f96ec78e45bc5bb2efbde Wed Sep 18 13:48:11 2019 -0700
    adding rotterdam workshop. bumping PAG out of the next-four list. adding OHSU
• src/hg/hubApi/list.c
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    ab553b2a1e248cdc8108d39f5e2a8d859216f15b Tue Sep 17 14:21:12 2019 -0700
    fix list chromosomes function for bigDataUrl tracks on database genomes refs #23589
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    3470ab0967e3c4775a6ba192b49eb0ab95c7827a Tue Sep 17 14:34:19 2019 -0700
    place output of list tracks for database genome in container refs #24127
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    7ecb25c2270135eabfeb50aeaca073cf9d899ccb Tue Sep 17 14:49:38 2019 -0700
    correct list chromosomes for a big* track from database where bigDataUrl is in a table refs #23589
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    06f2c99883ae9eba0185f49ef56fa33f48c33040 Tue Sep 17 15:07:11 2019 -0700
    verify fileName column exists before asking for it refs #23589
• src/hg/hubApi/tests/expected/list03.gz
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    3470ab0967e3c4775a6ba192b49eb0ab95c7827a Tue Sep 17 14:34:19 2019 -0700
    place output of list tracks for database genome in container refs #24127
• src/hg/hubApi/tests/expected/list09.gz
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    3470ab0967e3c4775a6ba192b49eb0ab95c7827a Tue Sep 17 14:34:19 2019 -0700
    place output of list tracks for database genome in container refs #24127
• src/hg/hubApi/tests/expected/list16.gz
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    ab553b2a1e248cdc8108d39f5e2a8d859216f15b Tue Sep 17 14:21:12 2019 -0700
    fix list chromosomes function for bigDataUrl tracks on database genomes refs #23589
• src/hg/hubApi/tests/expected/list17.gz
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    7ecb25c2270135eabfeb50aeaca073cf9d899ccb Tue Sep 17 14:49:38 2019 -0700
    correct list chromosomes for a big* track from database where bigDataUrl is in a table refs #23589
• src/hg/hubApi/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    ab553b2a1e248cdc8108d39f5e2a8d859216f15b Tue Sep 17 14:21:12 2019 -0700
    fix list chromosomes function for bigDataUrl tracks on database genomes refs #23589
  • lines changed 7, context: html, text, full: html, text
    7ecb25c2270135eabfeb50aeaca073cf9d899ccb Tue Sep 17 14:49:38 2019 -0700
    correct list chromosomes for a big* track from database where bigDataUrl is in a table refs #23589
• src/hg/inc/versionInfo.h
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    ecf836c5e37e333870adbc97ad3e38c1939056d1 Mon Sep 23 10:06:09 2019 -0700
    New version number v388
• src/hg/lib/hicUi.c
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    fef68995ad2ebf461ac6147fe67cd34de4e0c6a3 Fri Sep 20 16:29:54 2019 -0700
    Changes in response to code review, refs #24153
• src/hg/makeDb/avada/avada.as
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    4a819ccfe7f5074c2295daacd838731fe59534fb Tue Sep 17 02:16:07 2019 -0700
    new avada track, refs #24156
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    2aa6100449742684bbd3fc9d86ace72319e0308b Thu Sep 19 07:39:11 2019 -0700
    fixing tdb bug due to duplicated table name in as file
• src/hg/makeDb/avada/toBed.py
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    4a819ccfe7f5074c2295daacd838731fe59534fb Tue Sep 17 02:16:07 2019 -0700
    new avada track, refs #24156
• src/hg/makeDb/doc/hg19.txt
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    4a819ccfe7f5074c2295daacd838731fe59534fb Tue Sep 17 02:16:07 2019 -0700
    new avada track, refs #24156
• src/hg/makeDb/doc/hg38/crisprAll.txt
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    c90167e4248ec092a5c3be6aec0366759f65c95a Thu Sep 19 12:35:04 2019 -0700
    procedure completed refs #24172
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
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    c33114d442d7e717c3712e84c60e73ead55c982d Fri Sep 20 13:40:52 2019 -0700
    new Gencode M23 knownGene release
• src/hg/makeDb/mastermind/mastermind.as
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    2ae4d94adb7cb66f48c5c6f2b686cd9db29fca16 Fri Sep 20 05:50:51 2019 -0700
    removing mastermind files, now they are ottomatic
• src/hg/makeDb/mastermind/mastermindToBed.py
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    2ae4d94adb7cb66f48c5c6f2b686cd9db29fca16 Fri Sep 20 05:50:51 2019 -0700
    removing mastermind files, now they are ottomatic
• src/hg/makeDb/trackDb/human/avada.html
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    4a819ccfe7f5074c2295daacd838731fe59534fb Tue Sep 17 02:16:07 2019 -0700
    new avada track, refs #24156
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
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    0e3551f85282f521b80bd3284acfae077553b72b Mon Sep 16 16:11:27 2019 -0700
    Updating the version to the current v32, refs #24032
• src/hg/makeDb/trackDb/human/mastermind.html
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/hg/makeDb/trackDb/human/trackDb.ra
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    4a819ccfe7f5074c2295daacd838731fe59534fb Tue Sep 17 02:16:07 2019 -0700
    new avada track, refs #24156
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    ba37f18ca8b495b4f150f0639e6c739bb630a6fe Mon Sep 16 13:27:03 2019 -0700
    Updating http to https for braFlo1, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
  • lines changed 229, context: html, text, full: html, text
    666a852700dda342c2ba7aaa712e135025c9be44 Wed Sep 18 17:57:37 2019 -0700
    Correct ages in labels, etc. to include .5, as per input from Ren lab. refs #23880
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    67d66a7d1e5c5de9b9ecbea41238cb19f52515b7 Thu Sep 19 11:03:58 2019 -0700
    Remove superfluous metadata lines. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra
  • lines changed 58, context: html, text, full: html, text
    666a852700dda342c2ba7aaa712e135025c9be44 Wed Sep 18 17:57:37 2019 -0700
    Correct ages in labels, etc. to include .5, as per input from Ren lab. refs #23880
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    07c5245a60a9edfae0ea9f7b71a08e867db23ab9 Thu Sep 19 11:38:32 2019 -0700
    Add graphic of mouse development. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra
  • lines changed 1965, context: html, text, full: html, text
    666a852700dda342c2ba7aaa712e135025c9be44 Wed Sep 18 17:57:37 2019 -0700
    Correct ages in labels, etc. to include .5, as per input from Ren lab. refs #23880
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    67d66a7d1e5c5de9b9ecbea41238cb19f52515b7 Thu Sep 19 11:03:58 2019 -0700
    Remove superfluous metadata lines. refs #23880
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    df271bddabee40852bdef2312e616e8b49a9a4ff Thu Sep 19 11:37:24 2019 -0700
    Expand histone descriptive table and reorder subtracks based on input from data provider, D. Gorkin. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/encode3Reg.html
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    3e17a5dd38b22e37e7c31cb9983272e58900d41b Wed Sep 18 17:32:52 2019 -0700
    Add graphic of mouse developmental stages assayed by ENCODE 3, from Ren lab. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenAtac.html
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    6b2423fa6f1713f7d4f5d4569eebf5fecd13edf2 Wed Sep 18 13:46:07 2019 -0700
    Format citations and update based on input from data provider (D. Gorkin. refs #23880
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    3e17a5dd38b22e37e7c31cb9983272e58900d41b Wed Sep 18 17:32:52 2019 -0700
    Add graphic of mouse developmental stages assayed by ENCODE 3, from Ren lab. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html
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    6b2423fa6f1713f7d4f5d4569eebf5fecd13edf2 Wed Sep 18 13:46:07 2019 -0700
    Format citations and update based on input from data provider (D. Gorkin. refs #23880
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    3e17a5dd38b22e37e7c31cb9983272e58900d41b Wed Sep 18 17:32:52 2019 -0700
    Add graphic of mouse developmental stages assayed by ENCODE 3, from Ren lab. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.html
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    07c5245a60a9edfae0ea9f7b71a08e867db23ab9 Thu Sep 19 11:38:32 2019 -0700
    Add graphic of mouse development. refs #23880
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenHistone.html
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    6b2423fa6f1713f7d4f5d4569eebf5fecd13edf2 Wed Sep 18 13:46:07 2019 -0700
    Format citations and update based on input from data provider (D. Gorkin. refs #23880
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    3e17a5dd38b22e37e7c31cb9983272e58900d41b Wed Sep 18 17:32:52 2019 -0700
    Add graphic of mouse developmental stages assayed by ENCODE 3, from Ren lab. refs #23880
  • lines changed 42, context: html, text, full: html, text
    df271bddabee40852bdef2312e616e8b49a9a4ff Thu Sep 19 11:37:24 2019 -0700
    Expand histone descriptive table and reorder subtracks based on input from data provider, D. Gorkin. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.alpha.ra
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    c33114d442d7e717c3712e84c60e73ead55c982d Fri Sep 20 13:40:52 2019 -0700
    new Gencode M23 knownGene release
• src/hg/makeDb/trackDb/mouse/mm10/knownGeneOld11.html
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    c33114d442d7e717c3712e84c60e73ead55c982d Fri Sep 20 13:40:52 2019 -0700
    new Gencode M23 knownGene release
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    c33114d442d7e717c3712e84c60e73ead55c982d Fri Sep 20 13:40:52 2019 -0700
    new Gencode M23 knownGene release
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    a46f4b24ba0e7bc4c41deca3295ee0a2b87a2b40 Tue Sep 17 09:39:14 2019 -0700
    Updating http to https for ponAbe2 (orangutan), uiLinks cronjob.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
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    a46f4b24ba0e7bc4c41deca3295ee0a2b87a2b40 Tue Sep 17 09:39:14 2019 -0700
    Updating http to https for ponAbe2 (orangutan), uiLinks cronjob.
• src/hg/makeDb/trackDb/tetraodon/chainSelf.html
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    1dd16450a4d66999fa1341e1b206c4e27861c450 Mon Sep 16 13:23:25 2019 -0700
    Updating http to https for tetNig1, uiLinks cronjob.
• src/hg/makeDb/trackDb/tetraodon/netSelf.html
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    1dd16450a4d66999fa1341e1b206c4e27861c450 Mon Sep 16 13:23:25 2019 -0700
    Updating http to https for tetNig1, uiLinks cronjob.
• src/hg/utils/hubClone/hubClone.c
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    0bc408820ce1cc3b69dcaa49d72563ea0772b7af Wed Sep 18 17:04:02 2019 -0700
    Making hubClone allow multiple directories in genomes and trackDb file locations, reported by Lou
• src/hg/utils/otto/mastermind/buildMastermind.sh
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
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    fae82da25126fb8f6f14386243b858defe2f8ad5 Thu Sep 19 06:10:57 2019 -0700
    ottomating the archive for mastermind, refs #24157
• src/hg/utils/otto/mastermind/hg19/chromAlias.tab
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/hg/utils/otto/mastermind/hg38/chromAlias.tab
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/hg/utils/otto/mastermind/makefile
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/hg/utils/otto/mastermind/mastermind.as
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/hg/utils/otto/mastermind/mastermindToBed.py
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    b73a4247460859687b16ae03aa9b848f56576aa1 Tue Sep 17 02:40:05 2019 -0700
    ottomatizing mastermind, refs #24157
• src/inc/srcVersion.h
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    ecf836c5e37e333870adbc97ad3e38c1939056d1 Mon Sep 23 10:06:09 2019 -0700
    New version number v388
• src/lib/net.c
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    7807b5c21514ccf345d2b610e6ba1ed39725d269 Mon Sep 23 00:36:32 2019 -0700
    Incorporating change to support 307 and 308 redirect codes since the Encode portal seems to use them and customers are starting to ask for them.
• src/lib/udc.c
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    7807b5c21514ccf345d2b610e6ba1ed39725d269 Mon Sep 23 00:36:32 2019 -0700
    Incorporating change to support 307 and 308 redirect codes since the Encode portal seems to use them and customers are starting to ask for them.
• src/utils/qa/weeklybld/buildEnv.csh
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    2a2e0a5bf096f6bd7c01095d29e24914e822d46f Mon Sep 23 10:05:14 2019 -0700
    v388 final build, refs #24138

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• files changed: 83