All File Changes

v386_preview to v386_preview2 (2019-07-29 to 2019-08-05) v386

• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
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    7f1376a86f6b559c05763120e15b55c68ac7721d Fri Aug 2 15:58:08 2019 -0700
    Adding notice about it being obsolete really to usage message.
• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
  • lines changed 275, context: html, text, full: html, text
    84a3604cd4c2ef2edab9afd8470f8c880bba7dd5 Thu Aug 1 10:08:45 2019 -0700
    Slimmed down version of geoStormToHcaStorm. This one does not do any deletion or renaming of tags. It does do a few things that are hopefully worthwhile - reformatting dates, extracting accessions from URLs, and pasting together full addresses mostly. Typically run after geoToTagStorm.
  • lines changed 8, context: html, text, full: html, text
    34d918b704c7eb48b559eb7bb480520cfdee62fd Fri Aug 2 16:02:43 2019 -0700
    Removing protocol reprocessing, with the new schema not needed.
  • lines changed 123, context: html, text, full: html, text
    ace543bb0ea601a9d7e23dce57bfcf6cfc571f7d Sat Aug 3 09:00:04 2019 -0700
    Adding in sra info.
  • lines changed 1, context: html, text, full: html, text
    81262509982f63796d795d670d111094b080246c Sat Aug 3 09:08:51 2019 -0700
    Fixing typo in file.read_index.
• src/hca/fromGeo/geoToHcaStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    84a3604cd4c2ef2edab9afd8470f8c880bba7dd5 Thu Aug 1 10:08:45 2019 -0700
    Slimmed down version of geoStormToHcaStorm. This one does not do any deletion or renaming of tags. It does do a few things that are hopefully worthwhile - reformatting dates, extracting accessions from URLs, and pasting together full addresses mostly. Typically run after geoToTagStorm.
• src/hg/hgGene/pathways.c
  • lines changed 1, context: html, text, full: html, text
    d74dbff02dfc62a46cdeee1f3be9b8a6bb0d3537 Fri Aug 2 16:28:18 2019 -0700
    Updating reactome pathways linkout, refs #23940
• src/hg/hgTables/asFilter.c
  • lines changed 64, context: html, text, full: html, text
    d07a60844e7812764456164fb3dd1feb9cb12870 Tue Jul 30 14:42:10 2019 -0700
    hgTables: support bigBed autoSql enum/set filters. fixes #23926
• src/hg/hgTables/asFilter.h
  • lines changed 1, context: html, text, full: html, text
    d07a60844e7812764456164fb3dd1feb9cb12870 Tue Jul 30 14:42:10 2019 -0700
    hgTables: support bigBed autoSql enum/set filters. fixes #23926
• src/hg/hgTables/filterFields.c
  • lines changed 8, context: html, text, full: html, text
    939e96c53b6c0801e3ad9019e87097c13f2d53d1 Tue Jul 30 13:20:59 2019 -0700
    bigBed filter controls for enum/set columns need to support asColumnToSqlType formatting (in addition to SQL desc formatting). fixes #23925
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    184bc4943b88623ae01bda561a1e7024bc4cc21d Sun Aug 4 13:15:00 2019 -0700
    don't free tdb contents which might be in separately allocated memory
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 44, context: html, text, full: html, text
    62553262014b67dd654402b70b90fc76bb3f3aef Tue Jul 30 11:11:51 2019 -0700
    Adding note about U nucleotides on stand-alone blat, fixing tags #23890
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    d1f7caa72759548b36c87954a6b19f700658d7ae Mon Jul 29 15:45:10 2019 -0700
    Adding equCab3 to FAQrelease, refs #21223
  • lines changed 108, context: html, text, full: html, text
    7fd61a9b8e3db3a18bf285628ed3cd60cdf7731f Wed Jul 31 10:19:09 2019 -0700
    Updating old entries #23611
  • lines changed 5, context: html, text, full: html, text
    aea06327a4095872b6078777e50859e63b064a2c Thu Aug 1 13:21:27 2019 -0700
    Updating NCBI UCSC comparison of FAQrelease #23611
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 21, context: html, text, full: html, text
    8a64746755073e3980d4c1dbb1263157edc2d48b Mon Jul 29 16:42:43 2019 -0700
    Updating credits.html for equCab3, refs #21223
  • lines changed 16, context: html, text, full: html, text
    ea75935f71c3d2400057d34de5eb60f7fac9645f Tue Jul 30 10:43:59 2019 -0700
    Adding new assembly equCab3 to credits.html #21223
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    c92f92f8a9c97137534faa084991ca8d0154bc5e Mon Jul 29 16:10:35 2019 -0700
    Editing CyVerse path and adding new image for #23921
  • lines changed 1, context: html, text, full: html, text
    eea98aa0298a44fdbab938c30f7bb4c9250a5fd6 Wed Jul 31 09:43:36 2019 -0700
    Fixing path to cyVerse files #23921
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    cfe2ed16fc76ffdd709182eb83e80d3788805647 Thu Aug 1 08:59:07 2019 -0700
    fixing BLAT link
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 39, context: html, text, full: html, text
    a300d9e597facb8a3751a53f768084240a4d0d05 Tue Jul 30 11:17:29 2019 -0700
    Adding new assembly equCab3 to newsArch page #21223
  • lines changed 1, context: html, text, full: html, text
    9ad55bf14c88c7f011845479f4ea9932d0002342 Tue Jul 30 11:25:17 2019 -0700
    Adding new assembly equCab3 to indexNews page #21223
• src/hg/htdocs/images/cyverseEditedPaths.png
  • lines changed 0, context: html, text, full: html, text
    c92f92f8a9c97137534faa084991ca8d0154bc5e Mon Jul 29 16:10:35 2019 -0700
    Editing CyVerse path and adding new image for #23921
  • lines changed 0, context: html, text, full: html, text
    eea98aa0298a44fdbab938c30f7bb4c9250a5fd6 Wed Jul 31 09:43:36 2019 -0700
    Fixing path to cyVerse files #23921
  • lines changed 0, context: html, text, full: html, text
    6797c36baa29042d4cdac41e197644fd99d6852e Wed Jul 31 10:07:52 2019 -0700
    Replacing image, weirdly didnt load #23921
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    45b59b2951ea38252939c8805ded698ff2714e33 Wed Jul 31 10:31:49 2019 -0700
    Revert "Replacing image, weirdly didnt load #23921" This reverts commit 6797c36baa29042d4cdac41e197644fd99d6852e.
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    54d189f992b8fd585ade493a3e146f391be03077 Wed Jul 31 11:38:24 2019 -0700
    ampersands in URLs need to be encoded refs #23734
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    9ad55bf14c88c7f011845479f4ea9932d0002342 Tue Jul 30 11:25:17 2019 -0700
    Adding new assembly equCab3 to indexNews page #21223
• src/hg/htdocs/training/index.html
  • lines changed 17, context: html, text, full: html, text
    c235d4fcec8065db5ac56670cd2d0c0d92a03a66 Thu Aug 1 20:38:15 2019 -0700
    dropping completed grand rapids workshop and moving mayo clinic into top four
  • lines changed 1, context: html, text, full: html, text
    3e369fe7672c1d07f63d0f8be2fe397ab998d781 Thu Aug 1 20:42:49 2019 -0700
    fix one-char typo
  • lines changed 1, context: html, text, full: html, text
    deecef66ba49cdf0b041ed053e41b9a40fb2e08e Sat Aug 3 02:42:57 2019 -0700
    putting in better link to the hutch
• src/hg/hubApi/apiUtils.c
  • lines changed 1, context: html, text, full: html, text
    cc0fcb9762d1900766c7e1f1942cbb5561297854 Tue Jul 30 09:55:28 2019 -0700
    allow bigGenePred to open when it is just a bigDataUrl trackDb entry with no associated table refs #23900
• src/hg/hubApi/hubApi.c
  • lines changed 3, context: html, text, full: html, text
    afeeb82174da7dda62cffcbbf3ffab87194269d6 Fri Aug 2 15:37:49 2019 -0700
    show correct stats for each subTrack in a composite refs #23589
• src/hg/hubApi/list.c
  • lines changed 6, context: html, text, full: html, text
    c691103685d313c146aded7c45852ac7678267d1 Fri Aug 2 14:31:19 2019 -0700
    do not show itemCounts for containers, they have no items to count refs #23589
• src/hg/js/external/makefile
  • lines changed 2, context: html, text, full: html, text
    7185b2e8f64323c0858f25a5152ea325ee789e3b Fri Aug 2 16:03:22 2019 -0700
    adding sorttable.js to the output refs #23734
• src/hg/js/external/sorttable.js
  • lines changed 499, context: html, text, full: html, text
    3f229b7354bbc99a6fe98e71afd0a0d340c4cc6a Fri Aug 2 09:42:38 2019 -0700
    sorttable is properly an external script refs #23734
• src/hg/js/sorttable.js
  • lines changed 495, context: html, text, full: html, text
    8afe6f12967f38da19ce796d17a2510ec47b52ee Wed Jul 31 14:18:47 2019 -0700
    initial original source before jshint improvements refs #23734
  • lines changed 32, context: html, text, full: html, text
    b251152d660f0ccda8732d8312c631ffab31b52e Thu Aug 1 17:14:16 2019 -0700
    cleanup source due to jshint hints, not perfect yet refs #23734
  • lines changed 499, context: html, text, full: html, text
    3f229b7354bbc99a6fe98e71afd0a0d340c4cc6a Fri Aug 2 09:42:38 2019 -0700
    sorttable is properly an external script refs #23734
• src/hg/makeDb/doc/VGP/README.txt
  • lines changed 108, context: html, text, full: html, text
    b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700
    adding the .txt files and a README to describe the process refs #23734
• src/hg/makeDb/doc/VGP/amphibian.list
  • lines changed 2, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/doc/VGP/bird.list
  • lines changed 4, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/doc/VGP/build.run.list
  • lines changed 21, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/doc/VGP/commonNameOrder.list
  • lines changed 21, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/doc/VGP/commonNames.txt
  • lines changed 3, context: html, text, full: html, text
    b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700
    adding the .txt files and a README to describe the process refs #23734
  • lines changed 4, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
  • lines changed 2, context: html, text, full: html, text
    2dc3fec412b817b015deb93f5862e57aea0661b7 Thu Aug 1 16:06:05 2019 -0700
    also update groups.txt if updated here and run up sym links during a make refs #23734
• src/hg/makeDb/doc/VGP/fish.list
  • lines changed 12, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
  • lines changed 1, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
• src/hg/makeDb/doc/VGP/genomes.txt
  • lines changed 231, context: html, text, full: html, text
    b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700
    adding the .txt files and a README to describe the process refs #23734
• src/hg/makeDb/doc/VGP/groups.txt
  • lines changed 39, context: html, text, full: html, text
    b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700
    adding the .txt files and a README to describe the process refs #23734
• src/hg/makeDb/doc/VGP/hub.txt
  • lines changed 6, context: html, text, full: html, text
    b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700
    adding the .txt files and a README to describe the process refs #23734
  • lines changed 1, context: html, text, full: html, text
    7e2340e0b897f6a6d3102d2fd8e12d14796432e5 Thu Aug 1 14:19:57 2019 -0700
    Including hub.txt in the makefile, so changes can be made from tree #23734
  • lines changed 1, context: html, text, full: html, text
    6260111d7ae6ab49de776d35fa86fa626fa024fd Fri Aug 2 14:15:09 2019 -0700
    Fixing up the VGP pages #23734
• src/hg/makeDb/doc/VGP/makefile
  • lines changed 24, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
  • lines changed 4, context: html, text, full: html, text
    7e2340e0b897f6a6d3102d2fd8e12d14796432e5 Thu Aug 1 14:19:57 2019 -0700
    Including hub.txt in the makefile, so changes can be made from tree #23734
  • lines changed 13, context: html, text, full: html, text
    2dc3fec412b817b015deb93f5862e57aea0661b7 Thu Aug 1 16:06:05 2019 -0700
    also update groups.txt if updated here and run up sym links during a make refs #23734
• src/hg/makeDb/doc/VGP/mammal.list
  • lines changed 3, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
  • lines changed 1, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
• src/hg/makeDb/doc/VGP/mkAsmStats.pl
  • lines changed 264, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
  • lines changed 23, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
  • lines changed 1, context: html, text, full: html, text
    9f30c7b8a1cc0c6b082f96b0ff1a2f2011a5992e Fri Aug 2 09:15:01 2019 -0700
    Fixing some links to look better #23734
  • lines changed 9, context: html, text, full: html, text
    6260111d7ae6ab49de776d35fa86fa626fa024fd Fri Aug 2 14:15:09 2019 -0700
    Fixing up the VGP pages #23734
• src/hg/makeDb/doc/VGP/mkGenomes.pl
  • lines changed 123, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
  • lines changed 4, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
• src/hg/makeDb/doc/VGP/mkHubIndex.pl
  • lines changed 238, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
  • lines changed 33, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
  • lines changed 1, context: html, text, full: html, text
    9f30c7b8a1cc0c6b082f96b0ff1a2f2011a5992e Fri Aug 2 09:15:01 2019 -0700
    Fixing some links to look better #23734
  • lines changed 8, context: html, text, full: html, text
    6260111d7ae6ab49de776d35fa86fa626fa024fd Fri Aug 2 14:15:09 2019 -0700
    Fixing up the VGP pages #23734
• src/hg/makeDb/doc/VGP/mkSymLinks.sh
  • lines changed 21, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
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    d84a661a8c877c41a109a21ba4f095d0f26c12c4 Wed Jul 31 18:51:28 2019 -0700
    add assembly report and run during the make refs #23734
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    cef25c4a65ad872bda85799c6e2a6d237420c1bc Fri Aug 2 21:46:29 2019 -0700
    now symlink in the photograph for the gateway page refs #23734
• src/hg/makeDb/doc/VGP/perlPara.pl
  • lines changed 127, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/doc/VGP/reptile.list
  • lines changed 1, context: html, text, full: html, text
    89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700
    add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
• src/hg/makeDb/doc/VGP/runOneJob
  • lines changed 79, context: html, text, full: html, text
    d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700
    scripts used to build the VGP assembly hubs refs #23734
• src/hg/makeDb/trackDb/chainSelf.html
  • lines changed 1, context: html, text, full: html, text
    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/bgiCov.html
  • lines changed 2, context: html, text, full: html, text
    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/bgiGene.html
  • lines changed 1, context: html, text, full: html, text
    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/bgiSnp.html
  • lines changed 2, context: html, text, full: html, text
    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
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    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 1, context: html, text, full: html, text
    a182ee225d751458d96de06630d8d491d935080b Tue Jul 30 10:23:58 2019 -0700
    Updating http to https for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/horse/equCab3/description.html
  • lines changed 1, context: html, text, full: html, text
    6fb1eb33c6f91f4180595ce45b15f94707679e52 Mon Jul 29 15:43:12 2019 -0700
    Updating description page for 'twilight', refs #21223
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    5897274a97a6063fb6f6a3882aa63b4b3a97b50c Wed Jul 31 09:30:35 2019 -0700
    Updating http to https for calJac1, uiLinks cronjob.
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 1, context: html, text, full: html, text
    7d550538d9cdc37b2b3578970dc6cd38567e5a57 Mon Aug 5 09:05:05 2019 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 2, context: html, text, full: html, text
    24a0b8a64f89182c705fc822ea4f1fff03af95f2 Thu Aug 1 08:09:21 2019 -0700
    Updating http to https for tarSyr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html
  • lines changed 1, context: html, text, full: html, text
    7d550538d9cdc37b2b3578970dc6cd38567e5a57 Mon Aug 5 09:05:05 2019 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
  • lines changed 2, context: html, text, full: html, text
    7d550538d9cdc37b2b3578970dc6cd38567e5a57 Mon Aug 5 09:05:05 2019 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
  • lines changed 1, context: html, text, full: html, text
    7d550538d9cdc37b2b3578970dc6cd38567e5a57 Mon Aug 5 09:05:05 2019 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce2/netCb1.html
  • lines changed 1, context: html, text, full: html, text
    7d550538d9cdc37b2b3578970dc6cd38567e5a57 Mon Aug 5 09:05:05 2019 -0700
    Updating http to https for ce2, uiLinks cronjob.
• src/hg/mouseStuff/mafNoAlign/mafNoAlign.c
  • lines changed 100, context: html, text, full: html, text
    804466264c86aa3d9edc8edcfe1039a2f5392b20 Mon Jul 29 16:12:54 2019 -0700
    a utility to print out a bed file with regions that have no alignment in a maf file
• src/hg/mouseStuff/mafNoAlign/makefile
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    804466264c86aa3d9edc8edcfe1039a2f5392b20 Mon Jul 29 16:12:54 2019 -0700
    a utility to print out a bed file with regions that have no alignment in a maf file
• src/hg/mouseStuff/makefile
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    5e83e24792dcb04a419cff7e17f77814ea5f3def Mon Jul 29 16:18:10 2019 -0700
    add mafNoAlign to utils build
• src/hg/utils/automation/asmHubCpG.pl
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    1b17e173bde7713fe7080825f27efb8e952419f4 Thu Aug 1 14:51:39 2019 -0700
    updating text after QA comments refs #23734
• src/hg/utils/automation/asmHubGatewayPage.pl
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    1b17e173bde7713fe7080825f27efb8e952419f4 Thu Aug 1 14:51:39 2019 -0700
    updating text after QA comments refs #23734
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    100924e5f5169717677039f59ab4fb85099d68d8 Thu Aug 1 16:48:30 2019 -0700
    add VGP outlink refs #23734
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    192b2ae780feed3f18c415c42c1de1dbf7bf5be9 Fri Aug 2 21:48:00 2019 -0700
    now with gateway page images refs #23734
• src/hg/utils/automation/asmHubGc5Percent.pl
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    1b17e173bde7713fe7080825f27efb8e952419f4 Thu Aug 1 14:51:39 2019 -0700
    updating text after QA comments refs #23734
• src/hg/utils/automation/asmHubTrackDb.sh
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    1b17e173bde7713fe7080825f27efb8e952419f4 Thu Aug 1 14:51:39 2019 -0700
    updating text after QA comments refs #23734
• src/hg/utils/automation/doAssemblyHub.pl
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    bf57fe2786a732c3e49ae6453aed45b8062b6ed6 Thu Aug 1 14:57:57 2019 -0700
    add twoBitDup check and construct liftOver files and add doNcbiGene refs #23734
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    192b2ae780feed3f18c415c42c1de1dbf7bf5be9 Fri Aug 2 21:48:00 2019 -0700
    now with gateway page images refs #23734
• src/hg/utils/automation/gpToIx.pl
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    2f9ecbef0ea856db2838ef569c817f7bafd4de09 Thu Aug 1 14:55:29 2019 -0700
    correct word in usage message refs #23918
• src/hg/utils/hubCheck/hubCheck.c
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    56ec64d6672d5c2ef118bd5ef929ac8bf72b6e61 Mon Jul 29 15:19:36 2019 -0700
    First cut of having hubCheck output javascript arrays for jstree, refs #13428
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    6e0d7083fa223488bc745093350e449a30ad38f2 Tue Jul 30 09:11:59 2019 -0700
    Prepending genome name to track ids in hubCheck html output to force uniqueness, found by running on vgp hub
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    a6c175029974819a429e1074ea5d29d8b69f43ce Tue Jul 30 10:28:26 2019 -0700
    Forgot one place to prepend genome name after Hiram feedback
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    734dde02cf470fb185706ac6ed8954f9dc3f3465 Wed Jul 31 16:28:27 2019 -0700
    Making track hub errors show up in red from hubCheck
• src/lib/internet.c
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    7ada996f71680cb0f7b1555a01a6e16814a57a7f Sun Aug 4 04:30:55 2019 -0700
    Making TCP client connect more robust by trying each IP address returned by getaddrinfo() until one connects, or all have failed.
• src/lib/net.c
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    7ada996f71680cb0f7b1555a01a6e16814a57a7f Sun Aug 4 04:30:55 2019 -0700
    Making TCP client connect more robust by trying each IP address returned by getaddrinfo() until one connects, or all have failed.
• src/tabFile/makefile
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    0096b565ed86ed6a93d0d4b3a43fb8a192bb39be Fri Aug 2 15:36:08 2019 -0700
    Adding tabToTabDir to the compile chain.
• src/tabFile/tabToTabDir/in.tsv
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
• src/tabFile/tabToTabDir/inSpec.ra
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
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    e4a0012a8cf9d60fb362903b27935dc6bf15d771 Fri Aug 2 15:48:57 2019 -0700
    Adding a NULL check that is needed for a new test case.
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    56493b0353fe3cbc20ffebda1be16dba47577784 Fri Aug 2 15:49:12 2019 -0700
    Updating test case.
• src/tabFile/tabToTabDir/makefile
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
• src/tabFile/tabToTabDir/outDir/donor.tsv
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
• src/tabFile/tabToTabDir/outDir/project.tsv
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
• src/tabFile/tabToTabDir/outDir/sample.tsv
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
• src/tabFile/tabToTabDir/tabToTabDir.c
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    1bd63a5b1364a075195e59a06c8161244f934c59 Wed Jul 31 13:31:19 2019 -0700
    The tabToTabDir program seems to work.
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    3bac9e69c474bacd569daee6b3a4d7c9a14166b0 Fri Aug 2 12:40:26 2019 -0700
    Getting rid of some uglyf debugging messages and reducing verbosity.
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    fe122ae0b137be8ee4dbeb0e64d9185190bd7e51 Fri Aug 2 14:29:14 2019 -0700
    Made it so that you list output column name first and can use constants as well as input column names to say where it comes from.
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    41f5cd680816b869e17b611553b498fb4c2d859d Fri Aug 2 14:42:54 2019 -0700
    Making the index for a table be expressed in that tables fields rather than the big input tables fields.
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    73cd280d40a79a084f10dc029693e0760f8f9f3a Fri Aug 2 15:22:24 2019 -0700
    Making this able to have a field that is a foriegn key to the primary ID in another table.
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    b825492ab638f55020b2054d445c8009cd09c94e Fri Aug 2 15:26:02 2019 -0700
    Improving usage message.
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    e4a0012a8cf9d60fb362903b27935dc6bf15d771 Fri Aug 2 15:48:57 2019 -0700
    Adding a NULL check that is needed for a new test case.
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    95d91fe3bbf9be3217ae5f075b05549326489929 Fri Aug 2 17:38:48 2019 -0700
    Adding support for picking one element from a csv cell.
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    f2b012bfbb525fda8d876b13425f4237601522f7 Fri Aug 2 21:38:43 2019 -0700
    Adding a # operator that'll give you a sha1 hash of the value. Finishing implementing @ operator.
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    ff052c8366616779b8fe428bb6630b80c14d1d4d Fri Aug 2 22:18:37 2019 -0700
    Switching to somewhat shorter md5 hash. Making first line of stanza have to start with 'table' to make the formatting stand out a little better.
• src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
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    3a435016465624711bb3af8706398532d7b2f5b1 Fri Aug 2 15:55:45 2019 -0700
    Improving comment.
• src/tagStorm/tagStormToJson/tests/test.tags
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    b7c1b595e49b7bc00effe41db2b33fb1290c0e75 Fri Aug 2 15:53:42 2019 -0700
    Updating test set
• src/userApps/fetchKentSource.sh
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    d04d32c645edb005fc4811ea1f4e70de6c1c43a5 Tue Jul 30 17:05:54 2019 -0700
    fixup directory name clash for bedJoinTabOffset refs #23806
• src/utils/qa/qaAutoTrack.sh
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    fb895c82bef394408aff9fa5ce3008daa4cee6e3 Wed Jul 31 12:16:46 2019 -0700
    Fixed an issue with qaAutoTrack not properly checking date for grcIncidentDb tracks. Bumped up tooOld date for grcIncidentDb tracks to 6 months since updates seem to come infrequently from GRC. Fixed issue with runQaAutoTrack not deleting old log files. Added checks for grcIncidentDb track on danRer10 and galGal5. Removed check for danRer7 as GRC site does not seem to have data for this assembly anymore. no redmine
• src/utils/qa/runQaAutoTrack.sh
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    fb895c82bef394408aff9fa5ce3008daa4cee6e3 Wed Jul 31 12:16:46 2019 -0700
    Fixed an issue with qaAutoTrack not properly checking date for grcIncidentDb tracks. Bumped up tooOld date for grcIncidentDb tracks to 6 months since updates seem to come infrequently from GRC. Fixed issue with runQaAutoTrack not deleting old log files. Added checks for grcIncidentDb track on danRer10 and galGal5. Removed check for danRer7 as GRC site does not seem to have data for this assembly anymore. no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    bd5fb0ae8fa613e66280e73e9a6d517f395118db Mon Aug 5 10:36:14 2019 -0700
    v386 preview2, refs #23928

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