All File Changes

v359_base to v360_preview (2017-12-18 to 2018-01-08) v360

• confs/preview.hg.conf
  • lines changed 244, context: html, text, full: html, text
    04eb2e0196e538de9cce91739fc213a0f685ced0 Sun Dec 24 01:11:42 2017 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 8, context: html, text, full: html, text
    c2487553f4e16ce6cf28e2fb9c91f8613f0a86aa Tue Dec 19 15:17:16 2017 -0800
    Install curl on gbib if not already present, used for checking which mysql server is closest, refs #20733
  • lines changed 2, context: html, text, full: html, text
    2a47b16d4bd9eb1330e34e59de287ec5f8978a12 Tue Dec 19 23:59:42 2017 -0800
    gbib: making sure that mysql server is reset, refs #20733
• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
  • lines changed 1, context: html, text, full: html, text
    57a332d97df6f6006f2b94f9e6f7fd2623ef516a Wed Dec 20 15:07:39 2017 -0800
    Changing sra_run to insdc_run as per V4 of metadata spec.
• src/hca/toHca/hcaStormToTabDir/hcaStormToTabDir.c
  • lines changed 276, context: html, text, full: html, text
    b99f908b84e7bbbe46f81c8c997f7ea9aeecf5c9 Tue Dec 12 17:13:22 2017 -0800
    First cut of V4 tagstorm to tab-dir utility. Still needs some work to connect the various types of sample together.
  • lines changed 244, context: html, text, full: html, text
    37accb7ce70ae0c9389661ada545a9ed46453ef4 Wed Dec 13 16:22:08 2017 -0800
    Linking various types of samples together with an id/derived_from fields.
  • lines changed 31, context: html, text, full: html, text
    0788f3b055293f4322288962340134441f11ff9a Thu Dec 14 12:03:00 2017 -0800
    Copying species info to all sample pieces.
  • lines changed 13, context: html, text, full: html, text
    118817ab7e80ee7f55eb7bd30710e777e515df65 Thu Dec 14 12:16:37 2017 -0800
    Moving naked sample fields to last sample in chain.
  • lines changed 130, context: html, text, full: html, text
    7a33dcbd529c98acb9ea151a51acb3f6b4290a1b Thu Dec 14 16:44:57 2017 -0800
    Moving donor.submitted_id field, making experimental_design a || separated array as EBI is doing in their spreadsheets, and making unwinding array of publications in project.publications.tsv.
  • lines changed 12, context: html, text, full: html, text
    bc8e64c384c3d1c590df66ae323207de19415287 Thu Dec 14 17:04:17 2017 -0800
    Handling submitters and contibutors.
  • lines changed 1, context: html, text, full: html, text
    f76cf9d4287628507e2c9cfe7b5fd4b1807d961a Thu Dec 14 17:11:54 2017 -0800
    Oops, reversed some fields.
  • lines changed 48, context: html, text, full: html, text
    331c418086187ca1ba157a6e348cc61f9e126390 Thu Dec 14 17:40:10 2017 -0800
    Rescuing the donor. and cell_suspension. and so forth form the sample* files field names.
  • lines changed 91, context: html, text, full: html, text
    7e0407f574cc747c239e3af9de078d91302532d9 Fri Dec 15 10:59:54 2017 -0800
    Making sample.donor.disease into a simple string variable rather than array of ontology objects in output.
  • lines changed 13, context: html, text, full: html, text
    1cfc0ba46262593dc90cd427ced6c318c3ab5d46 Fri Dec 15 11:12:24 2017 -0800
    Fixing a few wrinkels on sample_id.
  • lines changed 7, context: html, text, full: html, text
    41f861d4acd7703e2b57805da5f8d245d9756654 Fri Dec 15 11:29:16 2017 -0800
    Fixing a wrinkle in sample_id
  • lines changed 80, context: html, text, full: html, text
    bfab7701cb473e0e271e23fb9c91ccc8d2a39ebf Fri Dec 15 14:50:39 2017 -0800
    Refactoring some code so as to reuse some logic for different sample subobjects assay subobjects.
  • lines changed 100, context: html, text, full: html, text
    6486bc630c9e3c6873409aba22dfb1631bec3d70 Fri Dec 15 15:55:46 2017 -0800
    Adding in assay_id to appropriate tabs.
  • lines changed 66, context: html, text, full: html, text
    dab69af66431bf99c7a8325cf5467ba6c27f4ddc Tue Dec 19 16:43:20 2017 -0800
    Creating a tagStormCopyTags function that gets called about 8 times now and replaces about 4 lines of code. Starting to work on file tab.
  • lines changed 104, context: html, text, full: html, text
    6cc4ab64bdd73fa2759d000749ca43383c855bde Tue Dec 19 18:04:43 2017 -0800
    Second pass at adding file tab. Seems to work for the arrayExpress ones anyway.
• src/hca/v3v4/fieldsFromJson.py
  • lines changed 33, context: html, text, full: html, text
    34c386768b974eea58ea8f61b7c396641ab24e5c Mon Dec 4 15:33:50 2017 -0800
    A python script that reads a json schema and write out the fields it describes. Not totally robust. Just works on the HCA json schema well enough.
• src/hca/v3v4/v3_fields
  • lines changed 238, context: html, text, full: html, text
    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
• src/hca/v3v4/v3v4
  • lines changed 284, context: html, text, full: html, text
    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
  • lines changed 59, context: html, text, full: html, text
    5f0479c39a7257c46305e8eb377f4bbc5d49d8b7 Thu Nov 30 13:30:55 2017 -0800
    Saving another round of changes, a little more than half way through manual pass through file.
  • lines changed 21, context: html, text, full: html, text
    44cc15f9add4a8190119eab297e93b07a3efce80 Mon Dec 4 13:38:05 2017 -0800
    Done first pass of conversion table.
  • lines changed 12, context: html, text, full: html, text
    e09f0fdb9dcecb24b2dd2de24801c09c238139c1 Tue Dec 5 11:01:14 2017 -0800
    Removing some trailing .[] that just confuse things.
  • lines changed 1, context: html, text, full: html, text
    00a7e5a92d475d0d32cc17c8b146fab00b6d82af Tue Dec 12 13:40:50 2017 -0800
    Fixing typo of period for tab.
  • lines changed 20, context: html, text, full: html, text
    cfa79208aac247b068c2049273305dfa279d9965 Wed Dec 20 16:43:31 2017 -0800
    A little polishing.
• src/hca/v3v4/v4_fields
  • lines changed 166, context: html, text, full: html, text
    a79774b4bdd70c5531339148277c84b9f7d3c209 Wed Nov 29 20:27:49 2017 -0800
    Working on v3 to v4 field-by-field conversion for tagstorms.
• src/hg/cirm/cdw/cdwFindSymlinkable/cdwFindSymlinkable.c
  • lines changed 62, context: html, text, full: html, text
    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
  • lines changed 18, context: html, text, full: html, text
    a5ab42be4520767f6a9ba7ca635c7e5457d504a5 Wed Dec 20 12:20:59 2017 -0800
    Handling special case of submits that failed validation.
  • lines changed 1, context: html, text, full: html, text
    9a033c715ff18c6350eb7acae2b788ad7647368b Wed Dec 20 14:32:39 2017 -0800
    Adding note explaing that currently it must be run as root when using -fixCdwMtimes
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 3, context: html, text, full: html, text
    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
• src/hg/cirm/cdw/cdwUnlockSubmittedFile/cdwUnlockSubmittedFile.c
  • lines changed 1, context: html, text, full: html, text
    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 9, context: html, text, full: html, text
    20b34092c7789385fb83f73b95c5fe3356a45727 Wed Dec 20 16:46:42 2017 -0800
    Documenting recent changes to cdwWebBrowse
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 23, context: html, text, full: html, text
    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
• src/hg/cirm/cdw/lib/resetCdw
  • lines changed 8, context: html, text, full: html, text
    f2920bdb18db3fe25189112594547986aab8095c Wed Dec 20 16:46:04 2017 -0800
    Fixing a wrong md5sum for a an assembly .2bit file. Also coping with option name change in cdwAddAssembly
• src/hg/hgCert/hgCert.c
  • lines changed 7, context: html, text, full: html, text
    22d1b7b1d2e0f48aee47675a9622e920dacadb0f Fri Jan 5 18:13:02 2018 -0800
    Fixing compile errors and encoding consistency, even though this code is obsolete.
• src/hg/hgCollection/hgCollection.c
  • lines changed 8, context: html, text, full: html, text
    c5a827f8f0c4094c20ff333acb191ded2bf86744 Wed Dec 20 11:36:10 2017 -0800
    ongoing work on hgCollection
  • lines changed 5, context: html, text, full: html, text
    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
  • lines changed 5, context: html, text, full: html, text
    2904a2f549264f1d81450c2eb9b0a36681c737f5 Wed Jan 3 11:38:20 2018 -0800
    explicitly set type in custom composites
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 11, context: html, text, full: html, text
    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
• src/hg/hgTracks/extTools.c
  • lines changed 15, context: html, text, full: html, text
    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/hgTracks/extTools.ra
  • lines changed 23, context: html, text, full: html, text
    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/hgTracks/longRangeTrack.c
  • lines changed 63, context: html, text, full: html, text
    4e5b41a3d4c933bffb2958c9b34f925bab023179 Tue Dec 12 13:07:26 2017 -0800
    Suppress labels on interchromosomal items if any on screen would overlap. Maybe later try packing, but this could be tricky. refs #17512
  • lines changed 4, context: html, text, full: html, text
    8c07287881e7745c1070a233cff3e649bc1fdf6b Wed Dec 20 09:59:56 2017 -0800
    Remove debug statement.
• src/hg/hgTracks/menu.c
  • lines changed 58, context: html, text, full: html, text
    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    c5a827f8f0c4094c20ff333acb191ded2bf86744 Wed Dec 20 11:36:10 2017 -0800
    ongoing work on hgCollection
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    4fae8edf7d8618583df86033fa9644ab098229bf Wed Dec 20 16:31:35 2017 -0800
    Announcing the panPan2 assembly release, refs #16036
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    4fae8edf7d8618583df86033fa9644ab098229bf Wed Dec 20 16:31:35 2017 -0800
    Announcing the panPan2 assembly release, refs #16036
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 3, context: html, text, full: html, text
    3c7a9115098e154946199e0f814549f472cefb2d Fri Jan 5 15:32:39 2018 -0800
    Fixing some URL addresses in bigBarChart text examples
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    07334064a7acc319895a676e5ba3a6e2e6efbd5e Tue Dec 19 13:27:09 2017 -0800
    Updating NCBI Map Viewer link to Genome Data Viewer. refs #18671
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 1, context: html, text, full: html, text
    40e16172fe0394d1544433a04ae7f50c4ca79e76 Wed Dec 20 10:41:36 2017 -0800
    Updating style reference from code review input refs #20726
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
  • lines changed 37, context: html, text, full: html, text
    4fae8edf7d8618583df86033fa9644ab098229bf Wed Dec 20 16:31:35 2017 -0800
    Announcing the panPan2 assembly release, refs #16036
  • lines changed 34, context: html, text, full: html, text
    0f64eb14e35556ac4a91ca3d82ea71df87149351 Fri Jan 5 16:22:17 2018 -0800
    Announcing the release of the Hoffman mappability tracks for hg38, refs #19154
• src/hg/htdocs/images/Anopheles_gambiae.jpg
  • lines changed 0, context: html, text, full: html, text
    77623908c6e6655852cf957a2ff956295de4f617 Thu Dec 21 08:25:52 2017 -0800
    photo for anoGam3 refs #20743
• src/hg/htdocs/images/Cavia_aperea.jpg
  • lines changed 0, context: html, text, full: html, text
    67fe54da819ba950c79fe57ef80494e1f53820e5 Thu Jan 4 10:12:53 2018 -0800
    phot from flickr www.flickr.com/photos/trekman/4712570295 Gustavo Fernando Durán
• src/hg/htdocs/images/phylo/galVar1_6way.png
  • lines changed 0, context: html, text, full: html, text
    ddf2311e413ff8c66180f54fbc29aa5013a761d1 Mon Dec 18 14:44:11 2017 -0800
    6-way alignment phylo tree for galVar1 no redmine
• src/hg/htdocs/images/phylo/tupChi1_5way.png
  • lines changed 0, context: html, text, full: html, text
    422ac9b87674259386ff82324f8643d4cb7ca147 Mon Dec 18 14:51:35 2017 -0800
    5-way alignment tree for tupChi1 no redmine
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 1, context: html, text, full: html, text
    c5a827f8f0c4094c20ff333acb191ded2bf86744 Wed Dec 20 11:36:10 2017 -0800
    ongoing work on hgCollection
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    4fae8edf7d8618583df86033fa9644ab098229bf Wed Dec 20 16:31:35 2017 -0800
    Announcing the panPan2 assembly release, refs #16036
  • lines changed 12, context: html, text, full: html, text
    0f64eb14e35556ac4a91ca3d82ea71df87149351 Fri Jan 5 16:22:17 2018 -0800
    Announcing the release of the Hoffman mappability tracks for hg38, refs #19154
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/inc/longRange.h
  • lines changed 3, context: html, text, full: html, text
    4e5b41a3d4c933bffb2958c9b34f925bab023179 Tue Dec 12 13:07:26 2017 -0800
    Suppress labels on interchromosomal items if any on screen would overlap. Maybe later try packing, but this could be tricky. refs #17512
• src/hg/inc/mathWig.h
  • lines changed 4, context: html, text, full: html, text
    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
• src/hg/js/hgCollection.js
  • lines changed 6, context: html, text, full: html, text
    c5a827f8f0c4094c20ff333acb191ded2bf86744 Wed Dec 20 11:36:10 2017 -0800
    ongoing work on hgCollection
  • lines changed 10, context: html, text, full: html, text
    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/lib/customPp.c
  • lines changed 11, context: html, text, full: html, text
    4bb6fa70811bad557c8f9083652cdb3597d551fd Wed Dec 20 10:45:16 2017 -0800
    fix "name too long" bug in bigBed custom tracks loaded directly #20708
• src/hg/lib/customTrack.c
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    82ded93d66a822e83a7b957ffa603304dcaa51cb Wed Jan 3 11:19:32 2018 -0800
    fix problem with custom track altColor as described in #20741
• src/hg/lib/hdb.c
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    d3c4dd4f1df4b3919520794bfcaac0a7d0935a7f Tue Dec 19 12:07:23 2017 -0800
    Replace hgTracks' links to NCBI's obsolete Map Viewer with the new & improved Genome Data Viewer. GDV has only the latest RefSeq assembly for all species except human; it wants GCF_... IDs, which we will have to keep updating in hdb.c. It's possible that someday NCBI may accept our db IDs instead of GCF_. refs #18671
• src/hg/lib/longRange.c
  • lines changed 9, context: html, text, full: html, text
    4e5b41a3d4c933bffb2958c9b34f925bab023179 Tue Dec 12 13:07:26 2017 -0800
    Suppress labels on interchromosomal items if any on screen would overlap. Maybe later try packing, but this could be tricky. refs #17512
• src/hg/lib/mathWig.c
  • lines changed 85, context: html, text, full: html, text
    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
• src/hg/lib/mdb.c
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    27b25a4e86b49bb8d618b61684beecd81fa84d7b Tue Jan 2 12:26:30 2018 -0800
    fix a problem with oligo track on assembly hubs
• src/hg/lib/trackHub.c
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    6f5408b67c1b4534efa4d795bc3776c6c667d586 Fri Dec 22 18:29:07 2017 -0800
    implement missing data handling in mathWigs
• src/hg/makeDb/doc/anoGam3/initialBuild.txt
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    b059002aee613e7743d7eacdfbd2717701f5eb64 Tue Dec 19 14:31:46 2017 -0800
    begin anoGam3 browser build no redmine
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    0c717a44adcac01499ad89f893a48a0865be7fe4 Tue Dec 19 16:17:10 2017 -0800
    continuing with RepeatMasker
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    8a65d0697c43d24e5add86d1921523beec1760c4 Wed Dec 20 18:02:46 2017 -0800
    waiting for genbank run to finish refs #20743
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    4969685a0d16a10c689d921e87281ae0a06320bc Thu Dec 21 09:57:14 2017 -0800
    QA ready refs #20743
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    abdaf2d94220c3ea7c63a314e0897e74dd740eb6 Thu Dec 21 10:00:22 2017 -0800
    reset base position refs #20743
• src/hg/makeDb/doc/cavPor3.txt
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    c99090b56ef946bbfe6beb4e9c2d428f8abad935 Mon Dec 18 13:47:18 2017 -0800
    multiple alignments enough done for a look see no redmine
• src/hg/makeDb/doc/criGri1.txt
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    1a2688ea3df2d63117cfb99e4127c6054accfd1e Sat Jan 6 20:50:50 2018 -0800
    liftOver to criGriChoV2 refs #20540
• src/hg/makeDb/doc/criGriChoV1/initialBuild.txt
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    7af7775c43dd5ae71f939ad98203d199106126da Sat Jan 6 20:49:06 2018 -0800
    liftOver to criGriChoV2 refs #20540
• src/hg/makeDb/doc/criGriChoV2/initialBuild.txt
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    1b2ecf649edc6355b87bd0a5f6fb646599469c5d Wed Jan 3 17:48:28 2018 -0800
    running up repeatMasker and simpleRepeat refs #20540
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    1200278b75d93b425005aab6d5c0b2224dcd72b8 Thu Jan 4 11:52:49 2018 -0800
    masking done, continuing build refs #20540
• src/hg/makeDb/doc/dipOrd2/initialBuild.txt
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    2696cff97946f81916d21b644f50018c62a8a2d3 Fri Dec 22 21:54:23 2017 -0800
    begin dipOrd2 build refs #20751
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    84ee80e78bb063ee24c602adca839d51504e2dca Wed Jan 3 11:51:35 2018 -0800
    browser is QA Ready refs #20751
• src/hg/makeDb/doc/ficAlb1/initialBuild.txt
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    066deef16280ed7c0e6b58bf0d9c39a79cb5fc68 Fri Jan 5 16:03:10 2018 -0800
    ready to work up genbank run refs #9870
• src/hg/makeDb/doc/fukDam1/initialBuild.txt
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    39cc657b345aad224493b760e875f4f95a356b68 Wed Jan 3 11:47:10 2018 -0800
    browser is QA Ready refs #20752
• src/hg/makeDb/doc/galVar1/multiz6way.txt
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    c99090b56ef946bbfe6beb4e9c2d428f8abad935 Mon Dec 18 13:47:18 2017 -0800
    multiple alignments enough done for a look see no redmine
• src/hg/makeDb/doc/hg11.txt
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    2212307d88c8d8d050d9c64d5e6d437f6fc22243 Fri Dec 22 22:01:53 2017 -0800
    liftOver from hg11 to hg19 and hg38 refs #20736
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    61ccc644d4988c210f98c5de776a3de7a5fe6c7a Wed Jan 3 10:29:08 2018 -0800
    lastz/chainNet to fukDam1 and dipOrd2 refs #20751 #20752
• src/hg/makeDb/doc/hg38/multiz5way.txt
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    c99090b56ef946bbfe6beb4e9c2d428f8abad935 Mon Dec 18 13:47:18 2017 -0800
    multiple alignments enough done for a look see no redmine
• src/hg/makeDb/doc/mm10.txt
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    6f3663cf583d51949f0149dd1c69a705596ba06f Mon Dec 18 10:42:51 2017 -0800
    fixed copy/paste error in mm10 track make doc
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    61ccc644d4988c210f98c5de776a3de7a5fe6c7a Wed Jan 3 10:29:08 2018 -0800
    lastz/chainNet to fukDam1 and dipOrd2 refs #20751 #20752
• src/hg/makeDb/doc/papAnu4/initialBuild.txt
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    98925e2605ed8669d0e88fca346ebfeded675efa Wed Jan 3 17:47:57 2018 -0800
    running up repeatMasker and simpleRepeat refs #20769
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    df9e377a17f4ad508c8c1bc547704c37a025110d Fri Jan 5 16:28:15 2018 -0800
    ready to run up genbank refs #20769
• src/hg/makeDb/doc/tupChi1/multiz5way.txt
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    c99090b56ef946bbfe6beb4e9c2d428f8abad935 Mon Dec 18 13:47:18 2017 -0800
    multiple alignments enough done for a look see no redmine
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    393adbd5597ac296698ee21c3a4f2d6a431a7ba9 Thu Dec 21 08:24:00 2017 -0800
    Added anoGam3 - malaria mosquito refs #20743
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    c2c870d22d20a0caa44aa498fea09cd985cae5d3 Mon Jan 1 19:57:04 2018 -0800
    adding fukDam1 and dipOrd2 to the update alignments refs #20752 #20751
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    50f490d8d606e9b72e92da2e42753fe817917265 Wed Dec 20 08:11:45 2017 -0800
    Added anoGam3; no redmine
  • lines changed 19, context: html, text, full: html, text
    41e7bfe29214a6018767d8a297cd5e9b00e010f0 Sun Dec 31 08:54:37 2017 -0800
    adding dipOrd2 Dipodomys ordii refs #20751
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    1739294775fb13c71d448f26e9e79afd9411157f Sun Dec 31 15:04:58 2017 -0800
    adding fukDam1 - Fukomys damarensis - Damara mole-rat refs #20752
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    393adbd5597ac296698ee21c3a4f2d6a431a7ba9 Thu Dec 21 08:24:00 2017 -0800
    Added anoGam3 - malaria mosquito refs #20743
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    c2c870d22d20a0caa44aa498fea09cd985cae5d3 Mon Jan 1 19:57:04 2018 -0800
    adding fukDam1 and dipOrd2 to the update alignments refs #20752 #20751
• src/hg/makeDb/genbank/etc/rr.dbs
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    c2e8a18d1eec89fb7247068f9443d629a8b0b186 Wed Dec 20 15:14:16 2017 -0800
    Turning on genbank updates for panPan2, refs #16036
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    1739294775fb13c71d448f26e9e79afd9411157f Sun Dec 31 15:04:58 2017 -0800
    adding fukDam1 - Fukomys damarensis - Damara mole-rat refs #20752
• src/hg/makeDb/schema/all.joiner
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    f858434bab25856f342151b173813d2f6e2b7668 Wed Dec 20 20:06:09 2017 -0800
    adding rules for anoGam3 refs #20743
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    bc3d13133e1265d493c24dff6bcd63fa0bdc808f Wed Jan 3 10:18:10 2018 -0800
    adding fukDam1 and dipOrd2 rules refs #20752 #20751
• src/hg/makeDb/trackDb/anopheles/anoGam3/description.html
  • lines changed 64, context: html, text, full: html, text
    3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800
    initial files for anoGam3 no redmine
• src/hg/makeDb/trackDb/anopheles/anoGam3/gap.html
  • lines changed 30, context: html, text, full: html, text
    3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800
    initial files for anoGam3 no redmine
• src/hg/makeDb/trackDb/anopheles/anoGam3/gold.html
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    3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800
    initial files for anoGam3 no redmine
• src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra
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    3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800
    initial files for anoGam3 no redmine
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    31fa3dbc54d190496af806c94008a2b82af5e7c0 Tue Dec 19 15:54:07 2017 -0800
    add gold table search rule no redmine
• src/hg/makeDb/trackDb/baboon/papAnu4/description.html
  • lines changed 64, context: html, text, full: html, text
    df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800
    adding papAnu4 to the build refs #20768
• src/hg/makeDb/trackDb/baboon/papAnu4/gap.html
  • lines changed 31, context: html, text, full: html, text
    df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800
    adding papAnu4 to the build refs #20768
• src/hg/makeDb/trackDb/baboon/papAnu4/gold.html
  • lines changed 34, context: html, text, full: html, text
    df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800
    adding papAnu4 to the build refs #20768
• src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800
    adding papAnu4 to the build refs #20768
  • lines changed 5, context: html, text, full: html, text
    b2852526011bd97e06679d7659b94715a650f029 Fri Jan 5 13:27:06 2018 -0800
    add assembly track search rule refs #20769
• src/hg/makeDb/trackDb/birds/ficAlb1/description.html
  • lines changed 64, context: html, text, full: html, text
    3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800
    adding ficAlb1 Collared Flycatcher to the browser refs #9870
• src/hg/makeDb/trackDb/birds/ficAlb1/gap.html
  • lines changed 31, context: html, text, full: html, text
    3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800
    adding ficAlb1 Collared Flycatcher to the browser refs #9870
• src/hg/makeDb/trackDb/birds/ficAlb1/gold.html
  • lines changed 34, context: html, text, full: html, text
    3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800
    adding ficAlb1 Collared Flycatcher to the browser refs #9870
• src/hg/makeDb/trackDb/birds/ficAlb1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800
    adding ficAlb1 Collared Flycatcher to the browser refs #9870
  • lines changed 5, context: html, text, full: html, text
    496dc581888967a547d75db1a0d109962d788e63 Fri Jan 5 16:01:52 2018 -0800
    add assembly track search rule refs #9870
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    497900bf7d2aa553c79802ff2ebed6229eecc905 Thu Jan 4 15:54:32 2018 -0800
    panTro4: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/criGri/criGriChoV2/description.html
  • lines changed 64, context: html, text, full: html, text
    c7354491a93371f7ed5e605b6c2eaad847689982 Wed Jan 3 16:53:45 2018 -0800
    initial files for criGriChoV2 refs #20540
• src/hg/makeDb/trackDb/criGri/criGriChoV2/gap.html
  • lines changed 31, context: html, text, full: html, text
    c7354491a93371f7ed5e605b6c2eaad847689982 Wed Jan 3 16:53:45 2018 -0800
    initial files for criGriChoV2 refs #20540
• src/hg/makeDb/trackDb/criGri/criGriChoV2/gold.html
  • lines changed 34, context: html, text, full: html, text
    c7354491a93371f7ed5e605b6c2eaad847689982 Wed Jan 3 16:53:45 2018 -0800
    initial files for criGriChoV2 refs #20540
• src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    c7354491a93371f7ed5e605b6c2eaad847689982 Wed Jan 3 16:53:45 2018 -0800
    initial files for criGriChoV2 refs #20540
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    290b86d4a2936265c8cb6162bf13df521439b988 Fri Jan 5 10:06:45 2018 -0800
    add assembly track search rule refs #20540
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 4, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcell.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcellNeg.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellI.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellII.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/muPIT.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/ncbiGenePfam.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/pdb.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/spAnnot.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/spMut.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/eboVir3/spStruct.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/gire2014FixedMissense.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/gire2014PolymorphicMissense.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/gire2014SpecificSnps.html
  • lines changed 1, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/ebola/gireReferences.html
  • lines changed 2, context: html, text, full: html, text
    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 2, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
  • lines changed 433, context: html, text, full: html, text
    940a472493cada80db6f3cdf904317203ea841cb Mon Dec 18 14:46:10 2017 -0800
    adding 6-way alignment no redmine
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.6way.ra
  • lines changed 102, context: html, text, full: html, text
    940a472493cada80db6f3cdf904317203ea841cb Mon Dec 18 14:46:10 2017 -0800
    adding 6-way alignment no redmine
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    940a472493cada80db6f3cdf904317203ea841cb Mon Dec 18 14:46:10 2017 -0800
    adding 6-way alignment no redmine
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    04f2e467b84625608a700ed92b6f7f855dc0aa77 Thu Jan 4 14:58:54 2018 -0800
    nomLeu3: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    ace45961b4ca91fb8b365525b62f6355533a375b Thu Jan 4 13:03:18 2018 -0800
    gorGor3: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/guineaPig/cavApe1/description.html
  • lines changed 64, context: html, text, full: html, text
    e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800
    adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
• src/hg/makeDb/trackDb/guineaPig/cavApe1/gap.html
  • lines changed 29, context: html, text, full: html, text
    e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800
    adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
• src/hg/makeDb/trackDb/guineaPig/cavApe1/gold.html
  • lines changed 33, context: html, text, full: html, text
    e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800
    adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
• src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800
    adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
  • lines changed 5, context: html, text, full: html, text
    71fced743cd036e9a9a1295dcf376fc335097be4 Thu Jan 4 15:34:32 2018 -0800
    add assembly track search rule refs #20770
  • lines changed 1, context: html, text, full: html, text
    ebfcb94f9b285ca27980668bbbd2569e77cb31e5 Sat Jan 6 17:16:49 2018 -0800
    new gold table new assembly track search rule refs @20770
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 251, context: html, text, full: html, text
    ac9a56fb921dfb228a34119dc2f0bc87cbeda2e2 Tue Jan 2 12:00:43 2018 -0800
    adding fukDam1 and dipOrd2 chainNet refs #20751 #29752
• src/hg/makeDb/trackDb/human/cnvDevDelay.html
  • lines changed 2, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 2, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/dgvPlus.html
  • lines changed 3, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 1, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 1, context: html, text, full: html, text
    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 1, context: html, text, full: html, text
    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
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    c9bea9750f88e570c6aee27f8299457b019e9635 Tue Jan 2 13:09:49 2018 -0800
    removing new label for hg19 gtex eQTL tracks, no RM
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 3, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
  • lines changed 438, context: html, text, full: html, text
    40b1280bc13ea274af99b4434a6af798a5405e64 Mon Dec 18 14:29:34 2017 -0800
    adding 5-way mammal alignment no redmine
• src/hg/makeDb/trackDb/human/hg38/crispr.html
  • lines changed 3, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 2, context: html, text, full: html, text
    68813efac90f262c8cf21dc23902820af1e969d5 Tue Dec 19 11:46:42 2017 -0800
    correct assembly accession ID no redmine
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
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    844a643864852f43bd1033c8fda3c7c59bdfc28c Fri Jan 5 14:58:47 2018 -0800
    add type bigWig with limits for all the bw files refs #19154
  • lines changed 2, context: html, text, full: html, text
    5c7b0ddad4939219f31e57b77bdb2d435bd5b119 Fri Jan 5 15:17:06 2018 -0800
    type bigWig for the composite allows the schema page to display refs #19154
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    8386de0f499d3fdd24c9becc50acbef3f587ef5f Fri Jan 5 15:38:25 2018 -0800
    Fixing a typo in a track name, removing 'viewUi on', and adding the 'New' tag for the release. refs #19154
• src/hg/makeDb/trackDb/human/hg38/lincRNAs.html
  • lines changed 1, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/mappability.html
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    6335df8abfda70e6251cef0dd5defe7be2978d90 Fri Jan 5 16:02:49 2018 -0800
    Updating the bigBedToBed and bigWigToWig commands to have the correct hgdownload links, refs #19154
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/omimDescriptionText.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/tcgaExpr.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/trackDb.5way.ra
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    40b1280bc13ea274af99b4434a6af798a5405e64 Mon Dec 18 14:29:34 2017 -0800
    adding 5-way mammal alignment no redmine
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    40b1280bc13ea274af99b4434a6af798a5405e64 Mon Dec 18 14:29:34 2017 -0800
    adding 5-way mammal alignment no redmine
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    f32a2489ffb3cd1f2b169fb64c9028543c2017e7 Fri Jan 5 10:08:14 2018 -0800
    Adding the beta release tag for the Hoffman mappability tracks, refs #19154
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    e6494e03a164a82e735d8877dc51635a5cafd2a2 Fri Jan 5 13:56:19 2018 -0800
    Removing release tags to release the Hoffman mappability track to the RR, refs #19154
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html
  • lines changed 1, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/hgIkmc.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/iscaComposite.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/omimDescriptionText.html
  • lines changed 1, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp141.shared.html
  • lines changed 32, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 32, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp144.shared.html
  • lines changed 32, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp146.shared.html
  • lines changed 31, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp147.shared.html
  • lines changed 32, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/snp150.shared.html
  • lines changed 32, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/human/stsMap.html
  • lines changed 2, context: html, text, full: html, text
    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/description.html
  • lines changed 64, context: html, text, full: html, text
    4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800
    adding dipOrd2 to the build refs #20751
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/gap.html
  • lines changed 30, context: html, text, full: html, text
    4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800
    adding dipOrd2 to the build refs #20751
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/gold.html
  • lines changed 33, context: html, text, full: html, text
    4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800
    adding dipOrd2 to the build refs #20751
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800
    adding dipOrd2 to the build refs #20751
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    f2b2b152a855f138e0660bfbb1f3147c5d29744b Fri Dec 22 21:47:36 2017 -0800
    add gold table search rule refs #20751
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    14247a325d82a7e0e35fbfdb196416d3a2c5e69a Fri Jan 5 09:33:40 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/lamprey/petMar1/phastConsElements6way.html
  • lines changed 1, context: html, text, full: html, text
    14247a325d82a7e0e35fbfdb196416d3a2c5e69a Fri Jan 5 09:33:40 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/makefile
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    3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800
    initial files for anoGam3 no redmine
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    4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800
    adding dipOrd2 to the build refs #20751
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    92fba655e042b9abfb9f74626895aaed04338607 Fri Dec 22 21:48:30 2017 -0800
    correctly dipOrd2 refs #20751
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    e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800
    add fukDam1 to the build refs #20752
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    df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800
    adding papAnu4 to the build refs #20768
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    e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800
    adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
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    3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800
    adding ficAlb1 Collared Flycatcher to the browser refs #9870
• src/hg/makeDb/trackDb/mammal/fukDam1/description.html
  • lines changed 64, context: html, text, full: html, text
    e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800
    add fukDam1 to the build refs #20752
• src/hg/makeDb/trackDb/mammal/fukDam1/gap.html
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    e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800
    add fukDam1 to the build refs #20752
• src/hg/makeDb/trackDb/mammal/fukDam1/gold.html
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    e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800
    add fukDam1 to the build refs #20752
• src/hg/makeDb/trackDb/mammal/fukDam1/trackDb.ra
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    e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800
    add fukDam1 to the build refs #20752
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    d83b17b1b9578f9278801befc40b9cc421670514 Sat Dec 23 00:02:12 2017 -0800
    adding gold track search rule refs #20752
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra
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    651ac05ccccc9302f65cd29ea7e0d7cbd0ba7cd4 Thu Jan 4 11:55:34 2018 -0800
    calJac3: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    999e1db7beebcc27b2b57f7ea48d09b96ce0fea5 Mon Dec 18 15:19:07 2017 -0800
    Adding in release notes for previous public versions of mm10 GENCODE, refs #20715
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    f71ebf567e4352695381fabd495b248a3b8a78cc Wed Dec 20 16:40:30 2017 -0800
    Woops forgot about current version vm14 on gencode super track description page, refs #20715
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.ra
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    265f4ca9967e766a4db855eddd01496f535c3377 Thu Dec 21 07:54:24 2017 -0800
    Turning off VM14 by default now that VM16 is released, refs #20715
• src/hg/makeDb/trackDb/mouse/mm6/description.html
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    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/mouse/mm7/description.html
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    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/mouse/mm8/description.html
  • lines changed 1, context: html, text, full: html, text
    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/mouse/mm9/description.html
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    44515905fdb7ae6baecf321b2d86139d0d5fa1f2 Tue Dec 19 13:26:20 2017 -0800
    Updating NCBI assembly statistics links from old mapview/stats/BuildStats.cgi to the current style of assembly pages, where possible. For some very old mouse assemblies, NCBI does not have assembly pages. I will leave those links alone so they'll work until NCBI really drops mapview/stats/BuildStats.cgi. refs #18671.
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
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    d87f9f32733862a6eac1d815f10ca699d134fdba Tue Dec 19 13:20:34 2017 -0800
    Fixing typo in GCA ID.
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    9f1029ca3ad842029132ff9d8df91f170a6e8383 Tue Dec 19 14:32:32 2017 -0800
    Updating Accession ID on the hgGateway page for oreNil2, no Redmine.
• src/hg/makeDb/trackDb/patSeq.html
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    20a430615d70b2e9c235b19c5512e00a97f0f924 Wed Jan 3 11:58:25 2018 -0800
    Fixing broken links for eboVir3, no Redmine.
• src/hg/makeDb/trackDb/pubs.html
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    8842557bf262d266bdc530956cdb950352f86785 Wed Jan 3 11:12:00 2018 -0800
    Fixing broken links for ci2, no Redmine.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.chainNet.ra
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    ed5d935ac41c9968506a2ea3f9adc5a481e8bc8f Thu Jan 4 16:29:43 2018 -0800
    rheMac2: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
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    ed5d935ac41c9968506a2ea3f9adc5a481e8bc8f Thu Jan 4 16:29:43 2018 -0800
    rheMac2: distinguishing human chainNet tracks, refs #20216
• src/hg/makeDb/trackDb/sgpGene.html
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    83c5e9668e55fbd9adc5699b103ecc8fee3110b6 Wed Dec 20 09:25:32 2017 -0800
    Fixing broken links found by the broken link report, no Redmine
• src/hg/makeDb/trackDb/squirt/gap.html
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    8842557bf262d266bdc530956cdb950352f86785 Wed Jan 3 11:12:00 2018 -0800
    Fixing broken links for ci2, no Redmine.
• src/hg/makeDb/trackDb/squirt/intronEst.html
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    8842557bf262d266bdc530956cdb950352f86785 Wed Jan 3 11:12:00 2018 -0800
    Fixing broken links for ci2, no Redmine.
• src/hg/makeDb/trackDb/squirt/refGene.html
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    8842557bf262d266bdc530956cdb950352f86785 Wed Jan 3 11:12:00 2018 -0800
    Fixing broken links for ci2, no Redmine.
• src/hg/makeDb/trackDb/squirt/xenoMrna.html
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    8842557bf262d266bdc530956cdb950352f86785 Wed Jan 3 11:12:00 2018 -0800
    Fixing broken links for ci2, no Redmine.
• src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra
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    ac9a56fb921dfb228a34119dc2f0bc87cbeda2e2 Tue Jan 2 12:00:43 2018 -0800
    adding fukDam1 and dipOrd2 chainNet refs #20751 #29752
• src/hg/makeDb/trackDb/trackDb.chainNet.insects.ra
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    6535b146f2e677145a09721b4a4ce74efff7028a Wed Dec 20 15:51:27 2017 -0800
    adding anoGam3 chainNet no redmine
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
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    ac1837db78e0e3c82532a32503901e232b4bf551 Mon Dec 18 14:52:59 2017 -0800
    adding 5-way alignment no redmine
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    3414b871c08ab28abffc0d5b00cc95e153ae13e0 Mon Dec 18 15:06:52 2017 -0800
    updated text no redmine
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.5way.ra
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    ac1837db78e0e3c82532a32503901e232b4bf551 Mon Dec 18 14:52:59 2017 -0800
    adding 5-way alignment no redmine
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra
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    ac1837db78e0e3c82532a32503901e232b4bf551 Mon Dec 18 14:52:59 2017 -0800
    adding 5-way alignment no redmine
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
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    795b40a5239dd63b93f63e5daf5b6c125eb3cb71 Wed Jan 3 16:30:05 2018 -0800
    Fixing broken links found by the broken link report for hg38, no Redmine.
• src/hg/oneShot/freen/freen.c
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    cf0b1e4a2737a97cd5d7d7fcf0ca60a871f5b94b Mon Dec 11 17:44:23 2017 -0800
    Working out some functions needed for substituting arrays.
• src/hg/utils/automation/EnsGeneAutomate.pm
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    7069b166edb308a0707ecee7cdc5bad852085ceb Fri Jan 5 10:36:22 2018 -0800
    fixup one of the path names for peptides criGriChoV2 refs #20696
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    36f7d91fe577f89a5d3a1cb62c40c5483010bfd3 Fri Jan 5 10:41:56 2018 -0800
    fixup one of the path names for peptides criGriChoV2 refs #20696
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    8f20120f8b5c935f3e0778a79de672b53f011888 Sat Jan 6 20:40:41 2018 -0800
    rename ficAlb1 to ficAlb0 for v91 refs #20696
• src/hg/utils/automation/chromAlias.pl
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    c44f0ad0ae624dbff869c4d89b552417bec5dd8c Wed Dec 20 15:36:24 2017 -0800
    improved procedure to allow duplicates from other names to same UCSC name refs #20696
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    a42a7cedfcc556c6f202a11483fd3dc3e3f9218f Fri Jan 5 10:00:26 2018 -0800
    fix error when one of the inputs only has one line refs #20540
• src/hg/utils/automation/prepConfig.pl
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    30689fbfc5863fcbc71712b0c0279e604d6b2b31 Wed Jan 3 15:10:29 2018 -0800
    was not recognizing the genbank accession ID and renameMySQLCommonName variable refs #20540 #20722
• src/hg/utils/phyloTrees/commonNames.sh
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    a512688e18eb437953bf87bfc331bdb3f3b000d7 Wed Jan 3 22:17:42 2018 -0800
    updating to new browser versions no redmine
• src/inc/portable.h
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    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
• src/inc/tagSchema.h
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    fae178c6d7f74bf2ec5966d559e3ea66dae42923 Wed Dec 20 16:44:37 2017 -0800
    Adding some new library functions that help handle arrays of objects.
• src/lib/htmshell.c
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    9ea546d042a47947ff825f973f0048dfdfe36496 Fri Jan 5 17:51:24 2018 -0800
    Fixing charset encoding, since utf-8 is not needed and iso-8859-1 is our standard. Also cleaned up some comments.
• src/lib/osunix.c
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    1b380f11932d8dd14c1ae935cdf9cdcced61f9f6 Wed Dec 20 12:04:52 2017 -0800
    Fixing cdw utils to preserve the original date of the submitted file, which helps speed up cdwSubmit for old files as well. They will not have to run md5sum manually if the file date has not changed so it can use the md5 from the record in the database.
• src/lib/tagSchema.c
  • lines changed 86, context: html, text, full: html, text
    fae178c6d7f74bf2ec5966d559e3ea66dae42923 Wed Dec 20 16:44:37 2017 -0800
    Adding some new library functions that help handle arrays of objects.
• src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormDeleteTags/tests/input/delete.tags
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormDeleteTags/tests/input/in.tags
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    af9e74e1bed088d7e073bde9fc313d63029cb689 Tue Dec 12 11:18:28 2017 -0800
    Making tagStormDeleteTags handle tags that represent fields in arrays of objects.
• src/tagStorm/tagStormInfo/tagStormInfo.c
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    b814e8fcbb40cc31b4346c7b86a75ec836d0d525 Wed Dec 20 16:47:42 2017 -0800
    Removing unneeded external function prototype.
• src/tagStorm/tagStormRenameTags/array.2col
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/array.out
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/array.tags
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
• src/tagStorm/tagStormRenameTags/tagStormRenameTags.c
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    cebd589a73275d27e129944f3f3b06e7ec26f0ee Tue Dec 12 11:46:56 2017 -0800
    Making tagStormRenameTags handle tags that are fields in an array of objects.
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    d6347dce5eca5a6bcc426434f2ee7d8878921006 Wed Dec 20 16:49:01 2017 -0800
    Adding noArray option, useful when you want to rename array.1.something to scaler.something among other things.
• src/utils/qa/backupCentral.csh
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    6a3417da58ef9207dfdad6981332a16e0e224cc8 Wed Jan 3 14:49:18 2018 -0800
    adding 10 million size limit to namedSessionDb backup
• src/utils/qa/weeklybld/buildEnv.csh
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    b3e9b8d78ae15ea27833b19d30045b171d954a67 Mon Jan 8 10:20:28 2018 -0800
    v360 preview1

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• files changed: 263