All File Changes

v392_preview2 to v392_base (2019-12-16 to 2020-01-06) v392

• confs/hgwdev.hg.conf
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    5e4d25103a55106172279bd20b102742c4c6b1d3 Sun Jan 5 01:11:27 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwCheckValidation/cdwCheckValidation.c
  • lines changed 31, context: html, text, full: html, text
    567bb801c1502dd59b886e1ed10e76bcaf72cca4 Wed Dec 18 13:33:36 2019 -0800
    Adding most recent validation stats to cdwCheckValidation status, per wrangler request (no ticket)
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 5, context: html, text, full: html, text
    59ce0cc28f54920ac4842b3fe8c39e57fa24480a Wed Dec 18 02:52:56 2019 -0800
    highlighting link to parent track for supertrack children, refs #24664
• src/hg/hgTracks/bamTrack.c
  • lines changed 25, context: html, text, full: html, text
    87165caa138700c2f604737f7448685797bf1954 Wed Dec 18 14:20:37 2019 -0800
    Apply same base and indel coloring defaults to BAM tracks in hgTrackUi as in hgTracks. refs #24674
• src/hg/hgTracks/hgTracks.c
  • lines changed 11, context: html, text, full: html, text
    0a2d8aa2d2c0f3895ab4b8d60d6457a583f4c384 Fri Dec 20 10:16:58 2019 -0800
    Adding explanation for black shaded items in pLI track to legend and track description. Also adding 'gnomAD' back to short and longlabels, refs #20394
• src/hg/hgTracks/lollyTrack.c
  • lines changed 93, context: html, text, full: html, text
    0846fb5a0028fcdcd90beeec64bc00adafcb9f61 Mon Dec 30 14:38:22 2019 -0800
    allow specifying colors for lollipops, turn off color in TCGA cancer track, make pack mode draw lollies instead of bed modes #24705
• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    b3d7beaa964c90d43a6acea6292f34eef5cd1b4d Wed Dec 18 16:10:12 2019 -0800
    In pack mode, sorting by position at draw time is too late -- items have been packed before draw time, so sort by position at load time.
• src/hg/hgc/geneReviewsClick.c
  • lines changed 2, context: html, text, full: html, text
    92d22aef00c95d22ddf0013f5a58d2d4c67a3100 Tue Dec 17 07:02:11 2019 -0800
    changes after code review, refs #24660
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 11, context: html, text, full: html, text
    29468b3e7a861865f59609512f3b9c8f4a961df1 Tue Dec 17 01:59:28 2019 -0800
    blat FAQ update, based on refs #24595
  • lines changed 104, context: html, text, full: html, text
    fafd6ff48ad2085bfb30d30f53bdf3dfecab63f3 Tue Dec 17 11:46:59 2019 -0800
    Editing repeat matches missing section and changeing Blat to BLAT refs #24595
  • lines changed 36, context: html, text, full: html, text
    19ab7e792d62a1764de8fced4b1adcd2e6ab1ef4 Tue Dec 17 11:49:43 2019 -0800
    Fixing merge conflict #24595
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 10, context: html, text, full: html, text
    1e0b1b2cbd35e8c79caff322317c93365c8cc5a8 Tue Dec 17 08:18:58 2019 -0800
    Removing td from htmlCheck and a section about rsync on gbib.html
• src/hg/htdocs/images/phylo/regenCho1_7way.png
  • lines changed 0, context: html, text, full: html, text
    bbb2c537ecb4b7736ccd5b4d038e3158ba71e382 Thu Dec 19 13:57:22 2019 -0800
    regenCho1 7-way phylo tree refs #24568
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    e4dab37a60243eaacbb099293ed997502dceef7d Wed Dec 18 09:07:07 2019 -0800
    adding link to ucla workshop
• src/hg/hubApi/apiUtils.c
  • lines changed 6, context: html, text, full: html, text
    e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
    update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
• src/hg/hubApi/getData.c
  • lines changed 2, context: html, text, full: html, text
    487174a2ad313bc229c6733ce263fb6a4413d50f Wed Dec 18 14:26:41 2019 -0800
    start=end=0 does not work for NIB fetch sequence refs #24666
• src/hg/hubApi/tests/expected/err45.gz
  • lines changed 0, context: html, text, full: html, text
    e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
    update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
• src/hg/hubApi/tests/expected/err47.gz
  • lines changed 0, context: html, text, full: html, text
    e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
    update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
• src/hg/hubApi/tests/expected/list03.gz
  • lines changed 0, context: html, text, full: html, text
    a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
    fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
• src/hg/hubApi/tests/expected/list09.gz
  • lines changed 0, context: html, text, full: html, text
    a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
    fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
• src/hg/hubApi/tests/expected/redmine24666.gz
  • lines changed 0, context: html, text, full: html, text
    e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
    update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
• src/hg/hubApi/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
    update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
  • lines changed 4, context: html, text, full: html, text
    a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
    fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    87165caa138700c2f604737f7448685797bf1954 Wed Dec 18 14:20:37 2019 -0800
    Apply same base and indel coloring defaults to BAM tracks in hgTrackUi as in hgTracks. refs #24674
• src/hg/inc/trackDb.h
  • lines changed 9, context: html, text, full: html, text
    3c7a0656f98136df2c2b6c2d5e36baea9e3bf8bc Wed Jan 1 14:10:09 2020 -0800
    add version number to trackDb cache so if the trackDb structure changes, the "wrong" cached values won't be used.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    daf028a3af7cea339f52f2be2aa1485eab315583 Mon Jan 6 10:08:11 2020 -0800
    New version number v392
• src/hg/js/dbDbTaxonomy.js
  • lines changed 271, context: html, text, full: html, text
    e2750fa753c592c9941e3e553bb4daf978fb935f Mon Dec 23 15:28:41 2019 -0800
    Updating the taxonomy tree as it's been a couple years (prepping for otter), no ticket
• src/hg/lib/hui.c
  • lines changed 34, context: html, text, full: html, text
    87165caa138700c2f604737f7448685797bf1954 Wed Dec 18 14:20:37 2019 -0800
    Apply same base and indel coloring defaults to BAM tracks in hgTrackUi as in hgTracks. refs #24674
• src/hg/lib/trackDbCache.c
  • lines changed 24, context: html, text, full: html, text
    3c7a0656f98136df2c2b6c2d5e36baea9e3bf8bc Wed Jan 1 14:10:09 2020 -0800
    add version number to trackDb cache so if the trackDb structure changes, the "wrong" cached values won't be used.
• src/hg/makeDb/doc/globalReference/README.txt
  • lines changed 36, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/accAsmId.list
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/commonNameOrder.list
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/commonNames.txt
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/ethnicGroup.txt
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/family.txt
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/groups.txt
  • lines changed 39, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/hub.txt
  • lines changed 6, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/human.list
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/isolate.txt
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/makefile
  • lines changed 28, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
  • lines changed 9, context: html, text, full: html, text
    8bde61c3efd8828518d70bfc287c600b86683f68 Thu Jan 2 13:22:14 2020 -0800
    add hub.txt and groups.txt copies refs #24354
• src/hg/makeDb/doc/globalReference/mkAsmStats.pl
  • lines changed 270, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
  • lines changed 8, context: html, text, full: html, text
    27228c7e494674469a64cdeb61d7c4e433102f24 Thu Jan 2 13:16:14 2020 -0800
    updated text to global reference wording refs #24534
• src/hg/makeDb/doc/globalReference/mkGenomes.pl
  • lines changed 116, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/mkHubIndex.pl
  • lines changed 254, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
  • lines changed 9, context: html, text, full: html, text
    27228c7e494674469a64cdeb61d7c4e433102f24 Thu Jan 2 13:16:14 2020 -0800
    updated text to global reference wording refs #24534
• src/hg/makeDb/doc/globalReference/mkSymLinks.sh
  • lines changed 53, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/perlPara.pl
  • lines changed 128, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/run10.list
  • lines changed 10, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/globalReference/runOne.sh
  • lines changed 153, context: html, text, full: html, text
    147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
    set of files for hub build refs @24354
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    db3443c1060188f5e7abe8e640e3f245bd7f8cb7 Thu Dec 19 11:57:34 2019 -0800
    load of gencode V33lift37 prerelease
• src/hg/makeDb/doc/primateAsmHub/groups.txt
  • lines changed 39, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/makefile
  • lines changed 37, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/mkAsmStats.pl
  • lines changed 258, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl
  • lines changed 127, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl
  • lines changed 237, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/mkList.sh
  • lines changed 25, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/mkSymLinks.pl
  • lines changed 172, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/primates.asmId.commonName.tsv
  • lines changed 23, context: html, text, full: html, text
    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/primateAsmHub/primates.commonName.asmId.orderList.tsv
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    2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
    initial set of files to create symlinks and index pages refs #20137
• src/hg/makeDb/doc/rn6.txt
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    54c4f85da2fcff075df03bbce841043e0d5acc28 Tue Dec 17 08:31:41 2019 -0800
    lastz chainNet run regenCho1 vs. rn6 refs #24568
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
  • lines changed 1, context: html, text, full: html, text
    9bab3e9da3138f67a9d9d4f80b609aefb80e02c9 Mon Dec 23 11:20:20 2019 -0800
    remove duplicates from knownToEnsembl and knownToGencodeV32
• src/hg/makeDb/genbank/etc/align.dbs
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    0bba6230e62c76e0b4d461b035b9ec66178ef8ed Mon Dec 23 16:02:30 2019 -0800
    Added enhLutNer1 - Southern sea otter refs #21152
• src/hg/makeDb/genbank/etc/genbank.conf
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    bc1bc0142ca75c78a0d1f183a293eb509e8e571c Mon Dec 23 15:54:23 2019 -0800
    Added enhLutNer1 rhesus/Macaca mulatta; refs #23771
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    0bba6230e62c76e0b4d461b035b9ec66178ef8ed Mon Dec 23 16:02:30 2019 -0800
    Added enhLutNer1 - Southern sea otter refs #21152
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    db3443c1060188f5e7abe8e640e3f245bd7f8cb7 Thu Dec 19 11:57:34 2019 -0800
    load of gencode V33lift37 prerelease
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetBirds.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetFish.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetvertebrate.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
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    c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
    7-way multiz alignment refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/regenAGP.html
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    dc4b56b6156979617a0a79a99746f63c0090dcd2 Fri Dec 20 13:42:30 2019 -0800
    descriptions for AGP and gap definitions from the Regeneron AGP file refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/regenAGPGap.html
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    dc4b56b6156979617a0a79a99746f63c0090dcd2 Fri Dec 20 13:42:30 2019 -0800
    descriptions for AGP and gap definitions from the Regeneron AGP file refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.7way.ra
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    c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
    7-way multiz alignment refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.ra
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    c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
    7-way multiz alignment refs #24524
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetRBestInsects.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/drosophila/dm6/chainNetSynInsects.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
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    07b62ff4770ca7b072ed3988e47c3898527c4c68 Wed Dec 18 09:46:43 2019 -0800
    David pointed out that the order of genotypes in GnomAD v2's GC tags was not obvious and not described by the INFO headers -- adding explanation. refs #24620
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
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    9628686f224420ec0b9e0631e2e99d60bdab3489 Tue Dec 17 13:26:13 2019 -0800
    added html for gnomAD pLI tracks, to preserve definition of LOEUF
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    16c6ad6abb06ed686a984572bac87ad30063a46a Wed Dec 18 16:30:52 2019 -0800
    Starting on gnomad pLI track description, refs #20394
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    1435e1b124ef9073dc881a70a0a22b3ceda0628f Thu Dec 19 17:15:07 2019 -0800
    Finished track description page for gnomad haploinsufficiency track, refs #20394
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    0a2d8aa2d2c0f3895ab4b8d60d6457a583f4c384 Fri Dec 20 10:16:58 2019 -0800
    Adding explanation for black shaded items in pLI track to legend and track description. Also adding 'gnomAD' back to short and longlabels, refs #20394
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    0ca4edff9bd7aefe16d3af95d137f61576539929 Tue Dec 17 16:51:47 2019 -0800
    Adding filters to gnomad pli track and small label changes, refs #24657
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    0a2d8aa2d2c0f3895ab4b8d60d6457a583f4c384 Fri Dec 20 10:16:58 2019 -0800
    Adding explanation for black shaded items in pLI track to legend and track description. Also adding 'gnomAD' back to short and longlabels, refs #20394
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    fdcff5c4bd60905706fc95d0f387a17e5031b679 Fri Jan 3 06:29:37 2020 -0800
    It seems that the 'release' tdb statement is not inherited? Hiram says something complained about them. refs #24449
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.html
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    0846fb5a0028fcdcd90beeec64bc00adafcb9f61 Mon Dec 30 14:38:22 2019 -0800
    allow specifying colors for lollipops, turn off color in TCGA cancer track, make pack mode draw lollies instead of bed modes #24705
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
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    e60a2fbdbcf11780a7d3119cbdeeacc1b09d8ba9 Fri Dec 13 16:03:11 2019 -0800
    just happened to notice a missing <dl> start tag before a list.
• src/hg/makeDb/trackDb/human/hg38/hicAndMicroC.html
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    8613d0e66f912daaf38bdaf11b6f265c45ccde74 Fri Dec 6 09:24:21 2019 -0800
    Line length change and em tags for CR refs #23579
• src/hg/makeDb/trackDb/human/hg38/liftHg19.html
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    6dce178c939360c13338d6a3df5fba7900932aae Fri Jan 3 09:08:45 2020 -0800
    adding a hg38 liftOver track for hg19, refs #24707
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6dce178c939360c13338d6a3df5fba7900932aae Fri Jan 3 09:08:45 2020 -0800
    adding a hg38 liftOver track for hg19, refs #24707
• src/hg/makeDb/trackDb/human/trackDb.ra
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    129c29c899a77f6ace96555dd586e43ed1b83812 Fri Dec 20 14:55:02 2019 -0800
    Adding 'release alpha' for dbSnp152 which will remain hgwdev-only. refs #24690
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    c8590c60ac575ab0116fb337c0aed307f8218df1 Fri Jan 3 06:31:58 2020 -0800
    fixing link to Gene reviews site, suggested by Anna
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    b53fd185ab2c76072f90c0acd09d0d08d15a7ebf Mon Jan 6 05:09:47 2020 -0800
    fixing up variants in papers track after feedback from Anna
• src/hg/makeDb/trackDb/human/varsInPubs.html
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    b53fd185ab2c76072f90c0acd09d0d08d15a7ebf Mon Jan 6 05:09:47 2020 -0800
    fixing up variants in papers track after feedback from Anna
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
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    9aa6bd8e92fd50cea40a4ac676493c9047ee03cd Fri Dec 20 13:15:54 2019 -0800
    documentation page for 7-way refs #21579
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    f495f9c663e82f6fd6935e01f5d3951b6317b6a5 Thu Dec 19 09:03:19 2019 -0800
    Updating redirected links for rn5 found by the uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.ra
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    06ea1a979e711030c97f2d8a6a3d52e8316dd998 Thu Dec 19 13:56:38 2019 -0800
    Changing o_db to o_Organism in Net/Alignment tracks per conversation in RM refs #24677
• src/hg/utils/automation/asmHubGatewayPage.pl
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    d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
    get the gateway page a bit more generic with argument to specify refs #20137
• src/hg/utils/automation/asmHubTrackDb.sh
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    12b4622b8e00524ac3a6acd375fbf9a408ff41a6 Mon Dec 23 10:39:46 2019 -0800
    symlinks should be relative, not absolute refs #24354
• src/hg/utils/automation/doAssemblyHub.pl
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    4ca6162650c6e0f213cf674642b7a2b6bcea9bc1 Fri Dec 27 00:50:12 2019 -0800
    now automatically eliminating duplicate sequences refs #24354
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    d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
    get the gateway page a bit more generic with argument to specify refs #20137
• src/hg/utils/automation/doXenoRefGene.pl
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    cb83116ca0be25e3e45c93468d951fe53cb2c1e4 Fri Dec 27 00:49:20 2019 -0800
    better partitioning of the target genome refs #24354
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    d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
    get the gateway page a bit more generic with argument to specify refs #20137
• src/hg/utils/tdbQuery/tdbQuery.c
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    18b6f4ccf6ea234dd5fb38710763ae335f63e2e7 Mon Dec 16 13:41:09 2019 -0800
    add the groking if filter*.* lines in trackDb to tdbQuery
• src/inc/basicBed.h
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    0846fb5a0028fcdcd90beeec64bc00adafcb9f61 Mon Dec 30 14:38:22 2019 -0800
    allow specifying colors for lollipops, turn off color in TCGA cancer track, make pack mode draw lollies instead of bed modes #24705
• src/inc/srcVersion.h
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    daf028a3af7cea339f52f2be2aa1485eab315583 Mon Jan 6 10:08:11 2020 -0800
    New version number v392
• src/lib/basicBed.c
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    0846fb5a0028fcdcd90beeec64bc00adafcb9f61 Mon Dec 30 14:38:22 2019 -0800
    allow specifying colors for lollipops, turn off color in TCGA cancer track, make pack mode draw lollies instead of bed modes #24705
• src/utils/qa/weeklybld/buildEnv.csh
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    6e8c1a4b9311aa91585a31a5b16716b754b6c1a8 Mon Jan 6 10:04:39 2020 -0800
    v392 final build, refs #24628

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