All File Changes

v444_preview to v444_preview2 (2023-02-06 to 2023-02-13) v444

• src/hg/encode/getTrackReferences/getTrackReferences
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    6f3ab158f7f53c7d3b4b9c07b02de26912c33f0f Mon Feb 6 14:22:01 2023 -0800
    Removing outdated comments, refs #30603
• src/hg/hgGenome/mainPage.c
  • lines changed 8, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/hgTables/bigBed.c
  • lines changed 4, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTables/bigWig.c
  • lines changed 5, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTables/hgTables.c
  • lines changed 37, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTables/hgTables.h
  • lines changed 6, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
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    2b92068862c6ab7a42e909ea5c914d67c953122a Thu Feb 9 02:09:23 2023 -0800
    tweak wiggle output in TB, remove the BED option and add a note helping users who don't know the wiggle data format. refs #30585
• src/hg/hgTables/schema.c
  • lines changed 36, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTables/vcf.c
  • lines changed 3, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
• src/hg/hgTracks/bedTrack.c
  • lines changed 2, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/chainSnakeTrack.c
  • lines changed 581, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
  • lines changed 1185, context: html, text, full: html, text
    2e6b73ac1803862338f283d9b353fe2e10aa0204 Sun Feb 12 14:17:18 2023 -0800
    rename file to be more generic since display works on chains and psls
• src/hg/hgTracks/chainTrack.c
  • lines changed 56, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/halSnakeTrack.c
  • lines changed 5, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    f833d05bcd60f1c4f71cacf777a25ee84d7268d9 Thu Feb 2 02:49:23 2023 -0800
    fixing typo in color, refs #30578
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    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/makefile
  • lines changed 2, context: html, text, full: html, text
    2e6b73ac1803862338f283d9b353fe2e10aa0204 Sun Feb 12 14:17:18 2023 -0800
    rename file to be more generic since display works on chains and psls
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/snake.c
  • lines changed 1185, context: html, text, full: html, text
    2e6b73ac1803862338f283d9b353fe2e10aa0204 Sun Feb 12 14:17:18 2023 -0800
    rename file to be more generic since display works on chains and psls
• src/hg/hgTracks/snake.h
  • lines changed 23, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/hgTracks/wigTrack.c
  • lines changed 2, context: html, text, full: html, text
    25d71da8cf5aa20351e797594d56ccea1fc3c2bd Fri Feb 10 14:17:34 2023 -0800
    fix bug where "logo" type wiggle crased if it had a parent with no "container" attribute
• src/hg/hgc/hgc.c
  • lines changed 48, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/htdocs/FAQ/FAQcite.html
  • lines changed 6, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/htdocs/cite.html
  • lines changed 1, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 7, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 1, context: html, text, full: html, text
    250615a9c51e8402340f9d982aab1d4e87a12152 Mon Feb 13 09:18:51 2023 -0800
    Adding bigLolly doc link to page, ref #30585
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    7f9ebf15a57b4c8529177fdb89e4b56f36e57a3b Mon Feb 6 16:45:36 2023 -0800
    Code review edits: adding variable to get current year for searchedTermsCron.py and updating the relative path for a URL in newsarch.html , refs #30536
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    312c1e12d9fc7aafb210507f3aa257f4eb07b7b2 Thu Feb 9 02:57:39 2023 -0800
    adding links to our release log and the github repo, no redmine, emails with Mark and Chris
• src/hg/hubApi/tests/expected/list03.gz
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    8f64dc6018ec35583b8f807758e0fb12d8d45e9c Tue Feb 7 11:56:45 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
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    a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800
    trackDb updates affect the results of tests, make sure up to date no redmine
• src/hg/hubApi/tests/expected/list09.gz
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    8f64dc6018ec35583b8f807758e0fb12d8d45e9c Tue Feb 7 11:56:45 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
  • lines changed 0, context: html, text, full: html, text
    a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800
    trackDb updates affect the results of tests, make sure up to date no redmine
• src/hg/hubApi/tests/expected/notSup02.gz
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    a0e18d1f64aa38a4d79895ddf426838ec139637a Tue Feb 7 12:58:57 2023 -0800
    use a local vcfTabix track to test not supported no redmine
• src/hg/hubApi/tests/expected/schema06.gz
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    e7071512b2fa2f30e99a5b47f32f30cbda67a4fe Tue Feb 7 12:02:48 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
  • lines changed 0, context: html, text, full: html, text
    a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800
    trackDb updates affect the results of tests, make sure up to date no redmine
• src/hg/hubApi/tests/expected/schema10.gz
  • lines changed 0, context: html, text, full: html, text
    e7071512b2fa2f30e99a5b47f32f30cbda67a4fe Tue Feb 7 12:02:48 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
  • lines changed 0, context: html, text, full: html, text
    a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800
    trackDb updates affect the results of tests, make sure up to date no redmine
• src/hg/hubApi/tests/expected/test0.gz
  • lines changed 0, context: html, text, full: html, text
    8f64dc6018ec35583b8f807758e0fb12d8d45e9c Tue Feb 7 11:56:45 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
• src/hg/hubApi/tests/expected/test41.gz
  • lines changed 0, context: html, text, full: html, text
    8f64dc6018ec35583b8f807758e0fb12d8d45e9c Tue Feb 7 11:56:45 2023 -0800
    updated expected test output to reflect today contents of tables on hgwdev no redmine
  • lines changed 0, context: html, text, full: html, text
    a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800
    trackDb updates affect the results of tests, make sure up to date no redmine
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 3, context: html, text, full: html, text
    4a3f103195afff216604e84a30fc1d1ed4e0cf82 Tue Feb 7 12:13:35 2023 -0800
    indicate comments which server is which CGI no redmine
  • lines changed 4, context: html, text, full: html, text
    9b5f1e2ef7c4e9636a3dc8d68c8780f7f979f271 Tue Feb 7 16:13:17 2023 -0800
    Let api tests use an environment variable for which server to use so we can verify our sandbox versions of the cgi function, refs Hiram email
• src/hg/hubApi/tests/makefile
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    1744d98b15270fdbeb3abf81ee065ddfbd20f884 Tue Feb 7 12:59:12 2023 -0800
    use a local vcfTabix track to test not supported no redmine
  • lines changed 178, context: html, text, full: html, text
    9b5f1e2ef7c4e9636a3dc8d68c8780f7f979f271 Tue Feb 7 16:13:17 2023 -0800
    Let api tests use an environment variable for which server to use so we can verify our sandbox versions of the cgi function, refs Hiram email
• src/hg/inc/asmEquivalent.h
  • lines changed 103, context: html, text, full: html, text
    4418dae2476e397d9c03c1301e573e2c45b1a58e Fri Feb 10 12:16:43 2023 -0800
    adding asmEquivalent functions to this library no redmine
• src/hg/lib/asmEquivalent.c
  • lines changed 53, context: html, text, full: html, text
    4418dae2476e397d9c03c1301e573e2c45b1a58e Fri Feb 10 12:16:43 2023 -0800
    adding asmEquivalent functions to this library no redmine
• src/hg/lib/asmEquivalent.h
  • lines changed 101, context: html, text, full: html, text
    cf9bdd51cff9f2d4c01f8041e4c0c4708887571b Fri Feb 10 12:18:15 2023 -0800
    moved asmEquivalent.h to ../inc where it belongs no redmine
• src/hg/lib/hdb.c
  • lines changed 5, context: html, text, full: html, text
    67a193695c84dcb0508c79bdc7f8549471e9c5a7 Fri Feb 10 12:50:06 2023 -0800
    using the asmEquivalent hgFixed table to get an assembly name for the GDV browser will also need to translate the chromsome name to get this to work no redmine
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    15746316e92290a4aee220a757cb35293176d6e8 Tue Feb 7 05:29:10 2023 -0800
    adding file download links directly to the table browser "schema / data format" button, refs #30491
  • lines changed 1, context: html, text, full: html, text
    2a99d78cddf4b7de673435f911262ee25b36c238 Sun Feb 12 14:14:18 2023 -0800
    ongoing work on snake display for chains and psls
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    4418dae2476e397d9c03c1301e573e2c45b1a58e Fri Feb 10 12:16:43 2023 -0800
    adding asmEquivalent functions to this library no redmine
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    b211be496cb00c0899c46fa90d70181efe41bef6 Mon Feb 6 16:20:57 2023 -0800
    Removing EPS output links for hgTracks/hgGenome, refs #30606
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    129709f4ebba14b4ed271d9ee0c71b250e38294d Mon Feb 6 15:04:25 2023 -0800
    adding GCF_900747795.2_fErpCal1.3 reedfish/Erpetoichthys_calabaricus to catch up for VGP no redmine
  • lines changed 1, context: html, text, full: html, text
    91c4d455cc5c40ca17b08695bcb9ed887c8374f7 Wed Feb 8 10:15:35 2023 -0800
    adding GCA_902829235.1_CLODIP2 mayflies C.dipterum (2020) per user request refs #29545
  • lines changed 7, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
  • lines changed 3, context: html, text, full: html, text
    e71cff44c70dc01dda7236b4d6696320c4e0e379 Fri Feb 10 08:20:38 2023 -0800
    adding two per user request refs #29545
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 5, context: html, text, full: html, text
    8c39e9cdaef1aae3e50691b4452a118a8ddb4fd8 Mon Feb 6 14:48:14 2023 -0800
    error out when clade definition is missing no redmine
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 10, context: html, text, full: html, text
    f8c99a35bd085c9ec73b730a382129fee2183570 Mon Feb 6 14:47:27 2023 -0800
    add in the repeatModeler download files no redmine
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
  • lines changed 2, context: html, text, full: html, text
    e71cff44c70dc01dda7236b4d6696320c4e0e379 Fri Feb 10 08:20:38 2023 -0800
    adding two per user request refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    e71cff44c70dc01dda7236b4d6696320c4e0e379 Fri Feb 10 08:20:38 2023 -0800
    adding two per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    91c4d455cc5c40ca17b08695bcb9ed887c8374f7 Wed Feb 8 10:15:35 2023 -0800
    adding GCA_902829235.1_CLODIP2 mayflies C.dipterum (2020) per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 4, context: html, text, full: html, text
    a34d583ea0c3e75e865ed31d8f32133c8f945383 Wed Feb 8 11:00:22 2023 -0800
    catch up for some missed completed builds no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    631b1158bd10f31933723570979fa8aec1de321d Mon Feb 6 15:26:37 2023 -0800
    updated assembly for reedfish GCF_900747795.1_fErpCal1.1 no redmine
  • lines changed 5, context: html, text, full: html, text
    a34d583ea0c3e75e865ed31d8f32133c8f945383 Wed Feb 8 11:00:22 2023 -0800
    catch up for some missed completed builds no redmine
  • lines changed 3, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
  • lines changed 1, context: html, text, full: html, text
    e71cff44c70dc01dda7236b4d6696320c4e0e379 Fri Feb 10 08:20:38 2023 -0800
    adding two per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a34d583ea0c3e75e865ed31d8f32133c8f945383 Wed Feb 8 11:00:22 2023 -0800
    catch up for some missed completed builds no redmine
  • lines changed 1, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    129709f4ebba14b4ed271d9ee0c71b250e38294d Mon Feb 6 15:04:25 2023 -0800
    adding GCF_900747795.2_fErpCal1.3 reedfish/Erpetoichthys_calabaricus to catch up for VGP no redmine
  • lines changed 2, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    64d447ba2e30d43e88dfdf32ee98ff045888ee60 Mon Feb 6 15:39:50 2023 -0800
    GCA_004115265.2 replaced by GCF_004115265.2 no redmine;
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    7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800
    adding four new VGP assemblies to catch up no redmine
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 29, context: html, text, full: html, text
    253725f97da38e647a3f7ac58043a0022b1c4847 Thu Feb 9 15:00:07 2023 -0800
    bring in Asiatic elephant, domestic cat, and platypus GenArk hub chain tracks into composite refs #30555
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 25, context: html, text, full: html, text
    253725f97da38e647a3f7ac58043a0022b1c4847 Thu Feb 9 15:00:07 2023 -0800
    bring in Asiatic elephant, domestic cat, and platypus GenArk hub chain tracks into composite refs #30555
• src/hg/makeDb/trackDb/human/hg38/recombRate.ra
  • lines changed 2, context: html, text, full: html, text
    bcb55e9710a49301872112a3ffa02d1acc08a36f Thu Feb 9 16:00:50 2023 -0800
    Removing release tag, shortening the shortLabel and updating the pennantIcon, refs #30044
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    457fefad7b49573179bf6469470d39ab74b944cb Mon Feb 6 17:07:38 2023 -0800
    Adding beta to release tag, refs #30044
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    bcb55e9710a49301872112a3ffa02d1acc08a36f Thu Feb 9 16:00:50 2023 -0800
    Removing release tag, shortening the shortLabel and updating the pennantIcon, refs #30044
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    a09016f0bee722e938fd61643fe3d8f60a403ac0 Sun Feb 12 14:40:50 2023 -0800
    remove demo snake tracks
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 206, context: html, text, full: html, text
    6a173139cd987a0438b9798b902e0f4ba5006062 Thu Feb 9 14:23:02 2023 -0800
    adding chainNet definitions for GCF_024166365.1 GCF_018350175.1 GCF_004115215.2 per user request refs #30555
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 8, context: html, text, full: html, text
    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/hg/utils/gff3ToGenePred/tests/expected/hprcTest.gp
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    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/hg/utils/gff3ToGenePred/tests/input/hprc.gff3
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    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/hg/utils/gff3ToGenePred/tests/makefile
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    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/hg/utils/otto/grcIncident/runUpdate.sh
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    267f04e1dd82e71c871c9dfb465e2d3b1aa5617e Fri Feb 10 09:53:48 2023 -0800
    add a bit more output in the failing case to help identify it and update GRCh38 to patch 14 no redmine
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
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    644aca2e8d7af3d037a6fc29a400c5d79484756e Wed Feb 8 20:49:24 2023 -0800
    Data-driven branch-specific masking: replaced the contents of maskDelta.sh with a YAML specification of branches and sites/ranges/reversions to mask and a python script that reads the spec and then makes a matUtils mask file and runs matUtils mask as before. Did this so I could point people to the YAML spec instead of a non-portable bash script when they asked what sites are masked in what branches. See https://github.com/yatisht/usher/issues/324
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    644aca2e8d7af3d037a6fc29a400c5d79484756e Wed Feb 8 20:49:24 2023 -0800
    Data-driven branch-specific masking: replaced the contents of maskDelta.sh with a YAML specification of branches and sites/ranges/reversions to mask and a python script that reads the spec and then makes a matUtils mask file and runs matUtils mask as before. Did this so I could point people to the YAML spec instead of a non-portable bash script when they asked what sites are masked in what branches. See https://github.com/yatisht/usher/issues/324
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    c4776f376543fd420aa6024619f950c49f651c30 Wed Feb 8 20:51:36 2023 -0800
    Added a few more sequences from cov-lineages/pango-designation#1505
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    644aca2e8d7af3d037a6fc29a400c5d79484756e Wed Feb 8 20:49:24 2023 -0800
    Data-driven branch-specific masking: replaced the contents of maskDelta.sh with a YAML specification of branches and sites/ranges/reversions to mask and a python script that reads the spec and then makes a matUtils mask file and runs matUtils mask as before. Did this so I could point people to the YAML spec instead of a non-portable bash script when they asked what sites are masked in what branches. See https://github.com/yatisht/usher/issues/324
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    b3beba6edcc5ba334a756b83a11b66ec9350255a Wed Feb 8 21:10:19 2023 -0800
    Ever more lineages. Changed XBB.1.5 to not require T17124C.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    18a7959f18910bf26ec02f4ae21b839024d94230 Wed Feb 8 20:52:35 2023 -0800
    Fixed some bash syntax so the usage message appears when needed.
• src/inc/gff3.h
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    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/lib/bigBed.c
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    208943a63d7d5620b78217bb5593e9a17335d858 Mon Feb 6 17:59:56 2023 -0800
    Problems found with newer gcc on Ubunto 20, compiled on a vm.
• src/lib/gff3.c
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    0362494184981193a406895a488aee5e92ece803 Tue Feb 7 14:24:25 2023 -0800
    support for converting HPRC GFF3 files from Ensembl. Not perfect, however, all genes get converted, so this can be fixed in post-preocessing
• src/lib/net.c
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    208943a63d7d5620b78217bb5593e9a17335d858 Mon Feb 6 17:59:56 2023 -0800
    Problems found with newer gcc on Ubunto 20, compiled on a vm.
• src/utils/qa/searchedTermsCron.py
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    7f9ebf15a57b4c8529177fdb89e4b56f36e57a3b Mon Feb 6 16:45:36 2023 -0800
    Code review edits: adding variable to get current year for searchedTermsCron.py and updating the relative path for a URL in newsarch.html , refs #30536
• src/utils/qa/weeklybld/buildEnv.csh
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    8076e5d305eddfa1b901e6335a7b7689f12b4698 Mon Feb 13 10:09:01 2023 -0800
    v444 preview2, refs #30618

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