All File Changes

v411_preview2 to v411_base (2021-02-22 to 2021-03-01) v411

• .gitignore
  • lines changed 3, context: html, text, full: html, text
    d8874392132c3e1fe3cd1850550aed635a5566dd Tue Feb 23 09:40:09 2021 -0800
    have git ignore js/react/*/compiled/ directories
• src/browserbox/root/updateBrowser.sh
  • lines changed 1, context: html, text, full: html, text
    630ec442be94b7101d52477cbebf06d66633427f Wed Feb 24 14:56:34 2021 -0800
    add fonts to GBiB
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 5, context: html, text, full: html, text
    630ec442be94b7101d52477cbebf06d66633427f Wed Feb 24 14:56:34 2021 -0800
    add fonts to GBiB
• src/hg/featureBits/featureBits.c
  • lines changed 6, context: html, text, full: html, text
    2306b0cbe3778fe985fa284367228b35fd9dae78 Tue Feb 23 11:27:38 2021 -0800
    added featureBits option to only consider primary chromosomes using UCSC naming convention
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 7, context: html, text, full: html, text
    627074545317c835b7de2119653fd86d0ce8bbea Fri Feb 26 16:40:53 2021 -0800
    Adding a link to hgLiftOver refs #27086
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 18, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 189, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
  • lines changed 86, context: html, text, full: html, text
    7c1221c572248594a25af2c26e99c123415efe26 Tue Feb 23 11:38:29 2021 -0800
    The hardcoded QC thresholds for the green/yellow/red coloring in the summary table are out of date. Loosen the defaults a bit to reflect what is now a normal amount of difference from the reference, and add a config file to make them easily adjustable in the future.
  • lines changed 42, context: html, text, full: html, text
    a2a68e8ad4ff5927b604b27898c183a519c9e5f4 Tue Feb 23 20:08:34 2021 -0800
    Instead of replacing small subtrees (usher -k) with the new single subtree option (-K), make both (unless a large number of sequences are uploaded; then just -K).
  • lines changed 128, context: html, text, full: html, text
    5956c40955854fd83b75627124f6420518a78960 Wed Feb 24 20:51:42 2021 -0800
    Add more columns from summary table to TSV summary file. Move PSL indel-tallying code upstream & store results for summaries.
  • lines changed 12, context: html, text, full: html, text
    3ab3206277c766565ec2f5419e3f51f04064212f Thu Feb 25 16:09:26 2021 -0800
    Allow protobuf.tab's description column to contain filenames so we can point to automatically updated latest public files.
  • lines changed 49, context: html, text, full: html, text
    17cdc50389b482ee9f3f1ce649ed297201269d53 Thu Feb 25 20:41:01 2021 -0800
    If usher's output includes clade and lineage assignments, parse them and include them in the summary table.
  • lines changed 241, context: html, text, full: html, text
    8441e4b8e776dea862c62a466f765c8cd94b1e3d Mon Mar 1 00:55:04 2021 -0800
    Add a TSV download file summarizing S (Spike) protein mutations, emphasizing antibody escape and Receptor Binding Domain mutations. Don't show too many buttons at the top. Try a little harder to find metadata for collapsed nodes in subtrees.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 26, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
  • lines changed 1, context: html, text, full: html, text
    a2a68e8ad4ff5927b604b27898c183a519c9e5f4 Tue Feb 23 20:08:34 2021 -0800
    Instead of replacing small subtrees (usher -k) with the new single subtree option (-K), make both (unless a large number of sequences are uploaded; then just -K).
  • lines changed 13, context: html, text, full: html, text
    5956c40955854fd83b75627124f6420518a78960 Wed Feb 24 20:51:42 2021 -0800
    Add more columns from summary table to TSV summary file. Move PSL indel-tallying code upstream & store results for summaries.
  • lines changed 2, context: html, text, full: html, text
    17cdc50389b482ee9f3f1ce649ed297201269d53 Thu Feb 25 20:41:01 2021 -0800
    If usher's output includes clade and lineage assignments, parse them and include them in the summary table.
  • lines changed 1, context: html, text, full: html, text
    8441e4b8e776dea862c62a466f765c8cd94b1e3d Mon Mar 1 00:55:04 2021 -0800
    Add a TSV download file summarizing S (Spike) protein mutations, emphasizing antibody escape and Receptor Binding Domain mutations. Don't show too many buttons at the top. Try a little harder to find metadata for collapsed nodes in subtrees.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 37, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
  • lines changed 57, context: html, text, full: html, text
    a2a68e8ad4ff5927b604b27898c183a519c9e5f4 Tue Feb 23 20:08:34 2021 -0800
    Instead of replacing small subtrees (usher -k) with the new single subtree option (-K), make both (unless a large number of sequences are uploaded; then just -K).
  • lines changed 32, context: html, text, full: html, text
    17cdc50389b482ee9f3f1ce649ed297201269d53 Thu Feb 25 20:41:01 2021 -0800
    If usher's output includes clade and lineage assignments, parse them and include them in the summary table.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 20, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
  • lines changed 6, context: html, text, full: html, text
    a9be614b7730455011e5bfcf1f804eecb81f28ec Tue Feb 23 20:09:52 2021 -0800
    Russ request: by default, color by sample type (uploaded vs. existing) and don't show labels (they hide branches and are unreadable when tree is large). Also update Nextstrain clade colors.
  • lines changed 2, context: html, text, full: html, text
    4311905d25fea6367820a25ef089674680cfa37f Wed Feb 24 13:03:14 2021 -0800
    Nextstrain colors in auspice JSON: make uploaded samples stand out, add 20A.EU2.
  • lines changed 3, context: html, text, full: html, text
    439c90e9ae6471a5e575cdc1a35a722ac040c745 Mon Mar 1 00:55:54 2021 -0800
    Don't offer GISAID clade coloring for public trees since we don't have GISAID clade info for them.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 63, context: html, text, full: html, text
    5956c40955854fd83b75627124f6420518a78960 Wed Feb 24 20:51:42 2021 -0800
    Add more columns from summary table to TSV summary file. Move PSL indel-tallying code upstream & store results for summaries.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 20, context: html, text, full: html, text
    7e58340888377874edaad1dbc5174e20295f890c Mon Feb 22 14:17:33 2021 -0800
    Support upload of more sequences, add TSV file summarizing sample variants and placements. Requested by Joe de Risi (UCSF). Increase timeout to 10 minutes; make TSV with each sample's ID, nuc muts, AA muts, imputed bases and path from root to sample. Also use Yatish's new -K subtree algorithm in usher: one subtree encompassing all uploaded samples, plus the specified number of samples randomly selected from the rest of the tree. Don't show every single sample name in the title because there can be 1000 samples in the same subtree now. :)
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    07cf356455818b5dea3ffb62e3f462ba5fa30937 Fri Feb 26 16:27:09 2021 -0800
    prevent crash of hgTracks when maxWindowToDraw is used on bigWigs
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    b08adb87ffe9706696cf47ea9356c05ab998ab5c Mon Feb 22 11:29:25 2021 -0800
    don't put up the query sequence for blat custom track which might have multiple sequences
  • lines changed 19, context: html, text, full: html, text
    7def57860cd7a395af34b06ff0fe04e32a7f3e97 Thu Feb 25 13:58:01 2021 -0800
    don't attempt to connect to database for blat results from user input, including hubs
• src/hg/htdocs/contacts.html
  • lines changed 184, context: html, text, full: html, text
    71b3dc26b7bccd706bf4dac10deba76eedf69aef Tue Feb 23 17:28:46 2021 -0800
    cleaned up wording and organization
• src/hg/htdocs/covid19.html
  • lines changed 27, context: html, text, full: html, text
    599d664ddcf01de9da445c09ada1f199ade1f5ed Tue Feb 23 13:07:19 2021 -0800
    Update intro paragraph and add news item to COVID landing page, to highlight variant and mutations tracks.
  • lines changed 4, context: html, text, full: html, text
    526789d6d6aeacc9e592921c8177591c30542704 Tue Feb 23 18:20:53 2021 -0800
    dropping link. discontinuing maintenance
  • lines changed 21, context: html, text, full: html, text
    c03e3225559110595d05d71774331201c15d914a Wed Feb 24 08:27:27 2021 -0800
    Update and tighten wording in intro, update Nextstrain link. refs #25217
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    c5175e018cba8066d44772fde36ee07f501030eb Thu Feb 25 14:34:52 2021 -0800
    Removing an extra closing paragraph tag, no redmine
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 137, context: html, text, full: html, text
    68f4a25ad329fe693a2b8702bdd0a9f072990822 Mon Feb 22 16:11:03 2021 -0800
    Correcting a line about exonNumbers in trackDbLibrary refs #26598
  • lines changed 137, context: html, text, full: html, text
    d5ea9083c0d4b05184061069c93777ddc44cad0e Mon Feb 22 16:32:21 2021 -0800
    Revert "Correcting a line about exonNumbers in trackDbLibrary refs #26598" When I made this above exonNumbers I had other 'git checkout oldCommit changes staged reverting them back" This reverts commit 68f4a25ad329fe693a2b8702bdd0a9f072990822.
  • lines changed 1, context: html, text, full: html, text
    63e24ab4403518aefb8bb36b09122d5b6b5c0cc6 Mon Feb 22 16:46:51 2021 -0800
    Fixing a stray quotation mark in trackDbHub.v2 refs #26598
  • lines changed 6, context: html, text, full: html, text
    7ac2e910cc1b8e35fcc1671b9e2484d00892d941 Mon Feb 22 16:54:24 2021 -0800
    Moving some items in tracDbHub.v2 that are incorrectly marked as required to new (required items are items required for all hubs to work, as seen in this hubCheck command hubCheck -settings -level=required) refs #26598
  • lines changed 1, context: html, text, full: html, text
    d6f4508d22791b9781486136152ab64284217e2e Wed Feb 24 13:28:44 2021 -0800
    Small link fix on trackDbHub.v2 refs #26598
  • lines changed 8, context: html, text, full: html, text
    0be6716d8b1b060e6ab7f28917f045fafc449de5 Thu Feb 25 15:07:52 2021 -0800
    Adding some <a name=newSetting</a> entries on trackDbHub.v2 so Table of Contents can find new settings refs #26598
  • lines changed 1, context: html, text, full: html, text
    b70e552ff81ad543742da2495abe2c9f67e9ea34 Thu Feb 25 16:10:46 2021 -0800
    Removing an extra <code> tag that was breaking hubCheck -settings refs #26598
  • lines changed 1, context: html, text, full: html, text
    ac5c899c29eacb4ba584f18c7f4f719807f04b6b Fri Feb 26 15:56:08 2021 -0800
    Changing meta from level base to full, base suggests Ensembl signed-up to support meta and no signs this is the case. refs #26598
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    68f4a25ad329fe693a2b8702bdd0a9f072990822 Mon Feb 22 16:11:03 2021 -0800
    Correcting a line about exonNumbers in trackDbLibrary refs #26598
  • lines changed 2, context: html, text, full: html, text
    d5ea9083c0d4b05184061069c93777ddc44cad0e Mon Feb 22 16:32:21 2021 -0800
    Revert "Correcting a line about exonNumbers in trackDbLibrary refs #26598" When I made this above exonNumbers I had other 'git checkout oldCommit changes staged reverting them back" This reverts commit 68f4a25ad329fe693a2b8702bdd0a9f072990822.
  • lines changed 2, context: html, text, full: html, text
    9ae061463d19f620146ec250559b766701ffb623 Mon Feb 22 16:36:36 2021 -0800
    Correcting a line about exonNumbers in trackDbLibrary (and this time not accidentally including /trackDbHub.v2.html changes from another unrelated change) refs #26598
  • lines changed 8, context: html, text, full: html, text
    b310d5be5f0bacd60157c2402183cb44271f10d9 Fri Feb 26 17:30:59 2021 -0800
    Adding a scoreFilter and scoreFilterLimits alternative note about filter.score and filterByRange.score
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    b4e4ced101475547568667c730b4aabf427fe58b Wed Jan 27 15:05:48 2021 -0800
    Updated Clay's job description.
  • lines changed 1, context: html, text, full: html, text
    bc89f09d68bb21e16ded15f13cc9f9424ff216b8 Thu Jan 28 10:30:41 2021 -0800
    Changed Parisa's role to Project Manager for both CIRM and HCA.
  • lines changed 1, context: html, text, full: html, text
    9f022fa572da7200e68e72c9ae654d0d63b44267 Thu Jan 28 14:41:37 2021 -0800
    Updated William's role to Senior Data Wrangler and Full Stack Developer.
  • lines changed 2, context: html, text, full: html, text
    0bce910863f40f364ba8f683ba5e25388e8fa727 Tue Feb 23 12:14:26 2021 -0800
    Updated staff image for 2021.
  • lines changed 1, context: html, text, full: html, text
    0d0738664f275d15e078b009a21953d0116c3d0d Tue Feb 23 13:02:12 2021 -0800
    Updated William's title to Senior Data Wrangler and Data Engineer.
• src/hg/hubApi/getData.c
  • lines changed 2, context: html, text, full: html, text
    3a98f0a9c8b6e1771f09cd38d2cf68a7a691c860 Mon Mar 1 08:22:44 2021 -0800
    need to use the appropriate chrom name column when getting full table refs #25840
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b8032901670f0266e9c228bd9fda6a74463c65b9 Mon Mar 1 10:07:38 2021 -0800
    New version number v411
• src/hg/js/ddcl.js
  • lines changed 2, context: html, text, full: html, text
    87cb31210c7b6339c24c568397725460d594c4f0 Wed Feb 24 11:15:40 2021 -0800
    change c-style to js for curly braces, thanks Kate for catching.
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    1506b9017098c2c5d657aa0946cb59622b005338 Wed Feb 24 03:43:59 2021 -0800
    fixing another right-click problem, refs #26687
• src/hg/js/hui.js
  • lines changed 2, context: html, text, full: html, text
    928a0042c83303e4dcce0fc204d32630c04f2d09 Wed Feb 24 23:06:16 2021 -0800
    Fixed existing bug causing "ASSERT: matChkBoxNormalize() called for dim ABC!". This occurred for old-style dimensions that were neither XY matrix nor filterComposite facets. refs #25012
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    4940e907275b34957f5182ca6daa7ac8a2679803 Mon Feb 22 15:44:04 2021 -0800
    check for a NULL cart
• src/hg/lib/liftOver.c
  • lines changed 27, context: html, text, full: html, text
    93bdf148d3a0408d7e668190c5046fd3b34eef90 Tue Feb 23 22:32:50 2021 -0800
    Fixing some bugs in liftOver. Increased max fields from 64 to 256. Now it requires 3 or more fields. It detects if the field counts are not consistent for all rows. And it detects if there are too many fields. Fixes annoying bug in bed 1 or bed 2 that would confabulate output. refs #27023
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    c7e73e987cddcd4ad7df539e29910cb362293909 Wed Feb 24 10:48:48 2021 -0800
    MarkD recommended
• src/hg/lib/protobuf.c
  • lines changed 2, context: html, text, full: html, text
    6bb6a4d5b9cd9812ed63d2d2e80580099b3bc557 Thu Feb 25 18:59:31 2021 -0800
    Fix bug in skipping unrecognized protobuf repeated field (put else clause in the right place).
• src/hg/lib/variantProjector.c
  • lines changed 6, context: html, text, full: html, text
    ec58e08d65dcad145657e4c4420988ce5c3e4b18 Mon Feb 22 14:22:40 2021 -0800
    Increase bufLen in genomeTxMismatch to accommodate overlapping blocks for ribosomal frameshift as in SARS-CoV-2.
• src/hg/liftOver/tests/expected/bedPlus3-256.bed
  • lines changed 6, context: html, text, full: html, text
    93bdf148d3a0408d7e668190c5046fd3b34eef90 Tue Feb 23 22:32:50 2021 -0800
    Fixing some bugs in liftOver. Increased max fields from 64 to 256. Now it requires 3 or more fields. It detects if the field counts are not consistent for all rows. And it detects if there are too many fields. Fixes annoying bug in bed 1 or bed 2 that would confabulate output. refs #27023
  • lines changed 6, context: html, text, full: html, text
    dec161384fad86ffbb284a47f302aa06f2399ed9 Thu Feb 25 11:45:47 2021 -0800
    Now that the limit was raised from 256 to 2048, this is not needed
• src/hg/liftOver/tests/input/bedPlus-256.bed
  • lines changed 6, context: html, text, full: html, text
    93bdf148d3a0408d7e668190c5046fd3b34eef90 Tue Feb 23 22:32:50 2021 -0800
    Fixing some bugs in liftOver. Increased max fields from 64 to 256. Now it requires 3 or more fields. It detects if the field counts are not consistent for all rows. And it detects if there are too many fields. Fixes annoying bug in bed 1 or bed 2 that would confabulate output. refs #27023
  • lines changed 6, context: html, text, full: html, text
    dec161384fad86ffbb284a47f302aa06f2399ed9 Thu Feb 25 11:45:47 2021 -0800
    Now that the limit was raised from 256 to 2048, this is not needed
• src/hg/liftOver/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    93bdf148d3a0408d7e668190c5046fd3b34eef90 Tue Feb 23 22:32:50 2021 -0800
    Fixing some bugs in liftOver. Increased max fields from 64 to 256. Now it requires 3 or more fields. It detects if the field counts are not consistent for all rows. And it detects if there are too many fields. Fixes annoying bug in bed 1 or bed 2 that would confabulate output. refs #27023
  • lines changed 9, context: html, text, full: html, text
    dec161384fad86ffbb284a47f302aa06f2399ed9 Thu Feb 25 11:45:47 2021 -0800
    Now that the limit was raised from 256 to 2048, this is not needed
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 49, context: html, text, full: html, text
    6964f094f71a69fa083dbe3a6d88dc84f60b0855 Thu Feb 25 11:44:28 2021 -0800
    expanded link to other hubs table refs #23891
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 355, context: html, text, full: html, text
    9a4fce5401a6b405d65f2c05e1e3424d6cf6892c Thu Feb 25 09:49:24 2021 -0800
    adding fungi run list refs #27072
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    0736936b377d71bc19c0aa3b4311bc3872f76d54 Thu Feb 25 11:40:51 2021 -0800
    catching up a few assemblies refs #23891
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 355, context: html, text, full: html, text
    96eadc884d440309b56203fcbdf7b2bfa9ab1a7c Wed Feb 24 13:38:18 2021 -0800
    initial set non-unique common names refs #27072
  • lines changed 345, context: html, text, full: html, text
    51d63f5c477d789b0cc6fc94ec9fd6387e7d99dc Wed Feb 24 13:39:08 2021 -0800
    and with unique common names refs #27072
• src/hg/makeDb/doc/fungiAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    96eadc884d440309b56203fcbdf7b2bfa9ab1a7c Wed Feb 24 13:38:18 2021 -0800
    initial set non-unique common names refs #27072
• src/hg/makeDb/doc/fungiAsmHub/makefile
  • lines changed 26, context: html, text, full: html, text
    96eadc884d440309b56203fcbdf7b2bfa9ab1a7c Wed Feb 24 13:38:18 2021 -0800
    initial set non-unique common names refs #27072
• src/hg/makeDb/doc/hg38/cactus241way.txt
  • lines changed 924, context: html, text, full: html, text
    b5ba1cd9de8155e0d9110426bb5e137b78f708d6 Sat Feb 27 17:50:21 2021 -0800
    rought notes on constructing the 241-way track from the cactus hal file no redmine
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f0874c9f03bf0f37bf7365813dce7e83d549f6d5 Thu Feb 25 12:38:39 2021 -0800
    adding the purple sea urchin refs #27032
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    08cee46a18fa261f2af2d711d666b4ec3dbfd855 Thu Feb 25 11:39:12 2021 -0800
    mRatBN7.2 became a GCF release refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    ebf2d6bb1cefc1fdf1dec9548002bd0b7600340d Thu Feb 25 11:40:21 2021 -0800
    catching up a few assemblies refs #23891
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    65e66bfd2166612d6aa23ab8741bea63e76417e7 Thu Feb 25 11:42:16 2021 -0800
    catching up a few assemblies refs #26765
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV36.sh
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    919f6584f7a27525a8c287e10eafc31f1d96987f Mon Mar 1 07:39:07 2021 -0800
    create knownGene short-circuit trix file from knownCanonical without pseudogenes
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    b4dc9b3c2392cdc04e21b7d7e0cbd4f0f44c291c Thu Feb 25 11:41:18 2021 -0800
    catching up a few assemblies refs #23891
• src/hg/makeDb/doc/wuhCor1/spikeMuts.txt
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    f759f4f5195bdfe940c7611bd28833eaa0478cfd Wed Feb 24 08:53:35 2021 -0800
    Add make doc. refs #27025
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
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    8b490c6462b2eadfa0d54ec6f101a08c4cb0723f Wed Feb 24 09:07:30 2021 -0800
    Add make doc. refs #26876
• src/hg/makeDb/doc/xenTro10/initialBuild.txt
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    00bf66b33a1aaf94662da3947525b151a3fb9fd8 Mon Feb 22 13:32:31 2021 -0800
    initial db done running up RM and TRF refs #24693
• src/hg/makeDb/schema/all.joiner
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    a001152197ed70e4192a3ecf1db4e9efc4e34ce4 Mon Feb 22 22:08:40 2021 -0800
    adding rules for xenTro10 refs #24693
• src/hg/makeDb/trackDb/human/cadd.ra
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    89c00b4ed4fbf5d84e80218e7f09d903cee87d87 Fri Feb 26 04:03:38 2021 -0800
    working around dense mode problem in bigBed with only-insertion track, refs #18492
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    7e93fffd4c1d86c4c3e8b71badf0fbaf184a2be3 Fri Feb 26 16:12:56 2021 -0800
    Commenting out the maxWindowToDraw trackDb statement since it is currently broken, refs #18492
• src/hg/makeDb/trackDb/human/caddAlpha.ra
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    68f6144e502ba1c506ad6fe2ebbf49cdeee6db39 Fri Feb 26 16:09:23 2021 -0800
    Creating an alpha release verison of the CADD track for hg19 and hg38. This version contains the maxWinToDraw trackDb statement, refs #18492
• src/hg/makeDb/trackDb/human/caddSuper.html
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    d9a3622d83a3ac9a862aed226bc3e445b99ddb32 Thu Feb 25 14:28:02 2021 -0800
    Removing the space between mouseover, refs #18492
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    2065b8b9a610a9fe59fdb593aabe88c76962c168 Thu Feb 25 14:30:45 2021 -0800
    Replacing double quotes with the HTML entity, refs #18492
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    04282647de9c5688da55b7c2debc412d92a7c3d7 Thu Feb 25 14:48:29 2021 -0800
    Making each line less than 100 characters, refs #18492
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    00d7ec5697fe5ff72b7d6a2a907bd4384fd0b9aa Thu Feb 25 14:56:48 2021 -0800
    Adding double quotes around _blank attribute. Making 'Online' lowercase. Making <h2> tag lowercase, refs #18492
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    b562435c1788de3cc23904a788ba12bfed7a7f72 Thu Feb 25 14:59:52 2021 -0800
    Removing extra colon, refs #18492
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    1f6c523fc3ae53172f655789b37abc1e702d47d6 Thu Feb 25 15:01:27 2021 -0800
    Fixing phyloP typo, refs #18492
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
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    f03f959fe751f07ac02fa3d992764f07c1445c3a Wed Feb 24 09:49:04 2021 -0800
    Update stale COVID track pennanticons
• src/hg/makeDb/trackDb/human/encRegTfbsClustered.html
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    2dbde83fa13ececaabf3f5c811e595bc22f402af Tue Feb 23 12:19:33 2021 -0800
    Code review changes, minor detail added refs #27042
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    409e9a9ccaec73be08e2ace7bab31e8080e8086d Thu Feb 25 10:35:25 2021 -0800
    Ana colleagues request, add versions to the gnomAD tracks, refs #25010
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    668f464a238fdf7970b73eb574931433449cc8a9 Wed Feb 24 09:32:47 2021 -0800
    Repackage new supertrack for miRNA sites properly with release tags. refs #26287
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
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    7c83bb80b409ab17a349d216d0b37c2428541d96 Wed Feb 24 12:16:38 2021 -0800
    HTML typo fixes and beta staging #26919
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    7c83bb80b409ab17a349d216d0b37c2428541d96 Wed Feb 24 12:16:38 2021 -0800
    HTML typo fixes and beta staging #26919
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    7c83bb80b409ab17a349d216d0b37c2428541d96 Wed Feb 24 12:16:38 2021 -0800
    HTML typo fixes and beta staging #26919
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
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    5bf335e0cbfdcf1de85d278e67538a6f5c526f1f Thu Feb 25 14:23:13 2021 -0800
    First draft for muscle single cell barChart track. refs #26968
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    7c83bb80b409ab17a349d216d0b37c2428541d96 Wed Feb 24 12:16:38 2021 -0800
    HTML typo fixes and beta staging #26919
• src/hg/makeDb/trackDb/human/trackDb.ra
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    f03f959fe751f07ac02fa3d992764f07c1445c3a Wed Feb 24 09:49:04 2021 -0800
    Update stale COVID track pennanticons
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    8484de5f08f542815e5efeb3f6c8757611e65863 Fri Feb 26 16:11:27 2021 -0800
    Staging the CADD track on hgwbeta for hg19 and hg38, refs #18492
• src/hg/makeDb/trackDb/makefile
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    81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800
    adding xenTro10 to the browser refs #24693
• src/hg/makeDb/trackDb/marmoset/calJac4/catV2.html
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    6c276764fa27ce3afe69d59a4607601675e5fc1e Wed Feb 24 17:40:55 2021 -0800
    added CAT genes and supporting isoseq to calJac4; still waiting for documentation
• src/hg/makeDb/trackDb/marmoset/calJac4/customRefSeqComposite.ra
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    41946fe619f5dd532050be9fdbf6a1af1ebcd198 Fri Feb 26 11:52:30 2021 -0800
    turning on refSeq all instead of just curated refs #27067
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.catV2.ra
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    6c276764fa27ce3afe69d59a4607601675e5fc1e Wed Feb 24 17:40:55 2021 -0800
    added CAT genes and supporting isoseq to calJac4; still waiting for documentation
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.isoseq.ra
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    6c276764fa27ce3afe69d59a4607601675e5fc1e Wed Feb 24 17:40:55 2021 -0800
    added CAT genes and supporting isoseq to calJac4; still waiting for documentation
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
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    6c276764fa27ce3afe69d59a4607601675e5fc1e Wed Feb 24 17:40:55 2021 -0800
    added CAT genes and supporting isoseq to calJac4; still waiting for documentation
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    41946fe619f5dd532050be9fdbf6a1af1ebcd198 Fri Feb 26 11:52:30 2021 -0800
    turning on refSeq all instead of just curated refs #27067
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    107792d9359c8992520019b64b8c88ea73b5b7b3 Mon Feb 22 12:40:04 2021 -0800
    change a wuhCor1 to $D
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    5f8722b1f6f1c6f38adf62a237493507b9c7072d Wed Feb 24 13:34:11 2021 -0800
    Adding status filter to Uniprot Regions of Interest track, refs #27069
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    73ddfa4b104d4415e53a40bb839d15278fe3a289 Fri Feb 26 12:08:15 2021 -0800
    Turning on filters for most of the Uniprot tracks, refs #27069
• src/hg/makeDb/trackDb/virus/wuhCor1/abEscape.ra
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    4fa6d811d81ed29019680c70211eca730ff1dc6e Wed Feb 24 09:50:27 2021 -0800
    Tweak wuhCor1 defaults
• src/hg/makeDb/trackDb/virus/wuhCor1/bloomEsc.ra
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    4fa6d811d81ed29019680c70211eca730ff1dc6e Wed Feb 24 09:50:27 2021 -0800
    Tweak wuhCor1 defaults
• src/hg/makeDb/trackDb/virus/wuhCor1/spikeMuts.Feb21.html
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    8ee79cb69c2e039ac29491677a2e558da9f6018a Thu Feb 18 21:11:38 2021 -0800
    Updated to include additional mutation (L452R, in CA variant), change coloring to reflect colocation in RBD domain and overlap with Bloom antibody escape, add nicknames. refs #27025
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    56734e00ddd5e16b4a16b2e02d4e2e580f1b61a2 Tue Feb 23 16:31:37 2021 -0800
    Add Data Access and Release Notes, after linking earlier files into archive dir for download. refs #27025
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    8ee79cb69c2e039ac29491677a2e558da9f6018a Thu Feb 18 21:11:38 2021 -0800
    Updated to include additional mutation (L452R, in CA variant), change coloring to reflect colocation in RBD domain and overlap with Bloom antibody escape, add nicknames. refs #27025
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    79857b1c0bedbfa1610f0591a106e0710f104fa1 Mon Feb 22 14:24:44 2021 -0800
    Retire some older pennant icons
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    0addfcaa8bfb7f36aea0cbc0e64218ffc7f7a662 Tue Feb 23 16:23:25 2021 -0800
    Update to spike mutations track refs #27025
• src/hg/makeDb/trackDb/virus/wuhCor1/treangen.ra
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    79857b1c0bedbfa1610f0591a106e0710f104fa1 Mon Feb 22 14:24:44 2021 -0800
    Retire some older pennant icons
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
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    4fa6d811d81ed29019680c70211eca730ff1dc6e Wed Feb 24 09:50:27 2021 -0800
    Tweak wuhCor1 defaults
• src/hg/makeDb/trackDb/xenTro/xenTro10/description.html
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    81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800
    adding xenTro10 to the browser refs #24693
• src/hg/makeDb/trackDb/xenTro/xenTro10/gap.html
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    81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800
    adding xenTro10 to the browser refs #24693
• src/hg/makeDb/trackDb/xenTro/xenTro10/gold.html
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    81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800
    adding xenTro10 to the browser refs #24693
• src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra
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    81c8061cf668e009c5222909840074a8ae57166e Mon Feb 22 12:22:11 2021 -0800
    adding xenTro10 to the browser refs #24693
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    2b386db2505e864fef06874aa394578431abfefc Mon Feb 22 13:26:52 2021 -0800
    adding gold table assembly track search rule refs #24693
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    98d802668211742e7f43a7563bb91f7830f7d54e Mon Feb 22 22:03:30 2021 -0800
    add refSeqComposite refs #24693
• src/hg/utils/automation/doAssemblyHub.pl
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    d08acbc51365288f679e20b71ebe3a51da8c80e1 Wed Feb 24 14:30:47 2021 -0800
    correctly process non-nuclear unlocalized sequence refs #27072
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    64d224c975cf63ad9f784e522ee6782cfe144abd Mon Feb 22 12:52:50 2021 -0800
    fixed gff3ToGenePred -refseqHacks to not SEGV on a CDS without a Name parameter
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
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    64d224c975cf63ad9f784e522ee6782cfe144abd Mon Feb 22 12:52:50 2021 -0800
    fixed gff3ToGenePred -refseqHacks to not SEGV on a CDS without a Name parameter
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp
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    64d224c975cf63ad9f784e522ee6782cfe144abd Mon Feb 22 12:52:50 2021 -0800
    fixed gff3ToGenePred -refseqHacks to not SEGV on a CDS without a Name parameter
• src/hg/utils/gff3ToGenePred/tests/input/ncbiProblems.gff3
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    64d224c975cf63ad9f784e522ee6782cfe144abd Mon Feb 22 12:52:50 2021 -0800
    fixed gff3ToGenePred -refseqHacks to not SEGV on a CDS without a Name parameter
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    0b0ce9ae275e9f648f37535a0fe627fccdf6807e Fri Feb 26 14:30:47 2021 -0800
    COG-UK metadata columns changed again.
• src/hg/utils/otto/sarscov2phylo/nextcladeCogUk.sh
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    acd9854d3c6537ff237c597534abd5b9afbb7a75 Thu Feb 25 10:40:45 2021 -0800
    Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.
• src/hg/utils/otto/sarscov2phylo/nextcladeNcbi.sh
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    acd9854d3c6537ff237c597534abd5b9afbb7a75 Thu Feb 25 10:40:45 2021 -0800
    Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.
• src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
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    acd9854d3c6537ff237c597534abd5b9afbb7a75 Thu Feb 25 10:40:45 2021 -0800
    Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    acd9854d3c6537ff237c597534abd5b9afbb7a75 Thu Feb 25 10:40:45 2021 -0800
    Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.
• src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
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    acd9854d3c6537ff237c597534abd5b9afbb7a75 Thu Feb 25 10:40:45 2021 -0800
    Adding cron scripts for nightly update of public tree, VCFs, metadata and protobufs for hgPhyloPlace.
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    0d28b81239a743f286ccc60328d0743a0fa9acbd Thu Feb 25 16:11:21 2021 -0800
    Make public-latest.* links in archive directory and hgPhyloPlaceData.
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    092adf5dfa56fee387d3836b3493ac46ee2c0281 Fri Feb 26 14:48:50 2021 -0800
    Add 'matUtils annotate' calls to add Nextclade and Pangolin assignments to protobuf for hgPhyloPlace.
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    ea4eb88f661eb1d288f61981093d402830496603 Mon Mar 1 01:01:43 2021 -0800
    matToVcf has been replaced by 'matUtils convert'. Also, use 'matUtils annotate's new -l option to clear old clade annotations before reassigning them on the updated protobuf.
• src/inc/srcVersion.h
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    b8032901670f0266e9c228bd9fda6a74463c65b9 Mon Mar 1 10:07:38 2021 -0800
    New version number v411
• src/product/installer/docker/Dockerfile
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    b231e8f80c91e35ca7dbce2f1a42bc841db1409f Wed Feb 24 08:49:14 2021 -0800
    docker does not accept the "latest" keyword anymore, so setting it to a valid version, no redmine yet
• src/product/installer/docker/README.md
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    3697ae3c4d8f0ae58e294ec25d067ccded1db65a Wed Feb 24 08:50:16 2021 -0800
    adding a README file for our dockerfile, no redmine yet
• src/utils/qa/weeklybld/buildEnv.csh
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    5af501d38abc47cb0cd991179169497821d6f363 Mon Mar 1 10:06:49 2021 -0800
    v411 final build, refs #27028
• src/utils/qa/weeklybld/sendLogEmail.pl
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    8b34eced1e2ac52f273c98e80faba0840430e6fd Mon Mar 1 10:03:55 2021 -0800
    Change Brianlee to Lou in code review email

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