All File Changes

v407_base to v408_preview (2020-11-16 to 2020-11-23) v408

• confs/hgwdev.hg.conf
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    6e69690ff17012c39162effae74faacecfb874ce Sun Nov 22 01:11:26 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPcr/hgPcr.c
  • lines changed 33, context: html, text, full: html, text
    577abc852567f4e4356b9f8c2438ade69221959a Fri Nov 20 13:18:26 2020 -0800
    changes to support isPcr in assembly hubs
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 408, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/makefile
  • lines changed 29, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/parsimonyProto.c
  • lines changed 275, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/parsimonyProto.h
  • lines changed 42, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1439, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 141, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 40, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 767, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 555, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 519, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 568, context: html, text, full: html, text
    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
    Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
  • lines changed 66, context: html, text, full: html, text
    deca5eaeff633b054ba0091c391298fc7dc34377 Sat Nov 21 12:29:43 2020 -0800
    finalizing freeType font work
  • lines changed 11, context: html, text, full: html, text
    f3f1e39e778e3a16206504e5d8b7ceacfae8464a Sat Nov 21 13:51:40 2020 -0800
    oops... wasn't setting the current font and style correctly
• src/hg/hgTracks/hgTracks.c
  • lines changed 48, context: html, text, full: html, text
    ff4af73ba2a52b18ce5423aae3104fae1d1a3473 Fri Nov 20 17:25:43 2020 -0800
    converted to single file for json data instead of one file for each track refs #21980
  • lines changed 3, context: html, text, full: html, text
    deca5eaeff633b054ba0091c391298fc7dc34377 Sat Nov 21 12:29:43 2020 -0800
    finalizing freeType font work
  • lines changed 15, context: html, text, full: html, text
    bc22cca38e8c981de982f705ff77a07e059e6854 Sun Nov 22 22:35:05 2020 -0800
    actually copy and replaceChars to make name for mouseOverJsonFile to make sure it is the same as pngTn names refs #21980
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
    Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
  • lines changed 5, context: html, text, full: html, text
    ff4af73ba2a52b18ce5423aae3104fae1d1a3473 Fri Nov 20 17:25:43 2020 -0800
    converted to single file for json data instead of one file for each track refs #21980
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    aa3b27394f87202be3140c6c961c05f934f928ca Thu Nov 19 03:28:16 2020 -0800
    fixing bug where knownGene on hg19 didn't show up the exon number mouseover, refs #25325
  • lines changed 15, context: html, text, full: html, text
    3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
    Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
• src/hg/hgTracks/wigTrack.c
  • lines changed 5, context: html, text, full: html, text
    d6f2b2dfc3960ffa2d4a54e47508f4c7a773abc0 Tue Nov 17 08:12:26 2020 -0800
    delay popup time set to 0.2 seconds and restore correct data construction function in wigTrack.c refs #21980
  • lines changed 32, context: html, text, full: html, text
    ff4af73ba2a52b18ce5423aae3104fae1d1a3473 Fri Nov 20 17:25:43 2020 -0800
    converted to single file for json data instead of one file for each track refs #21980
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 19, context: html, text, full: html, text
    b3a4aa8255c685882c37802308fb90e7f59f1431 Tue Nov 17 10:40:00 2020 -0800
    Fixing merge conflict on bigLolly.html
  • lines changed 21, context: html, text, full: html, text
    b7d562f6d2b90c3755c508c1a5b98c67648bf5b9 Tue Nov 17 14:16:52 2020 -0800
    Working with Gerardo to resolve a git merge on bigLolly.html and adding some </li> and punctuation changes after running htmlCheck validate on the page refs #26481
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    693072b3d6703b9ffd63ae17ba39db1b0a0d04a6 Fri Nov 13 10:40:49 2020 -0800
    Added quotes for CR #26499
  • lines changed 5, context: html, text, full: html, text
    b9835eeed840bf68dd1d425a45c7d2f70ec3b4f9 Tue Nov 17 14:01:06 2020 -0800
    CR edits refs #26543
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 12, context: html, text, full: html, text
    577abc852567f4e4356b9f8c2438ade69221959a Fri Nov 20 13:18:26 2020 -0800
    changes to support isPcr in assembly hubs
• src/hg/htdocs/goldenPath/help/metadata.html
  • lines changed 2, context: html, text, full: html, text
    8cafabb070141bf9e8646ffb893d833f6fa5c4aa Tue Nov 17 14:40:31 2020 -0800
    Correcting a link the static page cronjob found, and correcting a tagstom reference on the page
• src/hg/htdocs/goldenPath/help/qValue.html
  • lines changed 2, context: html, text, full: html, text
    f688dc8b0b0b4cff6962e70ebf6a16b4422b65ea Tue Nov 17 10:54:53 2020 -0800
    Fixed broken url
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 2, context: html, text, full: html, text
    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 11, context: html, text, full: html, text
    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    d6181a65b6a908408ca6e148b8f2ece2c31c9877 Mon Nov 16 15:20:50 2020 -0800
    Announcing the Genome in a Bottle tracks for hg19 and hg38, refs #25873 and #24349
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    d6181a65b6a908408ca6e148b8f2ece2c31c9877 Mon Nov 16 15:20:50 2020 -0800
    Announcing the Genome in a Bottle tracks for hg19 and hg38, refs #25873 and #24349
• src/hg/inc/barChartUi.h
  • lines changed 3, context: html, text, full: html, text
    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/inc/cartDb.h
  • lines changed 4, context: html, text, full: html, text
    a3388dd3d91dc0e5023cfbda12e249d419f3e960 Sun Nov 22 07:10:28 2020 -0800
    add ability to have a default cart other than the empty one.
• src/hg/inc/protobuf.h
  • lines changed 88, context: html, text, full: html, text
    ff6abb3b7f34ac95c918dd1f03a9e5d52c59fc20 Thu Nov 19 12:58:52 2020 -0800
    Very incomplete parser for Google's protobuf3 -- sufficient to read file generated by Yatish Turakhia's usher --save-mutation-annotated-tree. refs #25943
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    577abc852567f4e4356b9f8c2438ade69221959a Fri Nov 20 13:18:26 2020 -0800
    changes to support isPcr in assembly hubs
• src/hg/inc/trackLayout.h
  • lines changed 5, context: html, text, full: html, text
    3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
    Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
  • lines changed 1, context: html, text, full: html, text
    deca5eaeff633b054ba0091c391298fc7dc34377 Sat Nov 21 12:29:43 2020 -0800
    finalizing freeType font work
• src/hg/js/ajax.js
  • lines changed 6, context: html, text, full: html, text
    490360baa89b5522ed5c7381d7c6081d74b027d8 Wed Nov 18 11:48:12 2020 -0800
    Better to use feature detection than browser detection, also this solves a lingering issue with bowser not being defined on the first pass through in IE 11 (thanks Chris). No ticket.
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    d6f2b2dfc3960ffa2d4a54e47508f4c7a773abc0 Tue Nov 17 08:12:26 2020 -0800
    delay popup time set to 0.2 seconds and restore correct data construction function in wigTrack.c refs #21980
  • lines changed 38, context: html, text, full: html, text
    ff4af73ba2a52b18ce5423aae3104fae1d1a3473 Fri Nov 20 17:25:43 2020 -0800
    converted to single file for json data instead of one file for each track refs #21980
• src/hg/lib/barChartUi.c
  • lines changed 102, context: html, text, full: html, text
    7537f40b289d8ff6b05f41f66e683d97a130b794 Tue Nov 17 12:24:52 2020 -0800
    Rough cut adding category file setting to barChart. refs #22075
  • lines changed 97, context: html, text, full: html, text
    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/lib/cart.c
  • lines changed 24, context: html, text, full: html, text
    a3388dd3d91dc0e5023cfbda12e249d419f3e960 Sun Nov 22 07:10:28 2020 -0800
    add ability to have a default cart other than the empty one.
• src/hg/lib/cartDb.c
  • lines changed 10, context: html, text, full: html, text
    a3388dd3d91dc0e5023cfbda12e249d419f3e960 Sun Nov 22 07:10:28 2020 -0800
    add ability to have a default cart other than the empty one.
• src/hg/lib/defaultCart.as
  • lines changed 5, context: html, text, full: html, text
    a3388dd3d91dc0e5023cfbda12e249d419f3e960 Sun Nov 22 07:10:28 2020 -0800
    add ability to have a default cart other than the empty one.
• src/hg/lib/defaultCart.sql
  • lines changed 9, context: html, text, full: html, text
    a3388dd3d91dc0e5023cfbda12e249d419f3e960 Sun Nov 22 07:10:28 2020 -0800
    add ability to have a default cart other than the empty one.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    84285974728864d308855bd4bd62c0a6b42be4fd Mon Nov 23 05:04:22 2020 -0800
    change after code review, refs #26550
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    ff6abb3b7f34ac95c918dd1f03a9e5d52c59fc20 Thu Nov 19 12:58:52 2020 -0800
    Very incomplete parser for Google's protobuf3 -- sufficient to read file generated by Yatish Turakhia's usher --save-mutation-annotated-tree. refs #25943
• src/hg/lib/protobuf.c
  • lines changed 286, context: html, text, full: html, text
    ff6abb3b7f34ac95c918dd1f03a9e5d52c59fc20 Thu Nov 19 12:58:52 2020 -0800
    Very incomplete parser for Google's protobuf3 -- sufficient to read file generated by Yatish Turakhia's usher --save-mutation-annotated-tree. refs #25943
• src/hg/lib/trackHub.c
  • lines changed 48, context: html, text, full: html, text
    577abc852567f4e4356b9f8c2438ade69221959a Fri Nov 20 13:18:26 2020 -0800
    changes to support isPcr in assembly hubs
• src/hg/lib/trackLayout.c
  • lines changed 12, context: html, text, full: html, text
    3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
    Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
  • lines changed 15, context: html, text, full: html, text
    deca5eaeff633b054ba0091c391298fc7dc34377 Sat Nov 21 12:29:43 2020 -0800
    finalizing freeType font work
• src/hg/makeDb/doc/mm10.txt
  • lines changed 63, context: html, text, full: html, text
    fd20659e4f87569876e2827c566844b7871f4f45 Wed Nov 18 11:15:05 2020 -0800
    adding synNet and Rbest for ornAna1 and monDom5 per user request refs #26540
• src/hg/makeDb/doc/wuhCor1/cladeLineageColors.pl
  • lines changed 7, context: html, text, full: html, text
    9d643ff9f562c900533aac2a8dec11ebf8c90fcf Mon Nov 16 08:53:51 2020 -0800
    Add support for lineage D. refs #26530
• src/hg/makeDb/doc/wuhCor1/pbmShanghai.txt
  • lines changed 10, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 8, context: html, text, full: html, text
    7a8c6715c6b044e8e04ef55b2c9e4575112147f9 Mon Nov 16 16:46:01 2020 -0800
    Adding note that updates of sarsCov2Phylo and sarsCov2PhyloPub tracks are now done by scripts in hg/utils/otto/sarscov2phylo/ instead of copy-pasting from doc. refs #26530
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    ec38f362fff0731d414a123d8058f38ba5d14cae Fri Nov 13 11:27:43 2020 -0800
    Added period for Code Review #26499
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cd69498b2b6c061ac5900e57a7fc2cba0ffcb954 Wed Nov 18 11:20:53 2020 -0800
    fixing bug in exon numbers on knowngene, temporary fix, refs #25325
• src/hg/makeDb/trackDb/human/trackDb.giab.ra
  • lines changed 5, context: html, text, full: html, text
    d01fc76ae53ffedfb53bef76d85b6faebfd34995 Mon Nov 16 15:33:06 2020 -0800
    Capitalizing the 'Trios' view on the descripiton page. Adding the 'new' pennantIcon for the annoucnement. Shortening the shortLabel for the structural variants. Captializing 'in' to match the other tracks' longLabels. Removing an extra space in 'Chinese Trio'. refs #24349 and #25873
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b8f4e654488d1abf09073d1e6bb297b5963db8c7 Mon Nov 16 11:55:13 2020 -0800
    Removing the alpha,beta release tags now that the Genome in a Bottle tracks are ready to be released, refs #24349 and #25873
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    7efd3e53fb60cf072cd5349e65a01aec807b71f8 Mon Nov 16 15:49:20 2020 -0800
    LRG outlinks should go to http instead of ftp refs #24672
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    fdfd62aee9d6810c469b156f84687b7535604436 Thu Nov 19 04:46:08 2020 -0800
    adding more exonnumbers statements, refs #25325
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fdfd62aee9d6810c469b156f84687b7535604436 Thu Nov 19 04:46:08 2020 -0800
    adding more exonnumbers statements, refs #25325
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fdfd62aee9d6810c469b156f84687b7535604436 Thu Nov 19 04:46:08 2020 -0800
    adding more exonnumbers statements, refs #25325
• src/hg/makeDb/trackDb/tagTypes.tab
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    b409b5a3c5aef834f7604d6da332a1fe864b4e86 Tue Nov 17 17:02:17 2020 -0800
    Clean up code supporting barChartCategoryUrl. As bonus feature, dd support for r,g,b color spec. refs #22075
• src/hg/makeDb/trackDb/virus/wuhCor1/pbm.html
  • lines changed 38, context: html, text, full: html, text
    197fa6afb4fab13d463336fa222a5d61fe065b97 Tue Nov 17 14:07:45 2020 -0800
    Making each line less than 100 characters long. Adding 'target=_blank' to links, refs #26518
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    c0c882aa7b3361ceba983fddcfe85d6d1de8b879 Tue Nov 17 16:27:00 2020 -0800
    Updating the Data Access section with examples that apply to this track (fixing copy/paste typo). Also fixing a strange hyphen that was showing up on the track description page for 'SARS-COV-2', refs #26518
  • lines changed 5, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
  • lines changed 10, context: html, text, full: html, text
    2ed976a69da52347f6032f63fe5133ffe9ebce60 Mon Nov 23 05:36:04 2020 -0800
    Finally understood how the two wuhCor1 microarray tracks are different, adapting docs page a little, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbm.ra
  • lines changed 28, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
  • lines changed 3, context: html, text, full: html, text
    7a14c9fb3bffb6d1d8e8a4de933bd58281e163fb Fri Nov 20 10:30:07 2020 -0800
    Adding the HTML track description to the subtracks, refs #26518
  • lines changed 2, context: html, text, full: html, text
    90137cb28c399ecdb5783b6638a62865f728383b Fri Nov 20 12:52:03 2020 -0800
    Adding the type of antibody to the shortLabel, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIggCovid.ra
  • lines changed 2, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
  • lines changed 1, context: html, text, full: html, text
    7a14c9fb3bffb6d1d8e8a4de933bd58281e163fb Fri Nov 20 10:30:07 2020 -0800
    Adding the HTML track description to the subtracks, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIggHealthy.ra
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    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIgmCovid.ra
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    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
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    7a14c9fb3bffb6d1d8e8a4de933bd58281e163fb Fri Nov 20 10:30:07 2020 -0800
    Adding the HTML track description to the subtracks, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIgmHealthy.ra
  • lines changed 1, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmShanghai.html
  • lines changed 80, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
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    aec43620029610c138229ddd1f6fb5c8d9a3fddf Fri Nov 20 16:35:11 2020 -0800
    Replacing double quotes with the HTML entity. Making each line less than 100 characters, refs #26564
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    2ed976a69da52347f6032f63fe5133ffe9ebce60 Mon Nov 23 05:36:04 2020 -0800
    Finally understood how the two wuhCor1 microarray tracks are different, adapting docs page a little, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmShanghai.ra
  • lines changed 11, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmShanghaiIgg.ra
  • lines changed 604, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmShanghaiIgm.ra
  • lines changed 605, context: html, text, full: html, text
    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/pyle.html
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    0b6c3f4c2875e26b028cf720d81e535ca3981601 Thu Nov 19 10:44:04 2020 -0800
    Feedback from CR refs #26504
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a6a8319c0c26327bb3a2e01f3dd8a9dbf7a927cd Fri Nov 20 16:23:18 2020 -0800
    Adding the pbmShanghai.ra include in trackDb.ra file, refs #26564
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    03d425545a21bdb2c227c7c3af4112f5edc04999 Mon Nov 23 02:28:26 2020 -0800
    fixing include line of micoarray wuhCor1 tracks, refs #26564
• src/hg/makeDb/trackDb/virus/wuhCor1/treangen.html
  • lines changed 10, context: html, text, full: html, text
    0b6c3f4c2875e26b028cf720d81e535ca3981601 Thu Nov 19 10:44:04 2020 -0800
    Feedback from CR refs #26504
• src/hg/makefile
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    e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
    New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
• src/hg/utils/otto/sarscov2phylo/addUnmappedPublic.sh
  • lines changed 83, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/bioSampleIdToText.sh
  • lines changed 45, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/bioSampleTextToTab.pl
  • lines changed 129, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl
  • lines changed 179, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/extractUnmappedPublic.sh
  • lines changed 95, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
  • lines changed 119, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
  • lines changed 97, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 27, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 83, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/getRelease.sh
  • lines changed 80, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/mapPublic.sh
  • lines changed 94, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/processRelease.sh
  • lines changed 123, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/publicCredits.sh
  • lines changed 67, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/searchAllSarsCov2BioSample.sh
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    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
  • lines changed 66, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
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    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 62, context: html, text, full: html, text
    99599c7130790107ff0de9f043930da6aa7fddf1 Mon Nov 16 16:35:58 2020 -0800
    Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching sequences and metadata from several public sources, mapping GISAID IDs to public seq IDs, downloading the latest release of the phylogenetic tree from github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public sequences, and using github.com/yatisht/usher to resolve ambiguous alleles, make protobuf files for hgPhyloPlace, and add public sequences that have not been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive public tree+VCF. This is still not fully otto-mated because certain crucial inputs like GISAID sequences still must be downloaded using a web browser, but the goal is to automate as much as possible and maybe someday have it fully cron-driven. There are two main top-level scripts which call other scripts, which may in turn call scripts, in this hierarchy: updateIdMapping.sh getCogUk.sh getNcbi.sh searchAllSarsCov2BioSample.sh bioSampleIdToText.sh bioSampleTextToTab.pl gbMetadataAddBioSample.pl fixNcbiFastaNames.pl updateSarsCov2Phylo.sh getRelease.sh processRelease.sh cladeLineageColors.pl mapPublic.sh extractUnmappedPublic.sh addUnmappedPublic.sh many of the above: util.sh publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I figure out how to automate fetching of author/institution metadata from NCBI and COG-UK.
• src/hg/utils/tdbQuery/tdbQuery.c
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    e1e3339475b5276781bdbb69dc991f8fc6173ae2 Sat Nov 21 16:27:40 2020 -0800
    Fix for absence of a release tag in an include file ignoring a parent include's release tag, refs #26566
• src/hg/utils/vcfToBed/vcfToBed.c
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    d0c2e3ab43838885be6ee4759b697cd972cea4ba Fri Nov 20 09:33:59 2020 -0800
    Increasing number of extra fields allowed in vcfToBed after running up against in gnomAD v3 update, refs #26449
• src/inc/phyloTree.h
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    7ffce0e9718d585fa11cddf6ae4fa2be764e6795 Fri Jul 24 17:19:51 2020 -0700
    Added phyloCountInternalNodes. Allow Newick format tree node names to begin with '_'. refs #25943
• src/jkOwnLib/gfPcrLib.c
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    577abc852567f4e4356b9f8c2438ade69221959a Fri Nov 20 13:18:26 2020 -0800
    changes to support isPcr in assembly hubs
• src/lib/freeType.c
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    deca5eaeff633b054ba0091c391298fc7dc34377 Sat Nov 21 12:29:43 2020 -0800
    finalizing freeType font work
• src/lib/phyloTree.c
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    7ffce0e9718d585fa11cddf6ae4fa2be764e6795 Fri Jul 24 17:19:51 2020 -0700
    Added phyloCountInternalNodes. Allow Newick format tree node names to begin with '_'. refs #25943
• src/utils/bedFixBlockOverlaps
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    d0ab96bfa4307ef666f194cdd2bda05608972cd1 Mon Nov 23 04:44:23 2020 -0800
    trying to address a problem in bedFixBlockOverlaps that appears in the uniprot otto pipeline. This is a hacky fix, but the problem only appears in very unusual assemblies, not on any mammal. refs #25784
• src/utils/bigHeat
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    9e006b729dc772306ef1d23ca9171308051278b4 Fri Nov 20 06:49:57 2020 -0800
    Adding wuhCor1 track for protein binding microarray data for the S protein, refs #26564
• src/utils/chromToUcsc/chromToUcsc
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    262ca5711bd80d3df1f85cd1a836063e52a7a4e0 Mon Nov 23 04:43:33 2020 -0800
    small fix to chromToUcsc for the special case of a mix of fixedStep + bed-Graph, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    b529787d46b6fcd30ae04bed0bd157ea7a122764 Mon Nov 23 10:10:11 2020 -0800
    v408 preview1
• src/utils/vcfFilter/vcfFilter.c
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    8d5880a93fa01e34601d87638c775f5945f9b269 Tue Nov 17 15:32:54 2020 -0800
    Adding clarifications to usage message & code based on code review feedback, thanks Chris. refs #26546

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