All File Changes

v427_base to v428_preview (2022-02-21 to 2022-02-28) v428

• src/hg/gar/garTable.pl
  • lines changed 53, context: html, text, full: html, text
    d4fdeadb1c734b4bf4d9885f462fa93c79df55b7 Mon Feb 21 16:02:14 2022 -0800
    add tooltip doc on column headers refs #28930
  • lines changed 2, context: html, text, full: html, text
    98e1f23b286fccc2636e7cdeadb3c5cd1c936876 Tue Feb 22 14:00:08 2022 -0800
    change text on column hide show pull down manu refs #28930
  • lines changed 1, context: html, text, full: html, text
    2cf3578abce882ea76c4d4f1309972a07797ba4f Tue Feb 22 14:29:18 2022 -0800
    better cleaning of sort keys for submitter strings and h1 h2 headings on intro text refs #28930
  • lines changed 17, context: html, text, full: html, text
    1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 Thu Feb 24 14:05:28 2022 -0800
    add a column 1 tool tip to indicate request or browser refs #28930
  • lines changed 22, context: html, text, full: html, text
    dcc09e71de2cb1f61a19f0526e0595ceb8277bb3 Fri Feb 25 10:43:00 2022 -0800
    adding cell background coloring for the IUCN column and tri-state indication on the hideAll buttons refs #28930
  • lines changed 44, context: html, text, full: html, text
    e56876e545b21501152e96f655141eb3b229cf0c Fri Feb 25 16:19:26 2022 -0800
    add in bioSample and bioProject columns and control of IUCN display refs #28930
• src/hg/gar/garTable.sh
  • lines changed 62, context: html, text, full: html, text
    942526536cf6261f16915b8c8c127829d70be133 Tue Feb 22 13:14:24 2022 -0800
    rework the content of the introduction text refs #28930
  • lines changed 5, context: html, text, full: html, text
    2cf3578abce882ea76c4d4f1309972a07797ba4f Tue Feb 22 14:29:18 2022 -0800
    better cleaning of sort keys for submitter strings and h1 h2 headings on intro text refs #28930
  • lines changed 4, context: html, text, full: html, text
    1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 Thu Feb 24 14:05:28 2022 -0800
    add a column 1 tool tip to indicate request or browser refs #28930
  • lines changed 6, context: html, text, full: html, text
    dcc09e71de2cb1f61a19f0526e0595ceb8277bb3 Fri Feb 25 10:43:00 2022 -0800
    adding cell background coloring for the IUCN column and tri-state indication on the hideAll buttons refs #28930
• src/hg/gar/rebuild.sh
  • lines changed 3, context: html, text, full: html, text
    b1d778892148961ead898fc47ff04c594c1f2ad6 Fri Feb 18 11:53:16 2022 -0800
    do not overwrite index.html until it is finished and reinstate size limit filter and correctly sort the submitter column refs #28930
• src/hg/hgTables/bigBed.c
  • lines changed 7, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTables/bigWig.c
  • lines changed 4, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTables/hic.c
  • lines changed 4, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/barChartTrack.c
  • lines changed 34, context: html, text, full: html, text
    6dfb86f7f9c25c2fd3b332695b9e79dc0c5184ee Fri Feb 25 16:06:50 2022 -0800
    Fix 3 barChart issues: One allow users to define a bar width and padding, two fix bar drawing bug where dynamically sizing the bars based on zoom level was causing some bars to be drawn at inconsistent widths in the same chart, three fix barChartStretchToItem bug when zoomed in to the base level such that your window size is less than the item size, refs #28977
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/cds.c
  • lines changed 8, context: html, text, full: html, text
    7fbad72434b7fd7559b48236c2d331c79fb9f29f Fri Feb 25 21:05:12 2022 -0800
    move check for baseColorUseSequence setting until is is actually needed
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/hgTracks.c
  • lines changed 33, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 3, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/bigDbSnpClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/bigRmskClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 2, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/encodeClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/lrgClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/mafClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/togaClick.c
  • lines changed 3, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/transMapClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/hgc/wiggleClick.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 20, context: html, text, full: html, text
    4f1745372c2a56d52df86f6c4f65013ea84ca04e Tue Feb 22 10:48:05 2022 -0800
    Making edits to Track Sets paper announcement after feedback from b0b.
  • lines changed 20, context: html, text, full: html, text
    979f7584699eedd743c90a7cf59d9fac44de845d Thu Feb 24 23:11:26 2022 -0800
    Adding info and announcement for drug resistance track refs #28889
  • lines changed 1, context: html, text, full: html, text
    18229787bffe10b59c80ab7d9a47ffcb391b7a81 Fri Feb 25 10:26:38 2022 -0800
    Fixing typo refs #28889
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    979f7584699eedd743c90a7cf59d9fac44de845d Thu Feb 24 23:11:26 2022 -0800
    Adding info and announcement for drug resistance track refs #28889
• src/hg/htdocs/style/gar.css
  • lines changed 63, context: html, text, full: html, text
    d4fdeadb1c734b4bf4d9885f462fa93c79df55b7 Mon Feb 21 16:02:14 2022 -0800
    add tooltip doc on column headers refs #28930
  • lines changed 153, context: html, text, full: html, text
    f9d9bdc8e2612f9478370a867a4216fb3b0cf345 Tue Feb 22 13:17:05 2022 -0800
    clean up unused rules and add box shadows around the pull-down menu boxes refs #28930
  • lines changed 2, context: html, text, full: html, text
    6647ae199221972aa0fbd68d015f80aa0aeef58a Tue Feb 22 13:59:33 2022 -0800
    center the pull down menu anchor text refs #28930
  • lines changed 21, context: html, text, full: html, text
    1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 Thu Feb 24 14:05:28 2022 -0800
    add a column 1 tool tip to indicate request or browser refs #28930
  • lines changed 36, context: html, text, full: html, text
    dcc09e71de2cb1f61a19f0526e0595ceb8277bb3 Fri Feb 25 10:43:00 2022 -0800
    adding cell background coloring for the IUCN column and tri-state indication on the hideAll buttons refs #28930
  • lines changed 12, context: html, text, full: html, text
    8068dd517b970501ce9b10759142e0aa24e3102f Fri Feb 25 15:37:57 2022 -0800
    adding two new columns for bioSample and bioProject refs #28930
• src/hg/inc/barChartUi.h
  • lines changed 4, context: html, text, full: html, text
    6dfb86f7f9c25c2fd3b332695b9e79dc0c5184ee Fri Feb 25 16:06:50 2022 -0800
    Fix 3 barChart issues: One allow users to define a bar width and padding, two fix bar drawing bug where dynamically sizing the bars based on zoom level was causing some bars to be drawn at inconsistent widths in the same chart, three fix barChartStretchToItem bug when zoomed in to the base level such that your window size is less than the item size, refs #28977
• src/hg/inc/chromAlias.h
  • lines changed 18, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/js/gar.js
  • lines changed 4, context: html, text, full: html, text
    369fd3ec5b7eaf247fd3da2c8c9377a474161c14 Tue Feb 22 10:34:33 2022 -0800
    fixup correct text for content on filled-in form fields refs #28930
  • lines changed 5, context: html, text, full: html, text
    28bb2659b7500bceab10a942b68bbbea26f56d2a Tue Feb 22 13:15:40 2022 -0800
    extend the all argument to also turn on all rows refs #28930
  • lines changed 45, context: html, text, full: html, text
    1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 Thu Feb 24 14:05:28 2022 -0800
    add a column 1 tool tip to indicate request or browser refs #28930
  • lines changed 6, context: html, text, full: html, text
    dcc09e71de2cb1f61a19f0526e0595ceb8277bb3 Fri Feb 25 10:43:00 2022 -0800
    adding cell background coloring for the IUCN column and tri-state indication on the hideAll buttons refs #28930
  • lines changed 13, context: html, text, full: html, text
    e56876e545b21501152e96f655141eb3b229cf0c Fri Feb 25 16:19:26 2022 -0800
    add in bioSample and bioProject columns and control of IUCN display refs #28930
• src/hg/lib/chainNetDbLoad.c
  • lines changed 2, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/chromAlias.c
  • lines changed 248, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/customFactory.c
  • lines changed 4, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/hdb.c
  • lines changed 14, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/hic.c
  • lines changed 13, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/lib/trackHub.c
  • lines changed 8, context: html, text, full: html, text
    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/hg/makeDb/doc/ambMex2/initialBuild.txt
  • lines changed 5, context: html, text, full: html, text
    980a640fde4cdcd5aa34f24de2f71e51e3d0fe61 Fri Feb 25 10:50:52 2022 -0800
    stalled on cpgIslands refs #23367
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    53902497740c6def14977a0c32a0dc95765b0307 Tue Feb 22 19:57:35 2022 -0800
    adding assembly GCA_013030995.1_ASM1303099v1 per user request refs #28954
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8678a6ea54cde92af856614a789fc353b2dbd8e8 Tue Feb 22 20:00:22 2022 -0800
    adding assembly GCA_013030995.1_ASM1303099v1 per user request refs #28954
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 182, context: html, text, full: html, text
    e5cc2f7ad696bf39d67e79429e304a34d2ecbbbc Sun Feb 27 20:32:09 2022 -0800
    new track of dog SNVs from European Variation Archive. Refs #28894
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
  • lines changed 95, context: html, text, full: html, text
    c0a4905df836349697fb24147e35cf5b7f737a09 Fri Feb 25 10:54:49 2022 -0800
    lastz galGal6 to GCF_016699485.2 per user request refs #28336
• src/hg/makeDb/doc/hg38/multiz30way.txt
  • lines changed 323, context: html, text, full: html, text
    3b2dda0ff5910870d3279ffe52d987d5c5a7bb64 Fri Feb 25 10:55:54 2022 -0800
    phyloP experiment with SSREV parameter per user request no redmine
• src/hg/makeDb/doc/rn7/lastzRuns.txt
  • lines changed 17, context: html, text, full: html, text
    92caabd2ff459cd75f8b5451f9d0f7fa5043d3b9 Fri Feb 25 10:58:18 2022 -0800
    finished lastz to bosTau9 no redmine
• src/hg/makeDb/doc/wuhCor1/resist.txt
  • lines changed 4, context: html, text, full: html, text
    8e542522565e5fc4cffeb971d316699a74894a41 Thu Feb 24 06:28:03 2022 -0800
    fixing resistance drug for wuhCor1 after QA, refs #28889
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 2, context: html, text, full: html, text
    37bc410dee52a5ace2a6bc4e7c6edc959a26a263 Tue Feb 22 14:32:04 2022 -0800
    added definition of acronym
• src/hg/makeDb/trackDb/dog/canFam3/evaSnp.html
  • lines changed 108, context: html, text, full: html, text
    e5cc2f7ad696bf39d67e79429e304a34d2ecbbbc Sun Feb 27 20:32:09 2022 -0800
    new track of dog SNVs from European Variation Archive. Refs #28894
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    e5cc2f7ad696bf39d67e79429e304a34d2ecbbbc Sun Feb 27 20:32:09 2022 -0800
    new track of dog SNVs from European Variation Archive. Refs #28894
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 19, context: html, text, full: html, text
    a1e6ba20edee50a0a5380524d26a89968292f47b Fri Feb 25 10:59:53 2022 -0800
    experiment with phyloP with SSREV parameters per user request no redmine
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    08a640aa705033527c30391bf8a1cde3d9148995 Wed Feb 23 03:42:27 2022 -0800
    adding another clinvar link, hidden in trackDb, refs #28926
• src/hg/makeDb/trackDb/uniprotAlpha.html
  • lines changed 1, context: html, text, full: html, text
    a3ba48cd34f0fbdf7b73df2814b7d04ebd51ddeb Wed Feb 23 17:33:06 2022 -0800
    Code review edit for the uniprot track description page, refs #28969
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 6, context: html, text, full: html, text
    8c61ea37c63d86c8888f3d887c071c44f97d789f Wed Feb 23 03:41:02 2022 -0800
    updating NIAID credits language following email from Wiriya Rutvisuttinunt, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/resist.html
  • lines changed 26, context: html, text, full: html, text
    979f7584699eedd743c90a7cf59d9fac44de845d Thu Feb 24 23:11:26 2022 -0800
    Adding info and announcement for drug resistance track refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8e542522565e5fc4cffeb971d316699a74894a41 Thu Feb 24 06:28:03 2022 -0800
    fixing resistance drug for wuhCor1 after QA, refs #28889
  • lines changed 1, context: html, text, full: html, text
    979f7584699eedd743c90a7cf59d9fac44de845d Thu Feb 24 23:11:26 2022 -0800
    Adding info and announcement for drug resistance track refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 2, context: html, text, full: html, text
    c80ef374749927678e17f5a751d556b5a55e3dcc Thu Feb 24 06:17:45 2022 -0800
    adding codon colors to wuhcor1 final proteins, no ticket
  • lines changed 1, context: html, text, full: html, text
    5debb32078bc1789052843c5c0e09934f0f84e05 Thu Feb 24 06:24:05 2022 -0800
    fixing tdb syntax error in wuhCor1, no ticket
• src/hg/utils/automation/prepConfig.pl
  • lines changed 2, context: html, text, full: html, text
    e78b1f8b7121149606b00890d327b78c06cd2522 Fri Feb 25 11:01:10 2022 -0800
    cleaner determination of genBankAccession no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 4, context: html, text, full: html, text
    f286e5c10c6344503cf9cd73d594070b5f22a671 Wed Feb 23 03:13:57 2022 -0800
    adding the new links that ClinVar added a few months ago to our hgc page, refs #28926
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 1, context: html, text, full: html, text
    f286e5c10c6344503cf9cd73d594070b5f22a671 Wed Feb 23 03:13:57 2022 -0800
    adding the new links that ClinVar added a few months ago to our hgc page, refs #28926
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    4ea36876ef8f78f0e152ddb3c12565254fbb7c9b Wed Feb 23 11:36:01 2022 -0800
    Increasing frequency of ncbi otto, no RM
  • lines changed 1, context: html, text, full: html, text
    8860b7c9a541ef4587471528aab8c2da3668a0d7 Wed Feb 23 12:34:46 2022 -0800
    Reverting the crontab to once a week since it has a verbose output and is only updated ~yearly.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
  • lines changed 5, context: html, text, full: html, text
    9734d13d2c7ee8004001a7553145e65af763796a Tue Feb 22 11:06:40 2022 -0800
    Extract Nextstrain clade from full nextclade output now generated by getNcbi.sh and getCogUk.sh.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 1, context: html, text, full: html, text
    ecbbcd78daf00901ca5eac7cde487effd342a376 Thu Jan 13 11:33:31 2022 -0800
    Increase max-path-length so we don't lop off all of BA.2 and BA.3 which due to Delta contam & back-muts are on super-long paths.
  • lines changed 2, context: html, text, full: html, text
    d898714060e14c8a185e3fde3d84dafe32f93baa Tue Feb 22 11:05:07 2022 -0800
    Speed up compression by using more threads.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
  • lines changed 122, context: html, text, full: html, text
    fcaec96345053d29cc56fa0aa8b13f07ecd8951d Mon Feb 14 13:43:12 2022 -0800
    Use Nextclade's new output columns privateNucMutations.{reversionSubstitutions,labeledSubstitutions} to identify partial or contaminated Omicron sequences for removal.
• src/hg/utils/otto/sarscov2phylo/findRefBackfill.pl
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    3c022c2be4485ff1f369617943da75bf51e9da70 Tue Feb 22 10:52:54 2022 -0800
    Identify sequences with an implausibly low number of substitutions given sampling month so we can exclude them from the tree.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    35e80a80d8967505aca7819e6c50a224e7ab4338 Thu Jan 13 11:38:00 2022 -0800
    Fasta fetches were timing out. Compressed versions of most files are available, use those. If a fetch fails, resume at the point it failed. Increase split fasta size for nextclade run - more efficient.
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    573695f19d9d0217bf98e7e7d06114835a592388 Tue Feb 22 11:02:20 2022 -0800
    Use COG-UK's new compressed download files. Use latest version of nextclade and keep full output.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    72739f248f43d3685eb2ca5fd464f73102fb77a4 Thu Jan 13 11:36:29 2022 -0800
    Increase split fasta size for nextclade run - more efficient.
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    b038619ca5e7c1bf6ab5810bfb004dc4c702266b Tue Feb 22 11:02:56 2022 -0800
    Use latest version of nextclade and keep full output.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
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    5f1c3399aaa5c1bcd341470a156cb528073546d3 Thu Jan 13 11:39:32 2022 -0800
    Uniqueify to prevent dups from several possible sources.
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    3760b502d693a5e3e1540f5eb190c87a6a0e965f Tue Feb 22 11:04:44 2022 -0800
    Strip quotes from nextclade tsv output, speed up compression by using more threads & speed up sed by usin conditional.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    c3ac1c095777767dff7ad31b94d4e71318a6db67 Tue Feb 22 10:55:09 2022 -0800
    Use new scripts findDropoutContam.pl and findRefBackfill.pl to identify problematic sequences using nextclade annotations. Exclude those sequences (with an exception for reported recombinants, via new file includeRecombinants.tsv) from the tree.
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    41d0b771bd70603cad81d2985e31c8c4c81d223b Sun Feb 27 11:11:48 2022 -0800
    Add some IDs from recent pango-designation requests.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    a6d479158de520ee012585952f425eec7324bbad Thu Jan 13 11:48:43 2022 -0800
    Exclude problematic sequences upstream of alignment -- avoid waste of time & CPU.
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    c3ac1c095777767dff7ad31b94d4e71318a6db67 Tue Feb 22 10:55:09 2022 -0800
    Use new scripts findDropoutContam.pl and findRefBackfill.pl to identify problematic sequences using nextclade annotations. Exclude those sequences (with an exception for reported recombinants, via new file includeRecombinants.tsv) from the tree.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    00842797b9fda733465b9bf732648a492d133cac Wed Jan 12 10:00:10 2022 -0800
    Also mask 21302, 21304 and 21305 in Delta. Mask convergent deletion of 11291-11296 plus 3 bases to the left in Alpha, Beta and Gamma to prevent spurious 'SNVs' at deletion site from messing up the tree; may need to add this for Omicron eventually.
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    b96a4b4d3d3b9d7dd2e7a1934ff4e4e57fb1348b Tue Feb 22 11:07:42 2022 -0800
    Mask two new problematic-in-Delta positions (https://github.com/cov-lineages/pango-designation/issues/435)
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    b9cad96bd7acdb271b5672d6c7703b8819f70d06 Thu Jan 13 11:46:44 2022 -0800
    Tweak Nextstrain 21M (base Omicron) mutations.
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    4ef0e866319b686e8087578651bc4ed50586f1d9 Thu Jan 20 16:49:53 2022 -0800
    Mask more Omicron sites as the branch continues to get scrambled by new seqs with reference backfilling & contamination.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    cc81e6f15173ad421b5b2ce99756579e5bfedb9c Tue Jan 11 14:56:06 2022 -0800
    Path tweaks for BB.1 and AV.1
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    52fa1b2103b94d28b62bc7a25f67bd4d228fa25a Wed Jan 12 09:54:40 2022 -0800
    Added BA.1.1; renamed BB.1 to B.1.621.2 - pango-designation v1.2.122. Also mask AY.32's C21304T because 21302, 21304, 21305 are masked in Delta now (leave AY.89 unchanged so it doesn't conflict with AY.4; slated to be withdrawn.)
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    3d412101b5e9aaac062cb53e48c9fe859622fd05 Thu Jan 13 09:42:15 2022 -0800
    AY.89 has been withdrawn - pango-designation v1.2.123
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    4ef0e866319b686e8087578651bc4ed50586f1d9 Thu Jan 20 16:49:53 2022 -0800
    Mask more Omicron sites as the branch continues to get scrambled by new seqs with reference backfilling & contamination.
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    48a5cc05092c7a1b99fd7a1dffa6df4448724fe7 Thu Feb 3 17:43:51 2022 -0800
    Redo of B.1.1.529 mutations: require mutations common to BA.* except especially dropout-prone locations -- use Ns for those, and add Ns for all mtuations specific to one or two BA.*s.
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    4f080ddd47a4464800ae1f5244ccf430b08def3e Thu Feb 3 23:21:56 2022 -0800
    Added new lineages AY.3.4, AY.4.2.4, AY.4.11, AY.4.12, AY.24.1, AY.25.2, AY.25.3, AY.103.1, AY.103.2, AY.122.4 and AY.125.1 - pango-designation v1.2.124
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    329c8f653135142be828bf24aecc080eef030318 Tue Feb 15 14:24:20 2022 -0800
    Added AY.4.13, AY.4.14, AY.4.15, AY.4.16, AY.4.17 and AY.124.1.1 -- pango-designation v1.2.125
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    32275764350ba48ecfc7ba000716d0f5f886c94d Tue Feb 15 14:48:29 2022 -0800
    Added AY.5.6, AY.25.1.2, AY.39.3, AY.43.8, AY.122.5 and AY.127.2 -- pango-designation v1.2.126
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    00b35af5594324410825b5886ef475708a4075e4 Tue Feb 15 15:28:28 2022 -0800
    Added AY.43.9 -- pango-designation v1.2.127
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    409232efcfdb35f6fbeca6f009a39466a0d0006c Wed Feb 16 23:45:49 2022 -0800
    Added BA.1.[2-15] except BA.1.11 which is a reversion mirage :(, also BA.1.13.1 and BA.1.15.1 -- pango-designation v1.2.128
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    505a2b837cb74dc1ce22743580762cd340e4954b Mon Feb 21 11:52:10 2022 -0800
    Mask A28461G in AY.* lineages; remove AY.96 -- pango-designation v1.2.129
• src/hg/utils/otto/sarscov2phylo/pangoHash.sh
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    3ac59e25cc8fb9d681fcb5d52224151b41f36ce5 Mon Feb 14 12:15:00 2022 -0800
    Align, mask and compute md5sum in same was as pangolin, for constructing cache file.
• src/hg/utils/otto/sarscov2phylo/runNextclade.sh
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    1d99af58ff1f767eb3497d666eeacc1ab8ac166a Mon Feb 14 12:12:37 2022 -0800
    Script for running nextclade on compressed or uncompressed fasta, keeping full TSV & aligned fasta output, suitable for running on cluster.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    ecbbcd78daf00901ca5eac7cde487effd342a376 Thu Jan 13 11:33:31 2022 -0800
    Increase max-path-length so we don't lop off all of BA.2 and BA.3 which due to Delta contam & back-muts are on super-long paths.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    1345e556ff3da44f7efcf83adc5b67868e536044 Tue Feb 22 11:08:53 2022 -0800
    ncov-ingest file with accession mapping is now gzipped.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    03e6d9865fa98c05dda6bbf5d780b0a2b41d389c Tue Feb 22 11:11:08 2022 -0800
    Remove B.1.1.529 from lineageTree.pb to match pangoLEARN behavior & avoid applying Omicron label to sequences of very poor quality -- requested by Rachel Colquhoun & Andrew Rambaut.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    cf519593dadf5adb63837c46b3e242f3c1ab08c3 Thu Jan 13 11:43:51 2022 -0800
    Fetch from different sources in parallel. Guard against non-zero return from grep (thx Jonathan!)
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
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    d97010481bcf72f263f4a6a21010e46bf667c272 Thu Jan 13 11:45:32 2022 -0800
    Shorten time limit for matOptimize cluster run to 2 hours (probably could be 1) because it usually doesn't recognize when it's done.
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    665fe7dc2ae7d018811a15f79c42bb29904d8630 Tue Feb 22 11:12:28 2022 -0800
    Add a para push to wait loop, to help with rare problem of a node failure. Clean up intermediate protobuf files-to-be-merged.
• src/hg/utils/otto/sarscov2phylo/util.sh
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    716924d36cd6d25551bf5f590cb3f587e987df8b Tue Feb 22 10:56:18 2022 -0800
    Yet more GenBank title craziness to filter out
• src/hg/utils/phyloTrees/220way.nh
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    3ab681f0f137f69e14917a4cb67cf21dd923b2e3 Fri Feb 25 11:01:53 2022 -0800
    update a couple of identities to newer versions no redmine
• src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl
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    af7a004c8f3fa909cd8c2cfc2e5bea60e3421cd1 Fri Feb 25 11:02:46 2022 -0800
    cleaner determination of parameters no redmine
• src/inc/bbiFile.h
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/inc/bigBed.h
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/inc/bigWig.h
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/inc/common.mk
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    5430222afb16da6e196ba2bc67bb216f2975f84e Fri Feb 25 15:32:03 2022 -0800
    Removing definition of SSLDIR because it is no longer used in common.mk or any makefile. SSL_DIR is used elsewhere in common.mk.
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    1713494a42debdf12ab248a85ec5e4fc828f42b0 Sun Feb 27 11:10:42 2022 -0800
    When CONDA_BUILD is set, skip freetype and get openssl static libs from ${PREFIX}/lib.
• src/lib/bamFile.c
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    b2de9d458c5a1afbcb1eda2ee6d636e2fbc21c76 Mon Feb 21 15:04:36 2022 -0800
    correctly use specified index file for cram file types no redmine
• src/lib/bbiRead.c
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/lib/bigBed.c
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/lib/bwgQuery.c
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    b622d147b7dbac52dbf3ba26928cd18e02d42bd8 Sat Feb 26 12:34:37 2022 -0800
    add support for using a bigBed as the chromAlias file
• src/product/installer/browserSetup.sh
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    dfb3d71d8c2ad629c2c105049106268e2835ea75 Wed Feb 23 08:52:14 2022 -0800
    adapting browserSetup.sh for centos 8 stream, refs #28733
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    7f82e232d708c48e78b2059a2a3b4e41b8cdf43d Thu Feb 24 02:36:18 2022 -0800
    fixing needless typo in browserSetup.sh found by Jairo, refs #28733
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    ef4ddb08245f80a35f424650c4ee5c2ecca62419 Thu Feb 24 03:38:35 2022 -0800
    hopefully the last fix for centos8 stream mysql setup, refs #28733
• src/utils/qa/weeklybld/buildEnv.csh
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    2215daa7439e228a8423369f03ddfa5baea71537 Mon Feb 28 10:17:34 2022 -0800
    v428 preview1, refs #29014

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