All File Changes

v409_base to v410_preview (2021-01-18 to 2021-01-25) v410

• src/hca/hcaColorCells/hcaColorCells.c
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    04540fddd609dd1ff407d4907c89d8fa9e178f38 Thu Jan 14 11:53:20 2021 -0800
    Adding -cellMin option to improve coloring of FACS based data sets.
• src/hca/hcaColorCells/typeColors.tsv
  • lines changed 30, context: html, text, full: html, text
    85e43277a71fa053c5e71502e4307738e7971e98 Sat Jan 16 10:42:21 2021 -0800
    Adding this data file since it is important and not under source code control elsewhere, and is used by hcaColorCells at runtime most of the time.
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    c9066a2a9f398731accc46749ee4e986ec79b6c2 Sun Jan 17 16:15:55 2021 -0800
    Slightly improved coloring scheme for cells, mostly sorted by color.
• src/hca/hcaUnifyMatrix/hcaUnifyMatrix.c
  • lines changed 402, context: html, text, full: html, text
    3d815b5ddda4f027ed21ddc71995eebec2a8574b Wed Jan 20 01:46:40 2021 -0800
    This utility to help merge expression matrices across data sets built on different gene models is starting to work.
  • lines changed 85, context: html, text, full: html, text
    bfd7d15166c13c243f9d9a4bf1d6d50f168c4920 Wed Jan 20 09:14:39 2021 -0800
    Adding trackDb and stats options. Also adding scale factor per dataset.
  • lines changed 4, context: html, text, full: html, text
    24302c51b7a95f59436da8eb263b10706bc0ab9a Fri Jan 22 04:14:24 2021 -0800
    Reducing verbosity of status output.
• src/hca/hcaUnifyMatrix/makefile
  • lines changed 4, context: html, text, full: html, text
    3d815b5ddda4f027ed21ddc71995eebec2a8574b Wed Jan 20 01:46:40 2021 -0800
    This utility to help merge expression matrices across data sets built on different gene models is starting to work.
• src/hg/hgGateway/hgGateway.c
  • lines changed 31, context: html, text, full: html, text
    8dd7fb37563baba6ade31719a3b3cf5237f4348c Sat Jan 23 21:54:52 2021 -0800
    pass better lable string in json to have better indication of what species is being selected in the species search box refs #23891
• src/hg/hgTracks/barChartTrack.c
  • lines changed 13, context: html, text, full: html, text
    2f718ddd0797fc5c618bac72c546008d596ca9c1 Sun Jan 17 09:42:52 2021 -0800
    Making scaling of barChart bar widths overall slightly wider, and allowing more modulation.
  • lines changed 7, context: html, text, full: html, text
    272888a64de727315e0328a74b727d695fcb8db7 Mon Jan 18 20:26:56 2021 -0800
    Some fine adjustments to the scale of bars - honestly could make them wider but not wanting to make GTEX behave differently just yet.
  • lines changed 7, context: html, text, full: html, text
    43ebc9fee33b23d8ac12a77441a5e2140c0bcb0b Wed Jan 20 09:15:44 2021 -0800
    Adjusting padding and barWidth when have lots of bars.
  • lines changed 18, context: html, text, full: html, text
    58ecdffac6432e41d3a1a8d355e0e2eeda6e6d5d Thu Jan 21 13:41:35 2021 -0800
    Tweaking bar widths and spacing at different scales.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 3, context: html, text, full: html, text
    c0d5a48b95aae318fe5ab5f12b14149356d17753 Thu Jan 21 11:46:02 2021 -0800
    Support mouseOver trackDb setting for bigPsl (previously allowed but not supported) and add generic position information for bigPsl clicks, both to get lrg bigPsl otto track up to date with old version, refs #24672
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    22dd60838217f9e01a5420bab79a724f694da54c Fri Jan 22 17:21:30 2021 -0800
    correct sizing of assembly hub sequence when more than display limit refs #26584
• src/hg/hgc/barChartClick.c
  • lines changed 14, context: html, text, full: html, text
    22ee4e58588dbf633ee93b9c661e08349ff8e908 Mon Jan 18 20:28:29 2021 -0800
    Fixing it so underbar and space should be equivalent in the bar chart labels in the stats file.
  • lines changed 14, context: html, text, full: html, text
    6a6d27d0f45a9cb2a4f783f4641f0b2a0ecdca69 Fri Jan 22 04:16:19 2021 -0800
    Making right label of how big bar is use same calculations for string width as the left labels, and in process preventing them from getting clipped as often.
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    c0d5a48b95aae318fe5ab5f12b14149356d17753 Thu Jan 21 11:46:02 2021 -0800
    Support mouseOver trackDb setting for bigPsl (previously allowed but not supported) and add generic position information for bigPsl clicks, both to get lrg bigPsl otto track up to date with old version, refs #24672
  • lines changed 10, context: html, text, full: html, text
    73e45ce8ceee39823400e8c1c7e7fc9d1d363f4c Fri Jan 22 08:40:30 2021 -0800
    Support the standard bigBed URL substitutinos in bigPsl, refs #24672
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    968c83a0aa30b92e73d08cde8ad1d46a20cacd2a Fri Jan 22 16:45:23 2021 -0800
    Adding new assembly canFam5 to FAQreleases #25917
• src/hg/htdocs/cite.html
  • lines changed 24, context: html, text, full: html, text
    b04b513f9f81bf519c8e31d851fcc37fb5094c25 Fri Jan 22 11:06:23 2021 -0800
    Adding new covid citation, sprucing up doc #26737
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 130, context: html, text, full: html, text
    9f189423cbed741016319382c95500648d72d36e Mon Jan 25 07:21:06 2021 -0800
    fixing html weirdnesses in pandoc generated page, refs #25525
  • lines changed 47, context: html, text, full: html, text
    f6b3de50db0a119dfecd63bd243932bafa4ee1b1 Mon Jan 25 07:44:14 2021 -0800
    a few more fixed for the mirror docs, found by daniel, refs #25525
• src/hg/htdocs/goldenPath/history.html
  • lines changed 2, context: html, text, full: html, text
    f1328df2e24d57d982a336f705d0301852603bc0 Wed Jan 20 11:20:33 2021 -0800
    Fixing some typos found during code review, CR #26822
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    8fa6db788b44f96802b25ae1e8fb27524a90907f Fri Jan 22 10:17:42 2021 -0800
    Updating news for gnomAD track updates, refs #26449
• src/hg/htdocs/images/gnomAD_v3_1_newsarch.jpg
  • lines changed 0, context: html, text, full: html, text
    4688a5a98f345eaae451a73cb176c6741244a031 Thu Jan 21 11:52:20 2021 -0800
    Adding image for gnomAD track release, refs #26449
• src/hg/htdocs/images/gnomadV3_1.jpg
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    7313b349552e79d790b350a150af35896c764387 Fri Jan 22 09:08:54 2021 -0800
    Renamed the gnomAD v3.1 image for newsarch, refs #26449
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    85daa2a65c21635a56b049abc7c754af404d1518 Fri Jan 22 08:52:12 2021 -0800
    replace pull down menu item 16 mouse strains with link to all assembly hubs refs #26765
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    85daa2a65c21635a56b049abc7c754af404d1518 Fri Jan 22 08:52:12 2021 -0800
    replace pull down menu item 16 mouse strains with link to all assembly hubs refs #26765
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    8fa6db788b44f96802b25ae1e8fb27524a90907f Fri Jan 22 10:17:42 2021 -0800
    Updating news for gnomAD track updates, refs #26449
• src/hg/inc/hdb.h
  • lines changed 9, context: html, text, full: html, text
    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
  • lines changed 2, context: html, text, full: html, text
    ecba53cfcf13a435e7935340a5ddb73737c5006d Fri Jan 22 14:55:31 2021 -0800
    change the way we discover files on beta and the rr for the bigDataUrl check
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    221339e63d4378f833ad7472327b73e550a3769c Fri Jan 22 23:51:53 2021 -0800
    investigating the width calculation of the text window, and keep the text popUp in the graph area at all times refs #21980
  • lines changed 8, context: html, text, full: html, text
    2942a10cc7373047918e8b594405b840ca78a5c9 Mon Jan 25 05:17:19 2021 -0800
    fixing right-click menu description for tracks where "exonNumbers on", refs #26849
• src/hg/lib/hdb.c
  • lines changed 19, context: html, text, full: html, text
    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
  • lines changed 5, context: html, text, full: html, text
    ecba53cfcf13a435e7935340a5ddb73737c5006d Fri Jan 22 14:55:31 2021 -0800
    change the way we discover files on beta and the rr for the bigDataUrl check
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    fbca997208c852dc1ea6d11ef9ab7f42b4378625 Tue Jan 19 10:34:09 2021 -0800
    Bump up size of buffer for mrna description in search results, refs #26832
• src/hg/makeDb/doc/hg19.txt
  • lines changed 161, context: html, text, full: html, text
    59e2aee12d89650eba71c72ffebc62f26c74dc22 Thu Jan 14 15:59:20 2021 -0800
    Adding descriptions of how fetalGeneAtlas and skinSoleBoldo single cell RNA barchart supertracks were made.
  • lines changed 3, context: html, text, full: html, text
    6d4fc5c83c417afe88dc436f03117f0c128dfda9 Tue Jan 19 09:40:18 2021 -0800
    Updating mapping.bed and statistics
  • lines changed 4, context: html, text, full: html, text
    903a638e8959f088ca1c82531eded597c6c305bc Fri Jan 22 04:21:18 2021 -0800
    Coloring all of fetalGeneAtlas subtracks with same scheme. Coloring hepatocytes.
• src/hg/makeDb/doc/wuhCor1/abEscape.txt
  • lines changed 2, context: html, text, full: html, text
    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
• src/hg/makeDb/doc/wuhCor1/escape.as
  • lines changed 17, context: html, text, full: html, text
    2cac648786e4cd731e12f1e2aa8d8d141e2bf74a Thu Jan 21 05:18:41 2021 -0800
    makedoc for the whelan escape tracks, refs #26497
• src/hg/makeDb/doc/wuhCor1/escape.py
  • lines changed 39, context: html, text, full: html, text
    2cac648786e4cd731e12f1e2aa8d8d141e2bf74a Thu Jan 21 05:18:41 2021 -0800
    makedoc for the whelan escape tracks, refs #26497
• src/hg/makeDb/doc/wuhCor1/escape.txt
  • lines changed 4, context: html, text, full: html, text
    2cac648786e4cd731e12f1e2aa8d8d141e2bf74a Thu Jan 21 05:18:41 2021 -0800
    makedoc for the whelan escape tracks, refs #26497
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 6, context: html, text, full: html, text
    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
  • lines changed 22, context: html, text, full: html, text
    ecba53cfcf13a435e7935340a5ddb73737c5006d Fri Jan 22 14:55:31 2021 -0800
    change the way we discover files on beta and the rr for the bigDataUrl check
• src/hg/makeDb/trackDb/bats/rouAeg1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/birds/cotJap2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/birds/ficAlb1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/chinchilla/chiLan1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/human/cadd.ra
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    715d9a47267e8a712604e63bda6d7c99622c7419 Fri Jan 22 08:52:55 2021 -0800
    adding cadd insertions and deletions, refs #18492
• src/hg/makeDb/trackDb/human/hg19/fetalGeneAtlas.ra
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    73c045c8fce9058a333220a2f72e5750d5cd885a Mon Jan 18 20:37:32 2021 -0800
    Recoloring.
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    44cb9d5b6cdf1e4182e727d4f858da45fcc04bff Fri Jan 22 10:42:00 2021 -0800
    Updating colors and fixing 'sorted by' to be 'binned by' like elsewhere
• src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html
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    bd4fac8f72aba18803cbd06d0bd36aeded3d4c57 Fri Jan 22 09:36:27 2021 -0800
    Reason: Adding a description for the population frequency table and updating pennant icons for gnomad, refs #26449
• src/hg/makeDb/trackDb/human/hg19/skinSoleBoldo.ra
  • lines changed 78, context: html, text, full: html, text
    8e7dfd6577aea4f69a73b8f6ff6885cc1d05088b Thu Jan 21 09:33:11 2021 -0800
    Oops, forgot to include this.
• src/hg/makeDb/trackDb/human/hg19/targetScanMiRnaSitesV72.html
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    ab46ba9ff96bf6e3621c3cc902aeb16a61c14372 Fri Jan 22 17:08:25 2021 -0800
    Update TargetScan miRNA sites track. refs #26287
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    5f4b90f7d7f3494fe2c92c583c464979bd994d42 Tue Jan 19 11:40:39 2021 -0800
    Adding allele count to mouseover for gnomAD tracks refs #26835
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    9ec7400e0417bee94d0835a6f9327a9c9835c275 Thu Jan 21 12:22:15 2021 -0800
    changing mouseOvers for gnomAD tracks refs #26835
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    bd4fac8f72aba18803cbd06d0bd36aeded3d4c57 Fri Jan 22 09:36:27 2021 -0800
    Reason: Adding a description for the population frequency table and updating pennant icons for gnomad, refs #26449
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    ae1c89ec531bf7384e5091b93078a138a3a24494 Fri Jan 22 11:42:05 2021 -0800
    Removing default filter on annotation type for gnomad tracks, refs bob email
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    4a264baa33ac4a9116494b4369309178fd2727b3 Fri Jan 15 13:57:08 2021 -0800
    skinSoleBoldo single cell rna to hg19
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    ab46ba9ff96bf6e3621c3cc902aeb16a61c14372 Fri Jan 22 17:08:25 2021 -0800
    Update TargetScan miRNA sites track. refs #26287
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    4311e5f3bc98d10cc550ce45933d85a1c6481fe1 Fri Jan 22 17:09:32 2021 -0800
    Update TargetScan miRNA sites track. refs #26287
• src/hg/makeDb/trackDb/human/hg38/bloodHao.ra
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    68fb75be28315352c3047092ecdd85c9b5e62086 Fri Jan 15 13:58:05 2021 -0800
    Finished labels on bloodHao single cell RNA on hg38
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    a60ebb6be3010ad11c415ca1fabc3f5bdec86c09 Fri Jan 22 04:23:39 2021 -0800
    Shifting to common colors shared by others, sadly a little less distinct for this data set. Shifting from L2 to L1, less detailed, cell type annotations for main cell_type.
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
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    859a32a5037bf85d25806b4d9a21e0c78ca1289a Fri Jan 15 10:57:32 2021 -0800
    Adding colonWang, ileumWang, and rectumWang single cell RNA datasets.
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    3e71ea091b2f5ca3c882f8fc09909aaff75c64d4 Fri Jan 15 11:38:44 2021 -0800
    Stretching bars a little by reducing barChartLimit for Wang intestinal data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra
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    ddc40a5ed80272c0156240193c65cd1b1d6ee61a Fri Jan 15 13:59:05 2021 -0800
    Making cortexVelmeshev data set on hg38 a little less loud.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra
  • lines changed 16, context: html, text, full: html, text
    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
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    903a638e8959f088ca1c82531eded597c6c305bc Fri Jan 22 04:21:18 2021 -0800
    Coloring all of fetalGeneAtlas subtracks with same scheme. Coloring hepatocytes.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    5f4b90f7d7f3494fe2c92c583c464979bd994d42 Tue Jan 19 11:40:39 2021 -0800
    Adding allele count to mouseover for gnomAD tracks refs #26835
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    541f07b9713fea3044572b32906b5050ddcdb496 Tue Jan 19 14:43:57 2021 -0800
    Adding gnomAD v3 and pennantIcons to the gnomAD track, refs #26449
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    92ba2942672d7b3fc8949876783ec4f8b82dd7c2 Wed Jan 20 10:06:17 2021 -0800
    Fixing up release tags, fix up pennant icon, fix up population frequencies table name for gnomAD v3.1, refs #26449
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    50277afc74c5d842e51edaca23183ec6f63ebe2d Thu Jan 21 10:32:43 2021 -0800
    Fixing typo in population frequencies table title pointed out in email by Gerardo
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    9ec7400e0417bee94d0835a6f9327a9c9835c275 Thu Jan 21 12:22:15 2021 -0800
    changing mouseOvers for gnomAD tracks refs #26835
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    bd4fac8f72aba18803cbd06d0bd36aeded3d4c57 Fri Jan 22 09:36:27 2021 -0800
    Reason: Adding a description for the population frequency table and updating pennant icons for gnomad, refs #26449
  • lines changed 1, context: html, text, full: html, text
    ae1c89ec531bf7384e5091b93078a138a3a24494 Fri Jan 22 11:42:05 2021 -0800
    Removing default filter on annotation type for gnomad tracks, refs bob email
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1.html
  • lines changed 5, context: html, text, full: html, text
    bd4fac8f72aba18803cbd06d0bd36aeded3d4c57 Fri Jan 22 09:36:27 2021 -0800
    Reason: Adding a description for the population frequency table and updating pennant icons for gnomad, refs #26449
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra
  • lines changed 1, context: html, text, full: html, text
    db744228f428826b9eb757d8536fe21da6250b19 Fri Jan 15 14:00:18 2021 -0800
    reducing volume on a bars in heart and lung single cell data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/ileumWang.ra
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    859a32a5037bf85d25806b4d9a21e0c78ca1289a Fri Jan 15 10:57:32 2021 -0800
    Adding colonWang, ileumWang, and rectumWang single cell RNA datasets.
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    3e71ea091b2f5ca3c882f8fc09909aaff75c64d4 Fri Jan 15 11:38:44 2021 -0800
    Stretching bars a little by reducing barChartLimit for Wang intestinal data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra
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    51a9b5ae84b3979930d70a05b0fcf82a178e2678 Thu Jan 14 19:30:51 2021 -0800
    Adding skinSoleBoldo and liverMacParland single cell data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra
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    e2d27ce7b87c27ded55ea090a72364bd0327d75b Thu Jan 14 11:49:59 2021 -0800
    Adding lungTravaglini2020 dataset with both 10x and FACS arms.
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    db744228f428826b9eb757d8536fe21da6250b19 Fri Jan 15 14:00:18 2021 -0800
    reducing volume on a bars in heart and lung single cell data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra
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    1174aa23ca05f247d28cec79b7bb2b86ff90811b Fri Jan 15 09:36:35 2021 -0800
    Adding pancreasBaron single cell RNA track to hg38
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
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    7c4a3360752f7a5c32f2abb96d0af76036fb5043 Fri Jan 22 04:26:14 2021 -0800
    Lumping some cells, mostly immune, with small counts into an 'other' category in the pancreas. Making 'detailed cell type' track for unlumped version.
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
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    00feb5dea48777b397362387c307086d7268f3fa Sat Jan 16 10:11:49 2021 -0800
    Adding placentaVentoTorma single cell RNA seq data set.
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    5bdcedbdb55631ea78fe3896542e21d6e314c21f Sat Jan 16 10:18:32 2021 -0800
    Adjusting view limits of ss2 subset. It seems to be scaled about the same as the 10x somehow, or close to it, so bringing it back to the same, unlike in the lungTrav. dataset.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/rectumWang.ra
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    859a32a5037bf85d25806b4d9a21e0c78ca1289a Fri Jan 15 10:57:32 2021 -0800
    Adding colonWang, ileumWang, and rectumWang single cell RNA datasets.
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    3e71ea091b2f5ca3c882f8fc09909aaff75c64d4 Fri Jan 15 11:38:44 2021 -0800
    Stretching bars a little by reducing barChartLimit for Wang intestinal data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra
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    280f594f5ec2f99725f2d7b5effa38827d8a3694 Wed Jan 20 09:17:27 2021 -0800
    Adding singleCellMerged track.
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    52a806f70c35f8bdb1b7db3217203c591695c0ac Fri Jan 22 04:28:43 2021 -0800
    Changing scale from 0-2 to 0-100 for best viewing and calling units 'vn-100.' Reintegrating things to take in changes in component tracks, especially reducing number of categories in blood by a lot and pancreas by a little.
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra
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    51a9b5ae84b3979930d70a05b0fcf82a178e2678 Thu Jan 14 19:30:51 2021 -0800
    Adding skinSoleBoldo and liverMacParland single cell data sets.
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    13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800
    Recoloring and in some cases merging columns.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    e2d27ce7b87c27ded55ea090a72364bd0327d75b Thu Jan 14 11:49:59 2021 -0800
    Adding lungTravaglini2020 dataset with both 10x and FACS arms.
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    51a9b5ae84b3979930d70a05b0fcf82a178e2678 Thu Jan 14 19:30:51 2021 -0800
    Adding skinSoleBoldo and liverMacParland single cell data sets.
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    1174aa23ca05f247d28cec79b7bb2b86ff90811b Fri Jan 15 09:36:35 2021 -0800
    Adding pancreasBaron single cell RNA track to hg38
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    859a32a5037bf85d25806b4d9a21e0c78ca1289a Fri Jan 15 10:57:32 2021 -0800
    Adding colonWang, ileumWang, and rectumWang single cell RNA datasets.
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    00feb5dea48777b397362387c307086d7268f3fa Sat Jan 16 10:11:49 2021 -0800
    Adding placentaVentoTorma single cell RNA seq data set.
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    57dac7ba30fa3754d63f0046abf01a42b127f1ec Sun Jan 17 18:40:03 2021 -0800
    Commenting out lungVieiraBraga.ra until have time to curate their columns down to 20 for the great merged display.
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    280f594f5ec2f99725f2d7b5effa38827d8a3694 Wed Jan 20 09:17:27 2021 -0800
    Adding singleCellMerged track.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    432f2452afb5ee7f34e87456b4e2d8fc206fd158 Wed Jan 20 07:26:34 2021 -0800
    adding mccoy track to mutation escape tracks, refs #26806
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    c0d5a48b95aae318fe5ab5f12b14149356d17753 Thu Jan 21 11:46:02 2021 -0800
    Support mouseOver trackDb setting for bigPsl (previously allowed but not supported) and add generic position information for bigPsl clicks, both to get lrg bigPsl otto track up to date with old version, refs #24672
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    73e45ce8ceee39823400e8c1c7e7fc9d1d363f4c Fri Jan 22 08:40:30 2021 -0800
    Support the standard bigBed URL substitutinos in bigPsl, refs #24672
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/loadTracks
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    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
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    ecba53cfcf13a435e7935340a5ddb73737c5006d Fri Jan 22 14:55:31 2021 -0800
    change the way we discover files on beta and the rr for the bigDataUrl check
• src/hg/makeDb/trackDb/macaca/macNem1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/makefile
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    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
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    ecba53cfcf13a435e7935340a5ddb73737c5006d Fri Jan 22 14:55:31 2021 -0800
    change the way we discover files on beta and the rr for the bigDataUrl check
• src/hg/makeDb/trackDb/mammal/casCan1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/mammal/fukDam1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/otters/enhLutKen1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/poeRet/poeRet1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/primate/aotNan1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/primate/cebCap1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/primate/cerAty1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/primate/manLeu1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/primate/proCoq1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/turtle/chrPic2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/virus/wuhCor1/abEscape.html
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
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    432f2452afb5ee7f34e87456b4e2d8fc206fd158 Wed Jan 20 07:26:34 2021 -0800
    adding mccoy track to mutation escape tracks, refs #26806
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    6cb1b8697312f777c5121e7ed3d3a9a072127714 Fri Jan 22 14:22:03 2021 -0800
    Fixing up new escape super track refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/abEscape.ra
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
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    432f2452afb5ee7f34e87456b4e2d8fc206fd158 Wed Jan 20 07:26:34 2021 -0800
    adding mccoy track to mutation escape tracks, refs #26806
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    67f2f0991f154196707868a4e4025f30aba059d3 Wed Jan 20 07:27:55 2021 -0800
    typo in last commit
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    6cb1b8697312f777c5121e7ed3d3a9a072127714 Fri Jan 22 14:22:03 2021 -0800
    Fixing up new escape super track refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/bloomEsc.ra
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
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    6cb1b8697312f777c5121e7ed3d3a9a072127714 Fri Jan 22 14:22:03 2021 -0800
    Fixing up new escape super track refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/bloomEscapeMax.html
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/bloomEscapeTotal.html
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/lineageB_1_1_7_US.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainParsimony.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/problematicSites.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/rappuoli.html
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPubParsimony.html
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/spikeMuts.html
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    a5c4b7be2638f5e1960b5cc3c3c716b66199fa44 Tue Jan 19 12:12:58 2021 -0800
    Add link to new URL for this data (covariants.org). refs #26782
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    fa262379d1f359658d77766de29655ae45b9de65 Tue Jan 19 12:41:12 2021 -0800
    Fixing link on Description page refs #26782
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    9cd26024b3f91de3adf0adc1700270d3c09aa6bf Tue Jan 19 12:44:01 2021 -0800
    Fixing link typo on Description page refs #26782
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    f0d2abbbcf9846e49cbdbc428163aa6f5a19f7ad Tue Jan 19 08:39:12 2021 -0800
    Adding "antibody escape" supertrack, refs #26806
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    358cb04e473f162ceab9ae72bf83721a942d4b36 Tue Jan 19 11:07:04 2021 -0800
    Pushing phylo track to RR refs #26804
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    c724bce8fc605361d9fd0b6fc5c55fc314c5f54d Tue Jan 19 11:10:12 2021 -0800
    Fixing merge No RM
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    c28068f9599002cf1ad5d9f394feeaffcc5ea632 Wed Jan 20 13:28:58 2021 -0800
    Removing default status for SPike Muts wuhCor1 refs #26782
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    c36ffe3e1a45ff7977ebb772b0fdc937fe37bf9f Fri Jan 22 10:54:25 2021 -0800
    Add Nextstrain clade coloring for sarsCov2PhyloPub, release alpha only until the coloring file is pushed.
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    47acadc6d9b0ef631aab06eebb4bb4d21ea30189 Fri Jan 22 14:37:04 2021 -0800
    Removing release tags for new track refs #26806
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    9e408b45edbfe7761eb76edb6b0987fb0910060e Fri Jan 22 14:41:58 2021 -0800
    Removing previous trackDb stanza, as the track has now been collapsed into the escape superTrack refs #26806
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    4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800
    David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
• src/hg/makeDb/trackDb/whale/orcOrc1/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
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    57d038169fe7e1102e2b942f32ecf3308791b04d Wed Jan 20 17:11:45 2021 -0800
    add alpha tag to include refSeqComposite.ra for dbs that do not have the NCBI RefSeq files on gbdb yet refs #26696
• src/hg/pslStats/pslStats.c
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    365898605d0de79f306e48d26e7362a8b8a8063d Thu Jan 21 14:30:36 2021 -0800
    fixed bug pslStats -overallStats calculation of mean query coverage
• src/hg/pslStats/tests/expected/cdna2cdnaOverallTest.stats
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    365898605d0de79f306e48d26e7362a8b8a8063d Thu Jan 21 14:30:36 2021 -0800
    fixed bug pslStats -overallStats calculation of mean query coverage
• src/hg/pslStats/tests/expected/untransOverallTest.stats
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    365898605d0de79f306e48d26e7362a8b8a8063d Thu Jan 21 14:30:36 2021 -0800
    fixed bug pslStats -overallStats calculation of mean query coverage
• src/hg/pslStats/tests/expected/untransOverallUnalnTest.stats
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    365898605d0de79f306e48d26e7362a8b8a8063d Thu Jan 21 14:30:36 2021 -0800
    fixed bug pslStats -overallStats calculation of mean query coverage
• src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c
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    6eaed8d72f6b12600d7fc8f6bb94b14e396b0948 Mon Jan 18 20:31:32 2021 -0800
    Adding in refGene name2 column search as basically the last thing to try. The way it selects the best transcript out of the refGene pile-up is pretty ad-hoc, just favoring protein coding and better curated, and often just taking the first of many equivalently scoring ones.
• src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c
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    bf1922c6259ffc74a2041b8e8beb681fe5c927ff Mon Jan 18 20:33:04 2021 -0800
    Adding -miss and -target options. -target will look harder for hits within a database. -miss puts unmapped genes into a miss file.
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    7fd0b76aeb83144a908f8c15e6a5452ded39bed1 Wed Jan 20 09:19:41 2021 -0800
    Fixing bug where was ommitting thickEnd from bed output.
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    562a5ca722b958707b6ac1033d5dec067da96736 Sat Jan 23 14:25:01 2021 -0800
    Add source ~/.bashrc at beginning. Not sure why that was not necessary before but is now.
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    466fc186d05dd8e8bd27f91752bcb03d8edd63a6 Tue Jan 19 11:03:38 2021 -0800
    Add try/except to prevent some encoding problem when writing varPaths from crashing the script.
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    83eb31f4ea1896449dce8576697627091c6ff313 Thu Jan 21 10:54:13 2021 -0800
    Prevent excess warnings about varPaths problems.
• src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl
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    40960dac74599ef433b17978620bcc4ec06e8d08 Fri Jan 22 10:58:13 2021 -0800
    Update coloring for recently added Nextstrain clades; accept any letter for Pangolin lineages.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    4be38ba46f1cc49a9ac3dd60719bcf824aef8a0b Thu Jan 21 10:55:34 2021 -0800
    Tweak: use set -x in order to see which command fails when there's a silent failure (e.g. from wget -q).
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    2a551773f1cca84e8acb73cf1856f78111d53002 Fri Jan 22 10:57:17 2021 -0800
    Use curl not wget to avoid annoying .1, .2 files on retries.
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    c8d7abe94b3244702501b71b62d9e1ea6333228b Sat Jan 23 14:24:20 2021 -0800
    Grab COG-UK daily tree as Russ suggests; might want to try using it instead of GISAID tree.
• src/inc/portable.h
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    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
• src/lib/osunix.c
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    bd0a18827dcd91e4fae812f795e2a39968535627 Thu Jan 21 16:52:04 2021 -0800
    when building beta or public, check on hgwbeta and hgw0 for files referenced by bigDataUrl rather than assuming that they exist if they exist on dev
• src/product/mirrorDocs/staticPage.html
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    17b07a755e7881f0a795a6e1eade1282a2b8c04b Mon Jan 25 07:20:33 2021 -0800
    tiny comment change to markdown generated pages, no redmine
• src/product/mirrorManual.txt
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    fbef08bbf2e3c8234e769333463dcc8b1178fc37 Thu Jan 21 14:46:23 2021 -0800
    Fixing typos in doc for refs #25525
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    f6b3de50db0a119dfecd63bd243932bafa4ee1b1 Mon Jan 25 07:44:14 2021 -0800
    a few more fixed for the mirror docs, found by daniel, refs #25525
• src/utils/bedJoinTabOffset/bedJoinTabOffset.c
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/expectedOut1.bed
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/expectedOut2.bed
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/in.bed
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/in1.tab
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/in2.tab
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/makefile
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/bedJoinTabOffset/tests/out3.bed
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    1c36e8ebf0e5ddd3d5c3ee9fa2fd492bef5c41a0 Fri Jan 22 11:00:09 2021 -0800
    Allow bedJoinTabOffset to index on a field other than the name field, refs #26837
• src/utils/matrixClusterColumns/matrixClusterColumns.c
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    3cacf62418cf270f09b8b10df1daae429f191522 Sun Jan 17 11:39:41 2021 -0800
    Catching error condition of meta row labels not matching up to matrix column labels.
• src/utils/matrixRelabel/matrixRelabel.c
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    8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800
    Making checking on label counts matching matrix dimensions more robust, and catching file close error.
• src/utils/matrixRelabel/test.col
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    8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800
    Making checking on label counts matching matrix dimensions more robust, and catching file close error.
• src/utils/matrixRelabel/test.long
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    8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800
    Making checking on label counts matching matrix dimensions more robust, and catching file close error.
• src/utils/matrixRelabel/test.row
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    8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800
    Making checking on label counts matching matrix dimensions more robust, and catching file close error.
• src/utils/matrixRelabel/test.short
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    8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800
    Making checking on label counts matching matrix dimensions more robust, and catching file close error.
• src/utils/qa/weeklybld/buildEnv.csh
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    c8235bcb58cdf66ea753624c7be675f84724897f Mon Jan 25 10:02:38 2021 -0800
    v410 preview1

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