All File Changes

v399_preview to v399_preview2 (2020-05-18 to 2020-05-25) v399

• confs/rr.hg.conf
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    cc1c1406a9ca2f7d5a203704faaeeceeeac5ab09 Sun May 24 01:11:43 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/vcfTrack.c
  • lines changed 9, context: html, text, full: html, text
    7a16880260a6d93d0616bd8a1660fde60ac0bb3b Fri May 22 16:13:56 2020 -0700
    Use cart*ClosestToHome functions for setting trackUi vars so composite level track settings work correctly, refs #25585
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    443757e6a04336d7217fca4abe0e3774613323ea Fri May 22 16:22:33 2020 -0700
    Adding a comment to a function after code review, refs #25585
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 8, context: html, text, full: html, text
    2b2874d85add602f6753ae525337a1155d2298ea Mon May 25 06:35:18 2020 -0700
    allow for fine control of display of non-synonomous changes in mafSnp display
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    e13ac2383aa17a7f37bbea1526a8617af7b0f75d Tue May 19 09:58:20 2020 -0700
    Bugfix: itemLabel argument to printCustomUrlWithFields and printCustomUrlWithLabel was ignored. tangentially refs #25595 When a different itemLabel and itemName were passed into printCustomUrlWithFields, itemLabel was ignored for two reasons: 1. In printCustomUrlWithFields, itemName was passed into printCustomUrlWithLabel as both itemName and itemLabel arguments. 2. In printCustomUrlWithLabel, itemLabel was used only if it was the same as itemName, which kind of defeats the purpose of itemLabel.
• src/hg/hgc/vcfClick.c
  • lines changed 17, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/htdocs/covid19.html
  • lines changed 7, context: html, text, full: html, text
    f6c2c0b3577f894cf47d1c92bbbc2e7c77b8ea76 Tue May 19 22:37:10 2020 -0700
    Changing funding message on covid homepage as requested by Ann and Alexis
  • lines changed 1, context: html, text, full: html, text
    41df9b35fc8555ab404240a74723731bbe3af7ce Tue May 19 22:43:41 2020 -0700
    Changing funding message on covid homepage as requested by Ann and Alexis on Browser description page too
  • lines changed 1, context: html, text, full: html, text
    43781f8f66327ad8caa28e10007b6653e9ee003f Wed May 20 09:49:47 2020 -0700
    Making the anonymous donor plural.
  • lines changed 50, context: html, text, full: html, text
    ae5e1bdbe38c429212bb92a22d663eba4f161d60 Wed May 20 14:56:26 2020 -0700
    Adding CITRIS to funding and also moving it to a new section (along with news) on the coronavirus home page -checked with Ann
  • lines changed 1, context: html, text, full: html, text
    d955bcb6f1a8fc7508a1efbbd14c0af84923e295 Wed May 20 15:03:55 2020 -0700
    Removing additional and
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 2, context: html, text, full: html, text
    f7c079d1338892032d5e4a11168a4311ad762699 Thu May 21 12:50:14 2020 -0700
    Adding multiple pennantIcons documented, no RM
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    f7c079d1338892032d5e4a11168a4311ad762699 Thu May 21 12:50:14 2020 -0700
    Adding multiple pennantIcons documented, no RM
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 72, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/htdocs/images/GTExV8.png
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    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/htdocs/staff.html
  • lines changed 3, context: html, text, full: html, text
    afc6fb7714c9d18b60ffd0f38fb63dbc5a66270d Wed May 20 14:46:07 2020 -0700
    adding anna to staff list
• src/hg/inc/vcfUi.h
  • lines changed 1, context: html, text, full: html, text
    7a16880260a6d93d0616bd8a1660fde60ac0bb3b Fri May 22 16:13:56 2020 -0700
    Use cart*ClosestToHome functions for setting trackUi vars so composite level track settings work correctly, refs #25585
• src/hg/lib/vcfUi.c
  • lines changed 11, context: html, text, full: html, text
    7a16880260a6d93d0616bd8a1660fde60ac0bb3b Fri May 22 16:13:56 2020 -0700
    Use cart*ClosestToHome functions for setting trackUi vars so composite level track settings work correctly, refs #25585
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 26, context: html, text, full: html, text
    b99d9ad5adfa3176196acb5f4ace0c98f9742646 Fri May 22 14:13:48 2020 -0700
    eliminate other hub indexes for VGP page index refs #25555
• src/hg/makeDb/doc/panTro6/lastzRuns.sh
  • lines changed 84, context: html, text, full: html, text
    2e6b6889b0a4f2c0a730c1d2728f56dbdbf91c92 Tue May 19 15:41:00 2020 -0700
    per user request refs #25581
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    046d71e629864ab8a0e62344ad6b447a3f654543 Wed May 20 10:37:08 2020 -0700
    per user request panTro6 to ponAbe3 refs #25581
• src/hg/makeDb/doc/rheMac10/rhesusSNVs.txt
  • lines changed 13, context: html, text, full: html, text
    a94712cc61354fcdaea6de732191ae77749e6804 Tue May 19 11:39:13 2020 -0700
    added rheMac10 SNVs track
• src/hg/makeDb/trackDb/affyAllExonProbes.html
  • lines changed 1, context: html, text, full: html, text
    730d987244fc1ce83ff4fb23471292508420df6c Thu May 21 11:50:03 2020 -0700
    Updating http to https for mm8, uiLinks cronjob.
• src/hg/makeDb/trackDb/dog/canFam1/twinscan.html
  • lines changed 2, context: html, text, full: html, text
    5ae5cd62d836f712ed28ff78c110d9e50571ab8f Mon May 18 12:51:44 2020 -0700
    Updating http to https for canFam1
• src/hg/makeDb/trackDb/encodeCcreCombined.html
  • lines changed 164, context: html, text, full: html, text
    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 17, context: html, text, full: html, text
    93bfdd4cd73c04200bc783407316195cdbad7d5c Thu May 21 23:13:13 2020 -0700
    Adding southern sea otter (enhLutNer1) to mm10 and hg38 placental mammals chain/net, refs #21152
• src/hg/makeDb/trackDb/human/dbVarCommon.html
  • lines changed 3, context: html, text, full: html, text
    1bd2b1f3f86df6284bc45e1075fe011d215d1d78 Thu May 21 09:19:55 2020 -0700
    correct typos as in refs #25424
• src/hg/makeDb/trackDb/human/dbVarConflict.html
  • lines changed 3, context: html, text, full: html, text
    1bd2b1f3f86df6284bc45e1075fe011d215d1d78 Thu May 21 09:19:55 2020 -0700
    correct typos as in refs #25424
• src/hg/makeDb/trackDb/human/dbVarCurated.html
  • lines changed 2, context: html, text, full: html, text
    1bd2b1f3f86df6284bc45e1075fe011d215d1d78 Thu May 21 09:19:55 2020 -0700
    correct typos as in refs #25424
• src/hg/makeDb/trackDb/human/gtexGeneV8.html
  • lines changed 6, context: html, text, full: html, text
    8a6a5f100e276b967438cc6fb35d7cf80fe074bc Tue May 19 16:19:55 2020 -0700
    Minor edits for #25130
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 19, context: html, text, full: html, text
    2fb7246ce3bc2e617fd0194fa70fb11760ccf4e7 Mon May 18 14:44:05 2020 -0700
    hg19 description: Update the 'Note on chrM' to mention chrMT; add a bit more about p13 to 'Chromosome naming scheme'. refs #24648
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 23, context: html, text, full: html, text
    8301244fdedfac4e73bd039410be5b7c729abd70 Mon May 18 10:45:02 2020 -0700
    trackDb updates for release of hg19 p13+MT - thanks Ann for noticing we missed these earlier! refs #24648
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 32, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    8301244fdedfac4e73bd039410be5b7c729abd70 Mon May 18 10:45:02 2020 -0700
    trackDb updates for release of hg19 p13+MT - thanks Ann for noticing we missed these earlier! refs #24648
  • lines changed 17, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
  • lines changed 2, context: html, text, full: html, text
    7ae9d0e1bf12e39fc643f806d3251b6e3dca809a Thu May 21 16:54:10 2020 -0700
    Fixing error in size filter for clinGenCnv track, thanks Dan
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV26lift37.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV29lift37.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV30lift37.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV32lift37.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV33lift37.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/hg38/encode3.ccre.ra
  • lines changed 15, context: html, text, full: html, text
    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
  • lines changed 1, context: html, text, full: html, text
    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 151, context: html, text, full: html, text
    a398ef21403196d5d0fc0772e5ab39b6de73754a Wed May 20 14:22:25 2020 -0700
    Add scores and descriptive fields. refs #24668
  • lines changed 176, context: html, text, full: html, text
    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 18, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    b28304c11a843503e69b602da15458520b2cc930 Thu May 21 11:53:21 2020 -0700
    Pushing GENCODE and GTEX track releases #25130, #25164
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    7ae9d0e1bf12e39fc643f806d3251b6e3dca809a Thu May 21 16:54:10 2020 -0700
    Fixing error in size filter for clinGenCnv track, thanks Dan
  • lines changed 3, context: html, text, full: html, text
    81a2b1c5de6905ab22bf647d4b87e1f4277a7b32 Fri May 22 15:39:36 2020 -0700
    Woops forgot alternate names for trio individuals, refs #25585
  • lines changed 3, context: html, text, full: html, text
    7a16880260a6d93d0616bd8a1660fde60ac0bb3b Fri May 22 16:13:56 2020 -0700
    Use cart*ClosestToHome functions for setting trackUi vars so composite level track settings work correctly, refs #25585
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV33.ra
  • lines changed 1, context: html, text, full: html, text
    b28304c11a843503e69b602da15458520b2cc930 Thu May 21 11:53:21 2020 -0700
    Pushing GENCODE and GTEX track releases #25130, #25164
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.ra
  • lines changed 1, context: html, text, full: html, text
    b28304c11a843503e69b602da15458520b2cc930 Thu May 21 11:53:21 2020 -0700
    Pushing GENCODE and GTEX track releases #25130, #25164
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 56, context: html, text, full: html, text
    79a68220c380dfebcdb6bb0133d65f9c9321ed79 Thu May 21 11:13:23 2020 -0700
    Stagin new versions of clinGen tracks, refs #25562
  • lines changed 1, context: html, text, full: html, text
    7ae9d0e1bf12e39fc643f806d3251b6e3dca809a Thu May 21 16:54:10 2020 -0700
    Fixing error in size filter for clinGenCnv track, thanks Dan
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 2, context: html, text, full: html, text
    b28304c11a843503e69b602da15458520b2cc930 Thu May 21 11:53:21 2020 -0700
    Pushing GENCODE and GTEX track releases #25130, #25164
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    79a68220c380dfebcdb6bb0133d65f9c9321ed79 Thu May 21 11:13:23 2020 -0700
    Stagin new versions of clinGen tracks, refs #25562
• src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.html
  • lines changed 174, context: html, text, full: html, text
    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    93bfdd4cd73c04200bc783407316195cdbad7d5c Thu May 21 23:13:13 2020 -0700
    Adding southern sea otter (enhLutNer1) to mm10 and hg38 placental mammals chain/net, refs #21152
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.ra
  • lines changed 1, context: html, text, full: html, text
    56daeb5decf95a7de04411a0106f5b82cedb3b4c Fri May 22 16:29:39 2020 -0700
    Final push/ announce of GTEx and Gencode tracks #25130,25164,25167,25166
• src/hg/makeDb/trackDb/rhesus/rheMac10/rhesusSNVs.html
  • lines changed 138, context: html, text, full: html, text
    a94712cc61354fcdaea6de732191ae77749e6804 Tue May 19 11:39:13 2020 -0700
    added rheMac10 SNVs track
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    a94712cc61354fcdaea6de732191ae77749e6804 Tue May 19 11:39:13 2020 -0700
    added rheMac10 SNVs track
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    a398ef21403196d5d0fc0772e5ab39b6de73754a Wed May 20 14:22:25 2020 -0700
    Add scores and descriptive fields. refs #24668
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    d0b655a92d2b8ebfd006699ecc0dc888ca2cc1e5 Wed May 20 16:52:35 2020 -0700
    Polish schema, track description, and config based on ccomprehensive review and input by ENCODE DAC. refs #24668
• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
  • lines changed 137, context: html, text, full: html, text
    923192c09f92327447e8e0490691545486eba23a Tue May 19 11:33:32 2020 -0700
    eliminate discussions of phastCons and phyloP refs #25569
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 7, context: html, text, full: html, text
    41df9b35fc8555ab404240a74723731bbe3af7ce Tue May 19 22:43:41 2020 -0700
    Changing funding message on covid homepage as requested by Ann and Alexis on Browser description page too
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    43781f8f66327ad8caa28e10007b6653e9ee003f Wed May 20 09:49:47 2020 -0700
    Making the anonymous donor plural.
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    ae5e1bdbe38c429212bb92a22d663eba4f161d60 Wed May 20 14:56:26 2020 -0700
    Adding CITRIS to funding and also moving it to a new section (along with news) on the coronavirus home page -checked with Ann
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    d955bcb6f1a8fc7508a1efbbd14c0af84923e295 Wed May 20 15:03:55 2020 -0700
    Removing additional and
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 43, context: html, text, full: html, text
    c3ec4b2ef48608fa5788dd175b6e3fe0153bc6de Wed May 20 10:14:48 2020 -0700
    adding nanopore coverage track to wuhCor1, mostly for internal use for now
• src/hg/utils/paSNP/paSNP.c
  • lines changed 12, context: html, text, full: html, text
    2b2874d85add602f6753ae525337a1155d2298ea Mon May 25 06:35:18 2020 -0700
    allow for fine control of display of non-synonomous changes in mafSnp display
• src/inc/axt.h
  • lines changed 6, context: html, text, full: html, text
    2b2874d85add602f6753ae525337a1155d2298ea Mon May 25 06:35:18 2020 -0700
    allow for fine control of display of non-synonomous changes in mafSnp display
• src/lib/bamFile.c
  • lines changed 50, context: html, text, full: html, text
    6d058848117e130ca8c99f8d1c57f15e78616605 Wed May 20 14:40:34 2020 -0700
    add an understanding of the 'B' type to BAM parsing
• src/lib/vcf.c
  • lines changed 4, context: html, text, full: html, text
    30cb0185fefa49d413bdc67d45e11cb4bbf8d5ce Tue May 19 13:48:17 2020 -0700
    Adding check to vcf parsing for number of required headers after user's custom track caused hgCustom to crash, refs #25603
• src/utils/qa/weeklybld/buildEnv.csh
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    51397e9f6a12aa7c1aa6d11c296b8443d059c4f8 Mon May 18 09:59:53 2020 -0700
    v399 preview1
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    a7797ed59f866320289790d9c87e390d14306892 Mon May 25 10:01:32 2020 -0700
    v399 preview2

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• files changed: 77