All File Changes

v422_preview to v422_preview2 (2021-10-04 to 2021-10-11) v422

• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 167, context: html, text, full: html, text
    e2007fcc38456ee9241f55899ff3b124c22ad484 Mon Oct 4 14:49:29 2021 -0700
    Changes based on CR feedback: moved covid section to alpha order and removed i icon for ichida lab dataset as it doesn't have a desc, refs #28243
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    4f684d9f3528f106c33c8f71f36629972d95fdeb Tue Oct 5 17:42:23 2021 -0700
    Forgot to check for NULL... always check for NULL. Always.
  • lines changed 7, context: html, text, full: html, text
    fde62c7a689e744c436c75ebc8dc7640b0800239 Wed Oct 6 09:16:49 2021 -0700
    Add a note that trash files will expire in 2 days and should be downloaded if intended for long-term use.
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    33db6013f1b84f1ff59b285aec3a54414e928ad0 Mon Oct 11 06:26:58 2021 -0700
    removing the hg.conf dependency and changing "examples" help text to Jim's suggested text, refs #28072
• src/hg/htdocs/FAQ/index.html
  • lines changed 11, context: html, text, full: html, text
    daf7c41626443b53cd92b948a5419296b4e30232 Tue Oct 5 16:25:43 2021 -0700
    Adding a link to mailing list archives on master FAQs Search page
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 6, context: html, text, full: html, text
    6e155ea5e313e29b07fb8068ceb1771cf77efab1 Thu Oct 7 18:29:50 2021 -0700
    Clarifying tStrand stands for target strand, etc. No RM
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 6, context: html, text, full: html, text
    6b8b07d982d36546aa621c691562d95815592f65 Wed Oct 6 12:55:28 2021 -0700
    Adding an image about the new Refresh Cache button at CyVerse
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 1, context: html, text, full: html, text
    5bc3a3bbc872c129ad53f0dc335bafc9c85f126e Fri Oct 8 13:44:13 2021 -0700
    Fixing a typo of added ; by accident
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 3, context: html, text, full: html, text
    14c63e3f78773ecafc736870ed071304c9b542f2 Mon Oct 11 07:22:29 2021 -0700
    Adding a link to the FAQ on the query page
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    4468783a4df1769e596402996adb6ac568fff263 Fri Oct 8 13:47:12 2021 -0700
    Adding regex examples in the filterText section to help quick illustration.
• src/hg/htdocs/images/cyverseRefresh.png
  • lines changed 0, context: html, text, full: html, text
    6b8b07d982d36546aa621c691562d95815592f65 Wed Oct 6 12:55:28 2021 -0700
    Adding an image about the new Refresh Cache button at CyVerse
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    d068533815c7f9d3d2d2687910e577876f52d510 Mon Oct 4 17:07:29 2021 -0700
    adding link to nigeria virtual workshop
  • lines changed 2, context: html, text, full: html, text
    2b6ffc8cfb8f87942a2904320e04313599fe0448 Thu Oct 7 16:04:28 2021 -0700
    adding link to ucsf workshop
• src/hg/js/autocomplete.js
  • lines changed 8, context: html, text, full: html, text
    33db6013f1b84f1ff59b285aec3a54414e928ad0 Mon Oct 11 06:26:58 2021 -0700
    removing the hg.conf dependency and changing "examples" help text to Jim's suggested text, refs #28072
• src/hg/lib/liftOver.c
  • lines changed 17, context: html, text, full: html, text
    51aef9631658a9ec173d7c5aa8989738ae4a71ba Thu Oct 7 17:01:53 2021 -0700
    add a fix to a bug where liftOver elements with zero size that did *not* fit into a chain were flagges as an error rather than just marked as missing
• src/hg/lib/makefile
  • lines changed 4, context: html, text, full: html, text
    214027f89911627e70d5836ea64071b97487144b Mon Oct 4 12:35:07 2021 -0700
    fixup race condition to mkdir lib/MACHTYPE refs #28240
• src/hg/liftOver/tests/expected/zeroWidth.bed
  • lines changed 21, context: html, text, full: html, text
    51aef9631658a9ec173d7c5aa8989738ae4a71ba Thu Oct 7 17:01:53 2021 -0700
    add a fix to a bug where liftOver elements with zero size that did *not* fit into a chain were flagges as an error rather than just marked as missing
• src/hg/liftOver/tests/input/zeroWidth.bed
  • lines changed 17, context: html, text, full: html, text
    51aef9631658a9ec173d7c5aa8989738ae4a71ba Thu Oct 7 17:01:53 2021 -0700
    add a fix to a bug where liftOver elements with zero size that did *not* fit into a chain were flagges as an error rather than just marked as missing
• src/hg/liftOver/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    51aef9631658a9ec173d7c5aa8989738ae4a71ba Thu Oct 7 17:01:53 2021 -0700
    add a fix to a bug where liftOver elements with zero size that did *not* fit into a chain were flagges as an error rather than just marked as missing
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 4, context: html, text, full: html, text
    9d58bbf088d5889d9274d454a3fc6d1ecdf9ec0e Mon Oct 4 15:19:23 2021 -0700
    add note about invertebrate group containing more than just animals no redmine
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 98, context: html, text, full: html, text
    b42c37490f9b9d3dd976e98c95bbfd1e95c98ea6 Wed Oct 6 15:54:49 2021 -0700
    tardigrades lastz/chain/net no redmine
  • lines changed 14, context: html, text, full: html, text
    9e7949fb6dd9cbb6379327b52e762cdecde5341a Thu Oct 7 09:47:15 2021 -0700
    finish off lastz/chain/net procedure no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 6, context: html, text, full: html, text
    50bd805b6eddedc25a9db61f372f483319ba2987 Fri Oct 8 15:11:25 2021 -0700
    adding tardigrade and bacteria genomes requesed by users refs #28303
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    50bd805b6eddedc25a9db61f372f483319ba2987 Fri Oct 8 15:11:25 2021 -0700
    adding tardigrade and bacteria genomes requesed by users refs #28303
• src/hg/makeDb/doc/hg19.txt
  • lines changed 18, context: html, text, full: html, text
    61309f7c6fb5fb1d582fde243fbfa83559c1da21 Tue Oct 5 16:26:13 2021 -0700
    Fix float parsing bug in gtex transcript expression track on hg19 and hg38, refs #28280
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 7, context: html, text, full: html, text
    61309f7c6fb5fb1d582fde243fbfa83559c1da21 Tue Oct 5 16:26:13 2021 -0700
    Fix float parsing bug in gtex transcript expression track on hg19 and hg38, refs #28280
• src/hg/makeDb/doc/hg38/patchUpdate.13.txt
  • lines changed 81, context: html, text, full: html, text
    2574b18caca333a5d52d6d6b8ecc6424d403c7d7 Tue Oct 5 22:01:49 2021 -0700
    more p13 made properly versioned gc5Base files for top, intial, p12, p13, latest bigZips doownloads dirs. refs #25091
  • lines changed 89, context: html, text, full: html, text
    620c6d4617dc2b1fe159566b20c5e902821adb76 Wed Oct 6 16:31:09 2021 -0700
    adding correctly versioned hg38.chromAlias.txt to the various hg38 bigZips top, initial, p11, p12, p13 final dirs. refs #25091
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    6e1e750b5deddc08621ca5902d2cc8201a6965fc Wed Oct 6 13:33:36 2021 -0700
    adding two tardigrade genome assemblies per Max request no redmine
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 78, context: html, text, full: html, text
    1054d4e3c1d6bdb3d2799860d0eca70dfd35447c Mon Oct 4 10:27:27 2021 -0700
    mm39 vs. hg19 lastz/chain/net per Brian request no redmine
  • lines changed 3, context: html, text, full: html, text
    fae06a8f022bd67553c9e254fb1ecf98ca8d3e03 Wed Oct 6 14:12:49 2021 -0700
    fixup comment no redmine
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
  • lines changed 165, context: html, text, full: html, text
    e9341e4a870638ed3a9f855670e22f68f59c2f3d Mon Oct 4 15:55:56 2021 -0700
    Clean up make doc. refs #27926
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 1, context: html, text, full: html, text
    2dbcb08f6bbd8172fcfbde88dcf744062749c7ca Wed Oct 6 10:35:04 2021 -0700
    lower the priority of Gencode V36 since it's archived now
• src/hg/makeDb/trackDb/human/hg38/knownGeneV38.html
  • lines changed 12, context: html, text, full: html, text
    886dd609a731133e9e8295d6c4a50c0eedbd074e Tue Oct 5 13:49:59 2021 -0700
    update knownGeneV38.html with statistics table
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    3e628c524315ae7d3de8aac5d422c86cdabebcb7 Tue Oct 5 16:56:01 2021 -0700
    Releasing updated lrg tracks refs #24672
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 5, context: html, text, full: html, text
    9ef9b760d157a71c1ab0564b5b5f28597b015931 Mon Oct 4 14:23:58 2021 -0700
    no need to show error when looking for rmsk and it does not exist no redmine
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 2, context: html, text, full: html, text
    d2ea6b76f1d69dafb40ebdb6348fb7fbcc5c6e49 Fri Oct 8 15:12:35 2021 -0700
    manage the names for single sequences in bacteria refs #28303
• src/hg/utils/automation/doBigDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    504757947a40dcf788df653a4e00d8ba64c873c1 Thu Sep 30 01:08:34 2021 -0700
    updating default hg38 to p13 in dbsnp build utility
• src/hg/utils/automation/pairLastz.sh
  • lines changed 3, context: html, text, full: html, text
    280a2a6f10fd59284d182afba38fc5983dafc68f Mon Oct 4 10:26:35 2021 -0700
    updating spacing of makeDoc output no redmine
  • lines changed 3, context: html, text, full: html, text
    9e7949fb6dd9cbb6379327b52e762cdecde5341a Thu Oct 7 09:47:15 2021 -0700
    finish off lastz/chain/net procedure no redmine
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 3, context: html, text, full: html, text
    25f7f8e12a691157968e8a74b932418dd30b3a50 Wed Oct 6 12:33:13 2021 -0700
    Escaping text output by hubCheck's -htmlOut option so track hub developers can have quotes and other odd characters in their track name labels and the jstree will still work, refs Braney email
• src/hg/utils/otto/clinGen/clinGenWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 77, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 2, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 62, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 8, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/gwas/gwasWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/isca/iscaWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/lovd/lovd.long.as
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/lovd/lovd.short.as
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/omim/omimGene2ToBigBed.py
  • lines changed 3, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/omim/omimUploadWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/omim/omimWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/otto.crontab
  • lines changed 4, context: html, text, full: html, text
    a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700
    Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 2, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 1, context: html, text, full: html, text
    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
  • lines changed 2, context: html, text, full: html, text
    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 11, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
  • lines changed 4, context: html, text, full: html, text
    2bd08d43e884241b1e759bd87782e7bab62e1a5c Wed Oct 6 09:19:00 2021 -0700
    Oops, check more carefully for new optional arg.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 6, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
  • lines changed 4, context: html, text, full: html, text
    2bd08d43e884241b1e759bd87782e7bab62e1a5c Wed Oct 6 09:19:00 2021 -0700
    Oops, check more carefully for new optional arg.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
  • lines changed 1, context: html, text, full: html, text
    50c3ab948546ac10a2f0bf151ab51c8b836bafd9 Mon Oct 4 16:58:39 2021 -0700
    Use normal priority for cluster run.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    214027f89911627e70d5836ea64071b97487144b Mon Oct 4 12:35:07 2021 -0700
    fixup race condition to mkdir lib/MACHTYPE refs #28240
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    d8eaf7199fbe62ec8b6b565424306da70f571d99 Tue Oct 5 17:36:58 2021 -0700
    Don't forget the new hg/cgilib in the top-level libs and hgLib targets.
• src/utils/qa/hubPublicAutoUpdate
  • lines changed 20, context: html, text, full: html, text
    29c0f7fde4830831982258fb7dece05f0cd39eae Fri Oct 8 09:34:40 2021 -0700
    Changing query command to curl as requests did not support ftp, and adding a sanitizing function to escape quotes when found in labels, refs #28008
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    cb4fbb9fa0dd10f12642472971a197b2b17a94a3 Mon Oct 11 08:36:03 2021 -0700
    Adding full path to hgsql util for cron environment.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    f765bc85c29d5f67ef128016ee672d4bba938388 Mon Oct 11 10:10:47 2021 -0700
    v422 preview2, refs #28292

• lines changed: 1147
• files changed: 69