All File Changes

v456_preview2 to v456_base (2023-10-23 to 2023-10-30) v456

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 15, context: html, text, full: html, text
    d827b292f2da39b290412c402752b1bd68b37d2e Wed Oct 25 17:00:56 2023 -0700
    Adding a new condition to check for another regex expression. I found that two of the broken examples had spaces in the URL, so try to match on that and translate them. I also found one which had three backslashes incorrectly, so try to fix that too. I added it to a new loop so as not to affect the original functionality. This seems to cover all of the broken cases we had noted. Refs #31963
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    f38c6808e55c7a6f064085b8baea35c0526790fb Tue Oct 24 04:52:07 2023 -0700
    fixing null pointer crash, thanks to braney and chmalee, refs #32499
• src/hg/hgTables/schema.c
  • lines changed 0, context: html, text, full: html, text
    f38c6808e55c7a6f064085b8baea35c0526790fb Tue Oct 24 04:52:07 2023 -0700
    fixing null pointer crash, thanks to braney and chmalee, refs #32499
  • lines changed 2, context: html, text, full: html, text
    b8a5889bb0b33a6de78c81950aecdfdf4a280066 Tue Oct 24 04:55:34 2023 -0700
    fixing missing curly braces, thanks to braney, refs #32499
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    b6fb3bd6caadca912384f7e294d729d1b78f8c4a Fri Oct 27 17:23:00 2023 -0700
    Printed shortLabels on the hgTracks page should use HTML entities instead of special characters, refs #32512
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 9, context: html, text, full: html, text
    bcf0e9bf9e4fbde53c48293a625611a27a3c1d2f Wed Oct 25 13:51:28 2023 -0700
    Code review feedback edits and more updates for the release of the decorator.html, refs #32494 #30237
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    bcf0e9bf9e4fbde53c48293a625611a27a3c1d2f Wed Oct 25 13:51:28 2023 -0700
    Code review feedback edits and more updates for the release of the decorator.html, refs #32494 #30237
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 10, context: html, text, full: html, text
    c3bb05df9736fa214d0981a46aec9d3fe475fe09 Wed Oct 25 17:04:03 2023 -0700
    Adding a publication by Brittney, no RM
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    3f37c7999a4f1e808626906f2bc565d394e8c291 Mon Oct 30 10:36:31 2023 -0700
    New version number v456
• src/hg/lib/hdb.c
  • lines changed 11, context: html, text, full: html, text
    6093365dc43da304b632706394a77a1713965635 Tue Oct 24 12:58:59 2023 -0700
    stop checking for data accessibility on the assumption that the trackDb build already did that. Add a little side-effect up higher in the call chain. This should probably be somewhere else, but in fear of breaking something new, I'm just popping it up one link in the call chain.
  • lines changed 18, context: html, text, full: html, text
    5fad625c42342d49423acd17a40d95357c3aae64 Thu Oct 26 02:21:27 2023 -0700
    changes after code review, refs #32498
  • lines changed 18, context: html, text, full: html, text
    fb2ec3172f9e59b02a43f09307f189ee88321ac0 Thu Oct 26 09:12:52 2023 -0700
    Revert "changes after code review, refs #32498" This reverts commit 5fad625c42342d49423acd17a40d95357c3aae64.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 10, context: html, text, full: html, text
    d0bcef580cd0c19bbe20a2c401e0baf62410790c Thu Oct 26 12:52:03 2023 -0700
    add sanityCheck to prevent duplicate accession IDs from leaking into the tsv orderList refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 24, context: html, text, full: html, text
    0fb0515d36b58fbf20109d736e2c327e891430cd Tue Oct 24 11:17:50 2023 -0700
    VGP update adds 24 birds refs #29545
  • lines changed 23, context: html, text, full: html, text
    0b5a1f431e69714e84403c73c87ecfb48c78a553 Wed Oct 25 10:08:46 2023 -0700
    VGP update adding 23 fish refs #29545
  • lines changed 10, context: html, text, full: html, text
    af46043499a829ab8e1bafcc2b37c761139e24a8 Wed Oct 25 10:26:46 2023 -0700
    VGP update adding 10 vertebrate refs #29545
  • lines changed 9, context: html, text, full: html, text
    75479452cf7a3eeeb3844e02cec904789d2bc14a Wed Oct 25 15:01:28 2023 -0700
    VGP update adding 9 mammal assemblies refs #29545
  • lines changed 8, context: html, text, full: html, text
    f3b5d52f647e993599786170af8931721631259e Thu Oct 26 10:57:48 2023 -0700
    update adding 8 invertebrates refs #29545
  • lines changed 5, context: html, text, full: html, text
    c8cc281d9175f01aeda71372a49d3cd94b6eca90 Thu Oct 26 13:10:38 2023 -0700
    update adding 5 plants refs #29545
  • lines changed 4, context: html, text, full: html, text
    6fd3a06eb1fdeb0992cead0af6ab3bb6bcd4024d Thu Oct 26 13:39:44 2023 -0700
    update adding 2 fish and 2 birds refs @29545
  • lines changed 1, context: html, text, full: html, text
    71c76a53f1894e0dcff810c06a35cc14fad66bde Thu Oct 26 19:40:25 2023 -0700
    update Atlantic stingray hap1 from genbank to refseq refs #29545
  • lines changed 1, context: html, text, full: html, text
    e375c20d377485c5a56df45a9094833cb6738d54 Fri Oct 27 09:51:54 2023 -0700
    adding GCA_010365825.1_OtuSun1.0 Oriental scops-owl (oso-nibr-517 2020) per user request refs #29545
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 3, context: html, text, full: html, text
    411af8fc818febf61de8210a3cc05b019d9c8d2a Fri Oct 27 10:39:09 2023 -0700
    the missing files need to be marked as an error refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 33, context: html, text, full: html, text
    0fb0515d36b58fbf20109d736e2c327e891430cd Tue Oct 24 11:17:50 2023 -0700
    VGP update adds 24 birds refs #29545
  • lines changed 2, context: html, text, full: html, text
    6fd3a06eb1fdeb0992cead0af6ab3bb6bcd4024d Thu Oct 26 13:39:44 2023 -0700
    update adding 2 fish and 2 birds refs @29545
  • lines changed 1, context: html, text, full: html, text
    e375c20d377485c5a56df45a9094833cb6738d54 Fri Oct 27 09:51:54 2023 -0700
    adding GCA_010365825.1_OtuSun1.0 Oriental scops-owl (oso-nibr-517 2020) per user request refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 28, context: html, text, full: html, text
    0b5a1f431e69714e84403c73c87ecfb48c78a553 Wed Oct 25 10:08:46 2023 -0700
    VGP update adding 23 fish refs #29545
  • lines changed 2, context: html, text, full: html, text
    6fd3a06eb1fdeb0992cead0af6ab3bb6bcd4024d Thu Oct 26 13:39:44 2023 -0700
    update adding 2 fish and 2 birds refs @29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    6e2f28786bccefb4d632b6f127d81b061cfea92b Tue Oct 24 01:53:47 2023 -0700
    adding missing CKD track to emerge prs, refs #31546
• src/hg/makeDb/doc/hgFixed.txt
  • lines changed 11, context: html, text, full: html, text
    52e47105152b7e5dd2621b9e8439446e0d77336f Mon Oct 23 12:01:11 2023 -0700
    build Jaspar 2024 motif table
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    f3b5d52f647e993599786170af8931721631259e Thu Oct 26 10:57:48 2023 -0700
    update adding 8 invertebrates refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 7, context: html, text, full: html, text
    75479452cf7a3eeeb3844e02cec904789d2bc14a Wed Oct 25 15:01:28 2023 -0700
    VGP update adding 9 mammal assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    f3b5d52f647e993599786170af8931721631259e Thu Oct 26 10:57:48 2023 -0700
    update adding 8 invertebrates refs #29545
  • lines changed 2, context: html, text, full: html, text
    1b416ef57918a097a1da32249baa3fc7b675e18a Thu Oct 26 14:15:01 2023 -0700
    updated obsolte two birds refs #29545
  • lines changed 1, context: html, text, full: html, text
    71c76a53f1894e0dcff810c06a35cc14fad66bde Thu Oct 26 19:40:25 2023 -0700
    update Atlantic stingray hap1 from genbank to refseq refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    75479452cf7a3eeeb3844e02cec904789d2bc14a Wed Oct 25 15:01:28 2023 -0700
    VGP update adding 9 mammal assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    f3b5d52f647e993599786170af8931721631259e Thu Oct 26 10:57:48 2023 -0700
    update adding 8 invertebrates refs #29545
  • lines changed 2, context: html, text, full: html, text
    1b416ef57918a097a1da32249baa3fc7b675e18a Thu Oct 26 14:15:01 2023 -0700
    updated obsolte two birds refs #29545
  • lines changed 1, context: html, text, full: html, text
    71c76a53f1894e0dcff810c06a35cc14fad66bde Thu Oct 26 19:40:25 2023 -0700
    update Atlantic stingray hap1 from genbank to refseq refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    da4f13a10991eeea650596371fd2879b99222a9b Tue Oct 24 21:12:47 2023 -0700
    Eurasian badger v3.1 has moved to legacy refs #29545
  • lines changed 14, context: html, text, full: html, text
    75479452cf7a3eeeb3844e02cec904789d2bc14a Wed Oct 25 15:01:28 2023 -0700
    VGP update adding 9 mammal assemblies refs #29545
  • lines changed 1, context: html, text, full: html, text
    43e778085a841c112d25ff9d12da71083d1d99ec Thu Oct 26 12:05:46 2023 -0700
    illegal second copy of the same genome GCF_029834395.1 refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    c8cc281d9175f01aeda71372a49d3cd94b6eca90 Thu Oct 26 13:10:38 2023 -0700
    update adding 5 plants refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    af46043499a829ab8e1bafcc2b37c761139e24a8 Wed Oct 25 10:26:46 2023 -0700
    VGP update adding 10 vertebrate refs #29545
  • lines changed 2, context: html, text, full: html, text
    71c76a53f1894e0dcff810c06a35cc14fad66bde Thu Oct 26 19:40:25 2023 -0700
    update Atlantic stingray hap1 from genbank to refseq refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 112, context: html, text, full: html, text
    9db1c1b33a7d1db0f06783b71f81ed96a87ecb76 Fri Oct 27 15:01:53 2023 -0700
    VGP update to catch up with current listings refs #25555
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 119, context: html, text, full: html, text
    9db1c1b33a7d1db0f06783b71f81ed96a87ecb76 Fri Oct 27 15:01:53 2023 -0700
    VGP update to catch up with current listings refs #25555
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 176, context: html, text, full: html, text
    9db1c1b33a7d1db0f06783b71f81ed96a87ecb76 Fri Oct 27 15:01:53 2023 -0700
    VGP update to catch up with current listings refs #25555
• src/hg/makeDb/trackDb/chicken/galGal6/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/hg19/prs.html
  • lines changed 5, context: html, text, full: html, text
    2307e532192dd8a815adaf72cf743dc0cf328ed6 Tue Oct 24 01:55:57 2023 -0700
    prs docs update, refs #31546
• src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 1, context: html, text, full: html, text
    c014c28fd9dc9e242005a07430bd9f1a3edbd4a2 Wed Oct 18 12:44:02 2023 -0700
    oops fix typo
• src/hg/makeDb/trackDb/human/hg38/primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/hg38/t2tChain.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
  • lines changed 1, context: html, text, full: html, text
    0f9e84d70ea5f9b94011729c486ca220be9bcfcb Wed Oct 25 14:21:14 2023 -0700
    there is no o_organism for these refs #32455
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
  • lines changed 1, context: html, text, full: html, text
    0f9e84d70ea5f9b94011729c486ca220be9bcfcb Wed Oct 25 14:21:14 2023 -0700
    there is no o_organism for these refs #32455
• src/hg/makeDb/trackDb/mouse/mm39/mm39ChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
  • lines changed 1, context: html, text, full: html, text
    0f9e84d70ea5f9b94011729c486ca220be9bcfcb Wed Oct 25 14:21:14 2023 -0700
    there is no o_organism for these refs #32455
• src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
  • lines changed 1, context: html, text, full: html, text
    0f9e84d70ea5f9b94011729c486ca220be9bcfcb Wed Oct 25 14:21:14 2023 -0700
    there is no o_organism for these refs #32455
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 1, context: html, text, full: html, text
    736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700
    correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
• src/hg/perf/hgTracksRandom.c
  • lines changed 1, context: html, text, full: html, text
    89515354d525e9b4cc8d557a970cfd9faaea6721 Mon Oct 23 11:43:24 2023 -0700
    Adding a new condition to hgTracksRandom to complain if the response is too fast, which was what happened when hgCentral wend won and the page was responding instantly but with a mysql error. Refs GBPT 10/23/23
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 5, context: html, text, full: html, text
    9c779856e423e2f2030758080f93d8e1448b95b1 Fri Oct 27 10:44:05 2023 -0700
    do not need to do twoBitToFa twice in addMask, once is enough refs #29545
• src/hg/utils/chainInDel/chainInDel.c
  • lines changed 110, context: html, text, full: html, text
    136d37467b6957c38976c8bd98bdb942e8514bb6 Fri Oct 27 16:27:09 2023 -0700
    add chainInDel command to build HPRC indels track
• src/hg/utils/chainInDel/makefile
  • lines changed 3, context: html, text, full: html, text
    136d37467b6957c38976c8bd98bdb942e8514bb6 Fri Oct 27 16:27:09 2023 -0700
    add chainInDel command to build HPRC indels track
• src/hg/utils/otto/omim/doOmimGene2.sh
  • lines changed 2, context: html, text, full: html, text
    81ef31c5abe6dba3c4dfa96725f2912c2183fc8b Mon Oct 23 16:38:46 2023 -0700
    fix doOmimGene2.sh to not throw away items with the same start coordinate.
• src/hg/utils/otto/omim/makefile
  • lines changed 1, context: html, text, full: html, text
    81ef31c5abe6dba3c4dfa96725f2912c2183fc8b Mon Oct 23 16:38:46 2023 -0700
    fix doOmimGene2.sh to not throw away items with the same start coordinate.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    3f37c7999a4f1e808626906f2bc565d394e8c291 Mon Oct 30 10:36:31 2023 -0700
    New version number v456
• src/utils/qa/hubSearchUpdate
  • lines changed 2, context: html, text, full: html, text
    b29210d7c090241d05bf826c518787818613a467 Tue Oct 24 11:47:04 2023 -0700
    Go down one more level when generating public hubs search indexes, refs #30253
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    0c6eb63b03beeae304c59e52edb391e6b83e8beb Mon Oct 30 10:34:36 2023 -0700
    v456 final build, refs #32470

• lines changed: 904
• files changed: 76