All File Changes

v451_preview2 to v451_base (2023-07-10 to 2023-07-17) v451

• src/hg/cgilib/cartJson.c
  • lines changed 7, context: html, text, full: html, text
    f813e11a4d7798debd5a20c6222eb3a7be1bc0e0 Tue Jul 11 14:21:12 2023 -0700
    Fail more gracefully when a genbank table has been left on a server mistakenly, refs #31744
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 1, context: html, text, full: html, text
    96471ada1e945584ea0bbd8615fb1f54b743b011 Mon Jul 10 16:44:40 2023 -0700
    Add a bit more info to error message about subtree with no user sample IDs.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 8, context: html, text, full: html, text
    74badd35b7df2aef1be18519fb05beda8af1a4e4 Mon Jul 10 16:45:24 2023 -0700
    Doh, forgot to deal with strand in codonVpTxToAaChange, but MPXV has strands.
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 34, context: html, text, full: html, text
    9662dcb8b56ccc906aa0d2a2b92f4ed0be5e0217 Thu Jul 13 11:57:07 2023 -0700
    Adding documentation and examples for hgSearch API, refs #24113
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    9461b863e8b83742a6db23c5c701babd0e04a819 Mon Jul 17 11:27:32 2023 -0700
    New version number v451
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    ca540ace20beea2862dc268592d02f800816d1b3 Fri Jul 14 11:16:16 2023 -0700
    Fix html tags showing up when using arrow keys to select autocomplete items on hgGateway, refs #18255
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    da34e9cb9209ae2d8bce2b8a4b5102df58d94db5 Tue Jul 11 10:48:12 2023 -0700
    Forgot to pass the arguments through when binding to new function, refs #31742
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 2, context: html, text, full: html, text
    dc8ad8ee1ee8372436d900053d1c37c9f1f77425 Fri Jul 14 10:06:07 2023 -0700
    adding GCA_016920875.1_Utah_Ccol_1.0 slender pigeon louse (jgb_00001 2021) per user request and make the cp -p statements safe refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    f9e74d3251120c935a477d67be959df2e5d5d2f1 Wed Jul 12 13:55:41 2023 -0700
    adding GCF_000002415.2_ASM241v2 malaria parasite P. vivax (Salvador I 2009) per user request refs #31748
  • lines changed 1, context: html, text, full: html, text
    dc8ad8ee1ee8372436d900053d1c37c9f1f77425 Fri Jul 14 10:06:07 2023 -0700
    adding GCA_016920875.1_Utah_Ccol_1.0 slender pigeon louse (jgb_00001 2021) per user request and make the cp -p statements safe refs #29545
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 27, context: html, text, full: html, text
    a5cf15983b362b46e7818dc0f5b81f2b494577c1 Tue Jul 11 13:54:30 2023 -0700
    Staging the COSMIC track, refs #29625
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f9e74d3251120c935a477d67be959df2e5d5d2f1 Wed Jul 12 13:55:41 2023 -0700
    adding GCF_000002415.2_ASM241v2 malaria parasite P. vivax (Salvador I 2009) per user request refs #31748
  • lines changed 1, context: html, text, full: html, text
    dc8ad8ee1ee8372436d900053d1c37c9f1f77425 Fri Jul 14 10:06:07 2023 -0700
    adding GCA_016920875.1_Utah_Ccol_1.0 slender pigeon louse (jgb_00001 2021) per user request and make the cp -p statements safe refs #29545
• src/hg/makeDb/trackDb/human/genCC.ra
  • lines changed 2, context: html, text, full: html, text
    1962531867d517f98f6465d610b28de56c38f21d Wed Jul 12 02:23:54 2023 -0700
    adding outlink to GenCC gene page, no redmine
• src/hg/makeDb/trackDb/human/hg38/cosmicMuts.html
  • lines changed 83, context: html, text, full: html, text
    a5cf15983b362b46e7818dc0f5b81f2b494577c1 Tue Jul 11 13:54:30 2023 -0700
    Staging the COSMIC track, refs #29625
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 18, context: html, text, full: html, text
    b8553401fc82aa037b6ca053a25368f0a4ee5c5d Tue Jul 11 09:36:39 2023 -0700
    Adding IDT exome probeset track by user request, refs #31731
  • lines changed 4, context: html, text, full: html, text
    869c8a153ad5661072669e020618ef5c71913e94 Tue Jul 11 10:02:41 2023 -0700
    Cleaning up the trackDb and hiding the track by default, refs #31731
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    a5cf15983b362b46e7818dc0f5b81f2b494577c1 Tue Jul 11 13:54:30 2023 -0700
    Staging the COSMIC track, refs #29625
• src/hg/utils/gff3ToGenePred/tests/expected/errDupIdDiffParentsTest.out
  • lines changed 2, context: html, text, full: html, text
    c41c17e6c7251f5f93f68ad8e80ab6b0d0f348f6 Mon Jul 10 15:56:23 2023 -0700
    fixed SEGV with checking certain invalid GFF3s
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff
  • lines changed 265, context: html, text, full: html, text
    91e6c1e0eed9c2be10a8fbfea8126e3bc3093a81 Sat Jul 8 10:33:43 2023 -0700
    fix invalid GFF3 test file
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    91e6c1e0eed9c2be10a8fbfea8126e3bc3093a81 Sat Jul 8 10:33:43 2023 -0700
    fix invalid GFF3 test file
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
  • lines changed 9, context: html, text, full: html, text
    f070f343168fcb94a21b832d1cb20104b0670186 Fri Jun 30 15:08:56 2023 -0700
    There really should never be a clade-defining mutation on the first or last base of the genome (low/no coverage in most genomes), but this morning it happened, so at least prevent illegal overlapping blocks in nextstrainClade bed output.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 6, context: html, text, full: html, text
    d8a34f168b65a616fb185dbff94af89c426668b6 Mon Jul 10 12:02:02 2023 -0700
    Mask position 337 in BN.1.2.3 -- noisy.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 1, context: html, text, full: html, text
    6199485d849f1a1ecce4ce6f57fa01d4eb6097dd Mon Jul 10 12:02:57 2023 -0700
    No more pangolearn mode.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 2, context: html, text, full: html, text
    d746723d112678e33245af03ffd617f7076d775d Mon Jul 10 12:04:42 2023 -0700
    Adding a couple more IDs for sars-cov-2-lineages/lineage-proposals#174.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 63, context: html, text, full: html, text
    ddb2aa5ae97a44fce99c32afc22070c68deaca03 Mon Jul 10 12:01:42 2023 -0700
    Latest new lineages. Also mask 337 in descendants of BN.1.2.3 because it's masked in branchSpecificMask.yml (noisy).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 10, context: html, text, full: html, text
    18aba4871dfccf70dabe6fc328338c1442acb2bc Mon Jul 10 11:59:23 2023 -0700
    Have been using different matOptimize args since mid-May, see comment.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    9461b863e8b83742a6db23c5c701babd0e04a819 Mon Jul 17 11:27:32 2023 -0700
    New version number v451
• src/lib/gff3.c
  • lines changed 7, context: html, text, full: html, text
    c41c17e6c7251f5f93f68ad8e80ab6b0d0f348f6 Mon Jul 10 15:56:23 2023 -0700
    fixed SEGV with checking certain invalid GFF3s
• src/lib/tests/expected/gff3ErrorCasesTest.err
  • lines changed 3, context: html, text, full: html, text
    c41c17e6c7251f5f93f68ad8e80ab6b0d0f348f6 Mon Jul 10 15:56:23 2023 -0700
    fixed SEGV with checking certain invalid GFF3s
• src/utils/qa/longSessionCartDumps.sh
  • lines changed 21, context: html, text, full: html, text
    db5f73b743bbdabf1dc30218232ccb27ba65ab1c Thu Jul 13 09:02:26 2023 -0700
    Adding Brian Raney script and added the removal of long-running session cart dumps that are 2 weeks and older from directory, refs, #31585
• src/utils/qa/qaTestScript.py
  • lines changed 2, context: html, text, full: html, text
    07328609983300ad437d31fdfeee6c9ce964976f Thu Jul 13 16:08:17 2023 -0700
    Updating hgGeneGraph test case due to recent CGI changes, refs #31712
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 4, context: html, text, full: html, text
    03ce2704351e8dd64d48ffbe7e5daf6f77f456f4 Mon Jul 17 11:22:41 2023 -0700
    v451 final build, refs #31600

• lines changed: 602
• files changed: 33