All File Changes

v455_preview2 to v455_base (2023-10-02 to 2023-10-09) v455

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    d1f0ba05183b4fe97de2f40fefaa49e52ef9365b Fri Oct 6 15:56:24 2023 -0700
    Making small changes to the wording for the NCBI RefSeq parent link, refs #32263
• src/hg/hgTracks/simpleTracks.c
  • lines changed 38, context: html, text, full: html, text
    6777815b495172716ac5fe8f18a5b375a4196397 Wed Oct 4 15:09:41 2023 -0700
    Fix for label mapboxes not being drawn, refs #30237
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 0, context: html, text, full: html, text
    5d880eccee6e7beee8e1896931bba081883ac0a3 Wed Oct 4 09:04:29 2023 -0700
    Replace spaces with tabs in #CHROM header line of example VCF.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5ea537a921cd0adc0c6d14986f2e0f5581b0c6ed Mon Oct 9 09:36:00 2023 -0700
    New version number v455
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    30aaa1ec82ebf70d3349ffdd79334c0b0fe64c64 Wed Oct 4 11:38:32 2023 -0700
    Add a class to the icon in hui.c printInfoIcon() so javascript can know to make those tooltips appear, refs #32011
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    30aaa1ec82ebf70d3349ffdd79334c0b0fe64c64 Wed Oct 4 11:38:32 2023 -0700
    Add a class to the icon in hui.c printInfoIcon() so javascript can know to make those tooltips appear, refs #32011
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    b5545c453909057d382c04d36100e73d9ce18e0a Wed Oct 4 11:51:14 2023 -0700
    add GCA_025583915.1_AnoSag2.1 brown anole (Geneva1000 2022) per user request refs #29545
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 43, context: html, text, full: html, text
    631a7882f8c689b66f3d81fc8f25fbf98f73499a Mon Oct 2 16:55:41 2023 -0700
    remove the all genomes at once attachment option refs #29545
  • lines changed 17, context: html, text, full: html, text
    1ae12a1d8f166902e7697634f6a209fe15a70bf2 Wed Oct 4 14:48:52 2023 -0700
    adding outlink to IGV browser refs #29545
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    c41a4f1cb64b449dcba3318ec07c7569825d1ac9 Wed Oct 4 16:23:42 2023 -0700
    correctly indicate IGV link in common name column header title refs #29545
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 58, context: html, text, full: html, text
    d2346420237f134dff79722739380d022c5ec48d Fri Oct 6 16:02:11 2023 -0700
    Update to ncbiRefSeq Historical track now that I can make the proper cds ranges because NCBI provides the gbff file with the download set, refs #26016
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b5545c453909057d382c04d36100e73d9ce18e0a Wed Oct 4 11:51:14 2023 -0700
    add GCA_025583915.1_AnoSag2.1 brown anole (Geneva1000 2022) per user request refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    96c411aa4f02250ce383d99aff584395c5298f98 Tue Oct 3 09:44:59 2023 -0700
    update to the alternate list adding one refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 73, context: html, text, full: html, text
    ba37a4e86e631db3df00bf18b8eaf4d8d296387f Tue Oct 3 09:18:54 2023 -0700
    an update to the primary listing refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 26, context: html, text, full: html, text
    ba37a4e86e631db3df00bf18b8eaf4d8d296387f Tue Oct 3 09:18:54 2023 -0700
    an update to the primary listing refs #29545
  • lines changed 1, context: html, text, full: html, text
    96c411aa4f02250ce383d99aff584395c5298f98 Tue Oct 3 09:44:59 2023 -0700
    update to the alternate list adding one refs #29545
• src/hg/makeDb/trackDb/evaSnp.html
  • lines changed 2, context: html, text, full: html, text
    c0c874f6d123d68c0a58d59d89cd1f378fe2b18b Fri Oct 6 12:37:17 2023 -0700
    Removing confusing language about SNVs being simple nucleotide variants vs single nucroltide variants, refs email from Braney.
• src/hg/makeDb/trackDb/evaSnp4.html
  • lines changed 2, context: html, text, full: html, text
    c0c874f6d123d68c0a58d59d89cd1f378fe2b18b Fri Oct 6 12:37:17 2023 -0700
    Removing confusing language about SNVs being simple nucleotide variants vs single nucroltide variants, refs email from Braney.
• src/hg/makeDb/trackDb/evaSnp5.html
  • lines changed 2, context: html, text, full: html, text
    c0c874f6d123d68c0a58d59d89cd1f378fe2b18b Fri Oct 6 12:37:17 2023 -0700
    Removing confusing language about SNVs being simple nucleotide variants vs single nucroltide variants, refs email from Braney.
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 2, context: html, text, full: html, text
    28a0537782226f93bac8972e591eca140a182034 Tue Oct 3 12:07:25 2023 -0700
    updated longLabel per Benedict request refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 2, context: html, text, full: html, text
    28a0537782226f93bac8972e591eca140a182034 Tue Oct 3 12:07:25 2023 -0700
    updated longLabel per Benedict request refs #31528
  • lines changed 21, context: html, text, full: html, text
    7789aff7cff9c17e2ff56209af5225989b354916 Wed Oct 4 21:37:20 2023 -0700
    adding a phyloP track from Lukas for a primates subset their calculation refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    346fa22af4717e4d8bdaa6a22a873ac4324c357b Fri Oct 6 16:28:34 2023 -0700
    Change refSeqHistorical track to a bigGenePred, which it is now, refs #26016
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    346fa22af4717e4d8bdaa6a22a873ac4324c357b Fri Oct 6 16:28:34 2023 -0700
    Change refSeqHistorical track to a bigGenePred, which it is now, refs #26016
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 13, context: html, text, full: html, text
    69674723e539da023afcf3612d50bcc89be5f29f Wed Oct 4 14:58:09 2023 -0700
    adding cite reference stanza refs #29545
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 4, context: html, text, full: html, text
    5793028c4b37b6cb8300580e70d7b078abc516b2 Wed Oct 4 17:46:58 2023 -0700
    Mask deletion 21991-21993 in XBB.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 3, context: html, text, full: html, text
    afedd6d0dae5767b8ee9041119d72a65360f77e0 Wed Oct 4 17:46:28 2023 -0700
    Strip stuff past the accession in headers when making fasta for pangolin.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 34, context: html, text, full: html, text
    dc2399eba0ad110c5df9658b67da773e302b3bb0 Wed Oct 4 17:47:39 2023 -0700
    More requested exceptions to filters, thanks @aviczhl2.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 95, context: html, text, full: html, text
    9ddf9825cc02b849ed222d5a1274e4c385ba599b Wed Oct 4 17:45:17 2023 -0700
    Added new lineages and updated some existing ones.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 2, context: html, text, full: html, text
    87d8340f2b3cdce33de9043c4ecd9afdfef55b25 Wed Oct 4 17:48:43 2023 -0700
    Set prevDate at the beginning so we don't run into trouble for occasional epic long downloads from CNCB.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    5ea537a921cd0adc0c6d14986f2e0f5581b0c6ed Mon Oct 9 09:36:00 2023 -0700
    New version number v455
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 3, context: html, text, full: html, text
    01089c81628328a3a9083680e1705238e4246472 Mon Oct 2 15:45:51 2023 -0700
    tweak usage message to explain that relaxation of sorting requirement
• src/utils/bedToBigBed/tests/expected/notSorted.err
  • lines changed 1, context: html, text, full: html, text
    b5975d804a51167f783805828c78f811a3ef096b Mon Oct 2 14:45:30 2023 -0700
    some new tests for relaxed sorting
• src/utils/bedToBigBed/tests/input/hg38.chrom.sizes
  • lines changed 711, context: html, text, full: html, text
    b5975d804a51167f783805828c78f811a3ef096b Mon Oct 2 14:45:30 2023 -0700
    some new tests for relaxed sorting
• src/utils/bedToBigBed/tests/input/notSorted.bed
  • lines changed 1, context: html, text, full: html, text
    b5975d804a51167f783805828c78f811a3ef096b Mon Oct 2 14:45:30 2023 -0700
    some new tests for relaxed sorting
• src/utils/bedToBigBed/tests/input/oddSorted.bed
  • lines changed 923, context: html, text, full: html, text
    b5975d804a51167f783805828c78f811a3ef096b Mon Oct 2 14:45:30 2023 -0700
    some new tests for relaxed sorting
• src/utils/bedToBigBed/tests/makefile
  • lines changed 10, context: html, text, full: html, text
    b5975d804a51167f783805828c78f811a3ef096b Mon Oct 2 14:45:30 2023 -0700
    some new tests for relaxed sorting
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    e97bc01836d5b859a9f4aeed51b65955583eacff Mon Oct 9 09:32:02 2023 -0700
    v455 final build, refs #32270

• lines changed: 2110
• files changed: 38