All File Changes

v473_preview2 to v473_base (2024-10-21 to 2024-10-28) v473

• confs/hgwdev.hg.conf
  • lines changed 7, context: html, text, full: html, text
    0964e2a39a2b905eca2d26a673043261afb585a6 Sun Oct 27 01:11:18 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    3b525549f303d82e7ed569d733fdd7bc2ab712ee Fri Oct 25 13:50:35 2024 -0700
    Updating the message for maximum track load time, as well as changing the configure variable name and adding a descriptive mouseover. Refs #34638
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    3b525549f303d82e7ed569d733fdd7bc2ab712ee Fri Oct 25 13:50:35 2024 -0700
    Updating the message for maximum track load time, as well as changing the configure variable name and adding a descriptive mouseover. Refs #34638
  • lines changed 1, context: html, text, full: html, text
    60fae96e4ba45d4d541701591da1877c60d045a6 Fri Oct 25 15:04:09 2024 -0700
    Being more explicit in the error message to indicate the exact setting name, refs #34638
  • lines changed 1, context: html, text, full: html, text
    9f8af18e17cce3fdebd32a660fbb189a161a9cd8 Fri Oct 25 15:44:23 2024 -0700
    Final tweak to the message, removed one period so it only prints across two lines. Also added the setting to CTs. Refs #34638
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    6f13148b08b075f264d497776a84df283272aab1 Thu Oct 24 17:47:33 2024 -0700
    Revert "fix wigColorBy to work with linkedFeatures and on hubs" This reverts commit 94456e195ad86e3da7331bc8f014eceaa35a8ecc.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 48, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    3e6e726f55156e6611cedb85de6865419d6b0762 Mon Oct 28 10:50:33 2024 -0700
    New version number v473
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    7ebf7f76fdf869ed56d48f1b126114c6c7040ab6 Wed Oct 23 13:48:29 2024 -0700
    Tweaking the wording of the message, refs #34604
  • lines changed 1, context: html, text, full: html, text
    6c08a9c1a9dd5833cde3cfd3d893c3609eaa5365 Fri Oct 25 09:03:30 2024 -0700
    Don't click a button that doesn't exist anymore, refs #34604
  • lines changed 38, context: html, text, full: html, text
    532df37bf012ea6b52943707aaa6ab4a8b4f379f Fri Oct 25 14:50:53 2024 -0700
    hide others is getting worse and worse, need to address case that track to hide is a child itself and the problem that superTrack visibility is NOT (!) inherited by children. Encode regulation can be at hide, but the children are visible! refs #27890
• src/hg/js/utils.js
  • lines changed 32, context: html, text, full: html, text
    532df37bf012ea6b52943707aaa6ab4a8b4f379f Fri Oct 25 14:50:53 2024 -0700
    hide others is getting worse and worse, need to address case that track to hide is a child itself and the problem that superTrack visibility is NOT (!) inherited by children. Encode regulation can be at hide, but the children are visible! refs #27890
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    ad821f46184a2a2edac8bb6fdd109b19d8f48610 Thu Oct 24 14:14:46 2024 -0700
    when loading a genark hub, don't trash the existing hubUrl (if any) Refs #34699
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    9f8af18e17cce3fdebd32a660fbb189a161a9cd8 Fri Oct 25 15:44:23 2024 -0700
    Final tweak to the message, removed one period so it only prints across two lines. Also added the setting to CTs. Refs #34638
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    6f13148b08b075f264d497776a84df283272aab1 Thu Oct 24 17:47:33 2024 -0700
    Revert "fix wigColorBy to work with linkedFeatures and on hubs" This reverts commit 94456e195ad86e3da7331bc8f014eceaa35a8ecc.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 3, context: html, text, full: html, text
    3d843800810c738ed63e1af3f471c4c3f6316264 Wed Oct 23 17:10:21 2024 -0700
    no longer send out genomes.txt files, obsolete refs #34689
  • lines changed 14, context: html, text, full: html, text
    d72fcfd04dee8c6a6362a7dce10157f06b1af6f4 Wed Oct 23 17:49:13 2024 -0700
    no longer making the genomes.txt or hub.txt files, obsolete refs #34689
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 8, context: html, text, full: html, text
    e971cb3711d443360ac4a480b8dca4322b559cfa Wed Oct 23 16:54:01 2024 -0700
    no longer send out hub.txt files, obsolete refs #34689
  • lines changed 8, context: html, text, full: html, text
    098291ec429c92f2fae1b383c272bc5558ce6dfd Thu Oct 24 14:38:18 2024 -0700
    mistake, the hub.txt files do go out for the individual assembly refs #34689
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 44, context: html, text, full: html, text
    358e762de07c37fdfe7b8a0a03f16341e4fddf11 Wed Oct 23 17:21:16 2024 -0700
    adding assemblies for BRC project refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/trackDb/human/decipher.alpha.ra
  • lines changed 56, context: html, text, full: html, text
    691aa9e2e4f42cd650b092d338eb7bf67ce97bc4 Sun Oct 27 18:52:19 2024 -0700
    Nesting DECIPHER tracks into a single superTrack, refs #34702
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 48, context: html, text, full: html, text
    691aa9e2e4f42cd650b092d338eb7bf67ce97bc4 Sun Oct 27 18:52:19 2024 -0700
    Nesting DECIPHER tracks into a single superTrack, refs #34702
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 116, context: html, text, full: html, text
    691aa9e2e4f42cd650b092d338eb7bf67ce97bc4 Sun Oct 27 18:52:19 2024 -0700
    Nesting DECIPHER tracks into a single superTrack, refs #34702
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 11, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 7, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/makeDb/trackDb/human/hg38/knownGeneV47.html
  • lines changed 1, context: html, text, full: html, text
    af594073394815711c0cc6b7e3143060bb7c934a Tue Oct 22 12:26:28 2024 -0700
    Updating the GENCODE release month, refs #34219 #34218
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    de9dbe587d6fb8e55053465db0d6ef8eb26e0ce2 Tue Oct 22 13:20:37 2024 -0700
    Staging the GENCODE v47/vM36 KnownGene tracks on hgwbeta, refs #34219 #34218
  • lines changed 2, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 51, context: html, text, full: html, text
    691aa9e2e4f42cd650b092d338eb7bf67ce97bc4 Sun Oct 27 18:52:19 2024 -0700
    Nesting DECIPHER tracks into a single superTrack, refs #34702
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
  • lines changed 1, context: html, text, full: html, text
    ffd4832f6d2bd9559df45e7bbdaf99c1514410a4 Wed Oct 23 17:02:44 2024 -0700
    Archiving the mm39 VM35 knownGene track, refs #34218
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM36.html
  • lines changed 1, context: html, text, full: html, text
    af594073394815711c0cc6b7e3143060bb7c934a Tue Oct 22 12:26:28 2024 -0700
    Updating the GENCODE release month, refs #34219 #34218
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    de9dbe587d6fb8e55053465db0d6ef8eb26e0ce2 Tue Oct 22 13:20:37 2024 -0700
    Staging the GENCODE v47/vM36 KnownGene tracks on hgwbeta, refs #34219 #34218
  • lines changed 2, context: html, text, full: html, text
    717a49525e045cc82ee02b8cd9f906f97e8f348e Wed Oct 23 14:05:35 2024 -0700
    Staging and releasing the new GENCODE Known Gene tracks V47 and VM36, refs #34219 #34218
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 3, context: html, text, full: html, text
    ba227c00ba4786dcbe2482cc6282e36e867c778b Tue Oct 22 15:06:25 2024 -0700
    something fishy here not sure what refs #34685
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 16, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 3, context: html, text, full: html, text
    fb4ea088b4e255ba27b04ae59e86644dabe6eda7 Thu Oct 24 23:13:25 2024 -0700
    adding NCBI link outs on NCBI RefSeq gene tracks refs #34704
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 6, context: html, text, full: html, text
    2df91f181b1639297e87adfaee146fedcebd2f4a Mon Oct 21 13:53:37 2024 -0700
    now using hgwdev cluster for lastz runs and lastz only needs 3gb memory to run refs #34688
  • lines changed 15, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 18, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 16, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 16, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
  • lines changed 20, context: html, text, full: html, text
    0cf3bcb238f681f3df0decac63b08b4953d3f455 Sat Oct 26 23:25:21 2024 -0700
    getting TMPDIR set correctly refs #34685
• src/hg/utils/automation/doWindowMasker.pl
  • lines changed 32, context: html, text, full: html, text
    4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700
    the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
• src/hg/utils/automation/pairLastz.sh
  • lines changed 6, context: html, text, full: html, text
    2df91f181b1639297e87adfaee146fedcebd2f4a Mon Oct 21 13:53:37 2024 -0700
    now using hgwdev cluster for lastz runs and lastz only needs 3gb memory to run refs #34688
• src/hg/utils/otto/genCC/doGenCC.py
  • lines changed 2, context: html, text, full: html, text
    c5026c9eeaff1077f67822e478031ef9552fbd47 Tue Oct 22 17:35:33 2024 -0700
    I made a bonehead move when I first made this validation and did not re-assign the variable. This meant that the md5sum values always were md5sum+file name, and since the file names are always different the otto job always ran. This fixes the validation to only run when there is new data. No RM.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    3e6e726f55156e6611cedb85de6865419d6b0762 Mon Oct 28 10:50:33 2024 -0700
    New version number v473
• src/lib/freeType.c
  • lines changed 8, context: html, text, full: html, text
    2870ce9369e7839d7d47ca4c19aa31abb527e53b Tue Oct 22 09:29:43 2024 -0700
    fix strange bug where iconv returns byte order bytes only on the first conversion
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    43478dd5f7f99a50055922832b4b4f140f6cec61 Mon Oct 28 10:49:41 2024 -0700
    v473 final build, refs #34670

• lines changed: 707
• files changed: 55