All File Changes

v452_preview to v452_preview2 (2023-07-24 to 2023-07-31) v452

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8e8d65eb5a1505f99aa100474ef0e5e8ebb288c9 Sun Jul 30 01:11:25 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8e8d65eb5a1505f99aa100474ef0e5e8ebb288c9 Sun Jul 30 01:11:25 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8e8d65eb5a1505f99aa100474ef0e5e8ebb288c9 Sun Jul 30 01:11:25 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPcr/hgPcr.c
  • lines changed 2, context: html, text, full: html, text
    44f007c9ddb5379a7cb74cf44deb865a9fbf8c49 Mon Jul 24 14:34:59 2023 -0700
    disabling the "Append to.." checkbox in hgPcr because the code is broken and Chris is on vacation
  • lines changed 2, context: html, text, full: html, text
    2de160a334786c2168e379c5f02838f4aed40a3b Thu Jul 27 12:20:35 2023 -0700
    Fix two separate hgPcr related bugs. One, the primers entered by the user do not have to match the genome/transcript fully, and so when looking up the primers for showing mismatches we need to ensure we find them by relying on the psl qName rather than the primer file that holds the users input. Second, when clicking through to hgc, ensure that we check that the tStart and tEnd of the psl match what was clicked on so the right amplicon sequence can be shown, in the case that two separate searches that hit the same transcript are visible, refs #31784
• src/hg/hgTracks/cds.c
  • lines changed 18, context: html, text, full: html, text
    2de160a334786c2168e379c5f02838f4aed40a3b Thu Jul 27 12:20:35 2023 -0700
    Fix two separate hgPcr related bugs. One, the primers entered by the user do not have to match the genome/transcript fully, and so when looking up the primers for showing mismatches we need to ensure we find them by relying on the psl qName rather than the primer file that holds the users input. Second, when clicking through to hgc, ensure that we check that the tStart and tEnd of the psl match what was clicked on so the right amplicon sequence can be shown, in the case that two separate searches that hit the same transcript are visible, refs #31784
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/hgTracks/instaPortTrack.c
  • lines changed 104, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    7728ed94d30b671ee68497f22cbbf757e60c59ae Wed Jul 26 13:59:51 2023 -0700
    Updating spaceSaver to permit items to occupy more than one row, refs #31800
  • lines changed 5, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/hgc/hgc.c
  • lines changed 26, context: html, text, full: html, text
    2de160a334786c2168e379c5f02838f4aed40a3b Thu Jul 27 12:20:35 2023 -0700
    Fix two separate hgPcr related bugs. One, the primers entered by the user do not have to match the genome/transcript fully, and so when looking up the primers for showing mismatches we need to ensure we find them by relying on the psl qName rather than the primer file that holds the users input. Second, when clicking through to hgc, ensure that we check that the tStart and tEnd of the psl match what was clicked on so the right amplicon sequence can be shown, in the case that two separate searches that hit the same transcript are visible, refs #31784
  • lines changed 2, context: html, text, full: html, text
    124b0e19b769534dc9df4fde38a33bec0ef02948 Fri Jul 28 13:11:26 2023 -0700
    Quick fix - updating DECIPHER urls, refs #31809
• src/hg/htdocs/images/duplicateTrackUi_GENCODEV43.png
  • lines changed 0, context: html, text, full: html, text
    3a091b777a5bc4d99a1a8ba9cf01465247704614 Wed Jul 26 15:01:47 2023 -0700
    Updating images for the Track Duplication feature documentation, refs #30365
• src/hg/htdocs/images/duplicationHgTracks_GENCODEV43.png
  • lines changed 0, context: html, text, full: html, text
    3a091b777a5bc4d99a1a8ba9cf01465247704614 Wed Jul 26 15:01:47 2023 -0700
    Updating images for the Track Duplication feature documentation, refs #30365
• src/hg/htdocs/images/removeDuplicateTrackUi_GENCODEV43.png
  • lines changed 0, context: html, text, full: html, text
    3a091b777a5bc4d99a1a8ba9cf01465247704614 Wed Jul 26 15:01:47 2023 -0700
    Updating images for the Track Duplication feature documentation, refs #30365
  • lines changed 0, context: html, text, full: html, text
    64631b633b37ab4d68f3302c2a9b767ac69fbddb Thu Jul 27 13:45:36 2023 -0700
    Updating an image for the Track Duplication feature documentation, refs #30365
• src/hg/js/hgSearch.js
  • lines changed 2, context: html, text, full: html, text
    59fe82a7fcfef11d15cecee88ff2e3b7d20d78d8 Wed Jul 26 09:02:26 2023 -0700
    Fix hgSearch overwriting highlights because I was using the wrong variable to add new highlights to cart, refs #31758
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    54bb8a90b15d19a7af840e612125d1656111762d Mon Jul 31 10:16:21 2023 -0700
    Make changes to blue bar state persist in the cart, refs #19739
• src/hg/js/tutorial.js
  • lines changed 7, context: html, text, full: html, text
    36c7bf6775818acf0f16d1875e89fe5e8450cc7d Thu Jul 27 12:46:44 2023 -0700
    Log when users start and end the tutorial, refs Jairo email
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 83, context: html, text, full: html, text
    574a35c43eb5b7eb71a5499785f8e4671e566f53 Sun Jul 30 23:55:00 2023 -0700
    GCA_011100615.1 vs. mm39 lastz/chain/net run for user, refs #30834
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 95, context: html, text, full: html, text
    4bb0fd63fbf7a74d34283455dc3f872d5e0b2037 Sun Jul 30 23:58:44 2023 -0700
    hg38 vs. GCA_011100615.1 lastz/chain/net run for user, refs #30728
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 82, context: html, text, full: html, text
    d6045f07a6bd4aa42e2b415b97f043977a425944 Sun Jul 30 23:48:02 2023 -0700
    mm39 vs. GCA_001624445.1 lastz/chain/net run for user, refs #31040
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 467, context: html, text, full: html, text
    4bd1164a3a35175b1afee0b3e43c8c2d920a3460 Fri Jul 28 17:31:09 2023 -0700
    grouping 447-way into clades and beginning html documentation refs #31528
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 13, context: html, text, full: html, text
    c9dc8cccd55a31241dcc6f989d84e8400724577d Fri Jul 28 16:27:36 2023 -0700
    Fixing a bunch of 200s that became 300s after a global replace, refs #31794
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 1, context: html, text, full: html, text
    829216838880a8608d9acfcbbdf55053ccdb459a Thu Jul 27 18:37:10 2023 -0700
    turning on the summary track refs #31528
  • lines changed 13, context: html, text, full: html, text
    4bd1164a3a35175b1afee0b3e43c8c2d920a3460 Fri Jul 28 17:31:09 2023 -0700
    grouping 447-way into clades and beginning html documentation refs #31528
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.dev.ra
  • lines changed 212, context: html, text, full: html, text
    af6a0c5546f10af81f419b26cc9efe85dd9093fc Mon Jul 31 09:00:47 2023 -0700
    Removing old dev trackDb track that has a broken table associated with it, refs: Galt.
• src/hg/makeDb/trackDb/human/hs1/instaPortHg38.ra
  • lines changed 32, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5bb5421c6fb13dedfd18764abeba5857752bebe9 Fri Jul 28 12:09:25 2023 -0700
    Updating URL for DECIPHER CNVs track, refs #31809
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 5, context: html, text, full: html, text
    6d0dc8601b91fa9cbc3266992a8e26da73704dc5 Thu Jul 27 18:06:38 2023 -0700
    remove instaPort track type
  • lines changed 5, context: html, text, full: html, text
    4bd1164a3a35175b1afee0b3e43c8c2d920a3460 Fri Jul 28 17:31:09 2023 -0700
    grouping 447-way into clades and beginning html documentation refs #31528
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 1, context: html, text, full: html, text
    0ee89729a11ee96e74a5cb52f4acf3ecff24f601 Wed Jul 26 12:14:13 2023 -0700
    Add missing mutation A6948G to path for GJ.1.1 -- pointed out in sars-cov-2-variants/lineage-proposals#465
• src/inc/spaceSaver.h
  • lines changed 7, context: html, text, full: html, text
    7728ed94d30b671ee68497f22cbbf757e60c59ae Wed Jul 26 13:59:51 2023 -0700
    Updating spaceSaver to permit items to occupy more than one row, refs #31800
• src/lib/spaceSaver.c
  • lines changed 72, context: html, text, full: html, text
    7728ed94d30b671ee68497f22cbbf757e60c59ae Wed Jul 26 13:59:51 2023 -0700
    Updating spaceSaver to permit items to occupy more than one row, refs #31800
• src/utils/louisParse/louisParse.c
  • lines changed 13, context: html, text, full: html, text
    684570555dd19fe79c09d401a88efbc1f7ccb334 Tue Jul 25 15:46:35 2023 -0700
    more log data for Louis
• src/utils/qa/hubCheckDraftEmails.py
  • lines changed 1, context: html, text, full: html, text
    a36da3aabda1ec73fdb6a35c7001e53d53f6aff3 Sun Jul 30 21:36:20 2023 -0700
    Making the draftedMessages.txt output file visible through genecats.gi.ucsc.edu, refs #29319
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    dcefa87610e17db0c121768a131a91adbde2c653 Mon Jul 31 10:35:36 2023 -0700
    v452 preview2, refs #31799

• lines changed: 1288
• files changed: 39