All File Changes

v429_preview to v429_preview2 (2022-03-21 to 2022-03-28) v429

• src/hg/cgilib/annoStreamDb.c
  • lines changed 9, context: html, text, full: html, text
    5a884a9bce7e45d3f30423fd8e2e26bb7bc44b80 Wed Mar 23 10:50:57 2022 -0700
    Fix memory error revealed by Lou & valgrind: use rowBuf in nextRowFromSqlResult so hashJoin doesn't write past end of mysql row storage.
• src/hg/gar/garTable.pl
  • lines changed 4, context: html, text, full: html, text
    7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700
    most recent set of corrections refs #28961
• src/hg/gar/garTable.sh
  • lines changed 2, context: html, text, full: html, text
    7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700
    most recent set of corrections refs #28961
• src/hg/gar/rebuild.sh
  • lines changed 1, context: html, text, full: html, text
    7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700
    most recent set of corrections refs #28961
• src/hg/hgBlat/hgBlat.c
  • lines changed 4, context: html, text, full: html, text
    ddc80a927bfe5a53a792423cdc033f76f60f7977 Thu Mar 24 14:35:33 2022 -0700
    Adding links to BLAT json functionality to both the hgBlat CGI and the API page, refs #27193
• src/hg/hgSession/hgSession.c
  • lines changed 13, context: html, text, full: html, text
    07c4566bd0dc7ca669b4720b5b3a3e0b70f5a92b Mon Mar 28 01:48:37 2022 -0700
    Prevent adding a public session with no description from the 'edit details' checkbox, refs #21229
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    4801840ccde60df9698ce24f249392afac8fc55d Thu Mar 24 13:23:07 2022 -0700
    fix problem getting table dumps from hgTables on custom tracks on assembly hubs
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    6dc788ffecb06424dfa24f1ccae8970ecd8b9490 Thu Mar 24 13:36:11 2022 -0700
    restore alias printout when bigBed is used for alias refs #27228
  • lines changed 8, context: html, text, full: html, text
    cc2335c2d1f3f50ff9e1deb19172c2695db65339 Thu Mar 24 13:52:45 2022 -0700
    correctly link to chromAlias.txt instead of chromAlias.bb to display in the chromInfo page as a link to view refs #27228
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    e06f749516a194b916fb998122236a2c861fd455 Mon Mar 21 13:35:48 2022 -0700
    remove a check that prevents logo display on data sources with very small values
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 15, context: html, text, full: html, text
    172860595b76a888af59d255a98233983f2b14e1 Thu Mar 24 14:23:57 2022 -0700
    Adding entry about JSON url format for blat, refs #27193
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 2, context: html, text, full: html, text
    8a7cb4e91e585e31ef4cde11ee0e2e8a5798fc5b Mon Mar 21 14:34:46 2022 -0700
    Fixing a MySQL example I added that used hgsql in FAQgenes
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 2, context: html, text, full: html, text
    ddc80a927bfe5a53a792423cdc033f76f60f7977 Thu Mar 24 14:35:33 2022 -0700
    Adding links to BLAT json functionality to both the hgBlat CGI and the API page, refs #27193
• src/hg/htdocs/inc/garModal.html
  • lines changed 2, context: html, text, full: html, text
    7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700
    most recent set of corrections refs #28961
• src/hg/htdocs/style/gar.css
  • lines changed 7, context: html, text, full: html, text
    7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700
    most recent set of corrections refs #28961
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    41855a7fc178981d5b82c8b5bd7ad545763c738d Fri Mar 25 08:47:29 2022 -0700
    removing completed ASHG, adding NHGRI
  • lines changed 13, context: html, text, full: html, text
    e6a53c2fd65b6c6f1a5b3590fb211dc531b17b8d Sun Mar 27 14:02:14 2022 -0700
    adding netherlands course
  • lines changed 8, context: html, text, full: html, text
    ea4e30110f58e90834aa4ca91418018c6ae5a520 Sun Mar 27 14:50:04 2022 -0700
    adding Leiden workshop
• src/hg/js/gar.js
  • lines changed 40, context: html, text, full: html, text
    e1682f6a0c29bb52840fb969f636e62ef255120f Wed Mar 23 15:24:04 2022 -0700
    better clearing of the fields in the modal request form refs #28930
  • lines changed 1, context: html, text, full: html, text
    0fa05b3e9ee790c70332b1fdf90724c1f7ff8d30 Thu Mar 24 12:37:28 2022 -0700
    adding gar.js to the build refs #28930
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    0fa05b3e9ee790c70332b1fdf90724c1f7ff8d30 Thu Mar 24 12:37:28 2022 -0700
    adding gar.js to the build refs #28930
• src/hg/lib/evaSnp.as
  • lines changed 2, context: html, text, full: html, text
    ba8f65526e0188c88d6f493077eb0203e3607269 Mon Mar 21 10:33:02 2022 -0700
    swapped two fields to more logical order
  • lines changed 1, context: html, text, full: html, text
    4d295f9eff3c03708dfbac9b85e144b9cbf2d291 Mon Mar 21 10:38:39 2022 -0700
    make clear its a different type of class than EVA class
  • lines changed 1, context: html, text, full: html, text
    8792e23284008aaca386cbb63d0b760370a45b61 Mon Mar 21 18:56:15 2022 -0700
    Changing aaChange to lstring since it can be over 256 char limit. No RM
  • lines changed 0, context: html, text, full: html, text
    161a2d866f2d8f5a3360f3add176142a891757c3 Mon Mar 21 19:00:04 2022 -0700
    Removing little extra space added accidentally.
• src/hg/lib/joiner.c
  • lines changed 2, context: html, text, full: html, text
    4801840ccde60df9698ce24f249392afac8fc55d Thu Mar 24 13:23:07 2022 -0700
    fix problem getting table dumps from hgTables on custom tracks on assembly hubs
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 1, context: html, text, full: html, text
    9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 90, context: html, text, full: html, text
    7026265ab12f9aa4715453d5c84cdb703d2f4220 Mon Mar 21 16:30:12 2022 -0700
    water buffalo GCF_003121395.1 vs. Cow BosTau9 lastz/chain/net run for user, refs #29082
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 20, context: html, text, full: html, text
    9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
  • lines changed 3, context: html, text, full: html, text
    06c419b9e75122f425657acb9e4fbde86cce7786 Sat Mar 26 07:56:58 2022 -0700
    wait until v429 code gets out to turn on use of chromAlias.bb refs #27228
• src/hg/makeDb/doc/asmHubs/mkSendList.pl
  • lines changed 1, context: html, text, full: html, text
    9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 2, context: html, text, full: html, text
    9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 737, context: html, text, full: html, text
    442a1805ac02af026daeb9b8461de17b4a9ed1f4 Mon Mar 21 14:05:56 2022 -0700
    updated track to include VAI annotations. Refs #28894
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
• src/hg/makeDb/trackDb/dog/canFam3/evaSnp.html
  • lines changed 41, context: html, text, full: html, text
    442a1805ac02af026daeb9b8461de17b4a9ed1f4 Mon Mar 21 14:05:56 2022 -0700
    updated track to include VAI annotations. Refs #28894
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    442a1805ac02af026daeb9b8461de17b4a9ed1f4 Mon Mar 21 14:05:56 2022 -0700
    updated track to include VAI annotations. Refs #28894
• src/hg/makeDb/trackDb/human/hg38/snpCnvArrays.html
  • lines changed 23, context: html, text, full: html, text
    d51a86191aebb935efb9ff366d170f9e7098c729 Thu Mar 24 10:50:42 2022 -0700
    Wording changes form snp track #23591
• src/hg/utils/automation/aliasBedToCt.pl
  • lines changed 85, context: html, text, full: html, text
    1dea84ee820d50f05255371bdaaf6d7b98f220ca Wed Mar 23 17:03:10 2022 -0700
    adding construction of bigBed file for chromAlias refs #29111
  • lines changed 22, context: html, text, full: html, text
    57a8f0f882e83e90b2eb0546bc84225530690689 Thu Mar 24 12:40:59 2022 -0700
    and construct the test custom track files and bigBeds refs #29111
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 11, context: html, text, full: html, text
    1dea84ee820d50f05255371bdaaf6d7b98f220ca Wed Mar 23 17:03:10 2022 -0700
    adding construction of bigBed file for chromAlias refs #29111
• src/hg/utils/automation/asmHubChromAlias.pl
  • lines changed 162, context: html, text, full: html, text
    1dea84ee820d50f05255371bdaaf6d7b98f220ca Wed Mar 23 17:03:10 2022 -0700
    adding construction of bigBed file for chromAlias refs #29111
  • lines changed 6, context: html, text, full: html, text
    2113f4ab5376a69e9169e34db99d99a6ce20f8d5 Fri Mar 25 12:05:18 2022 -0700
    better name for refSeq variable refs #29111
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 19, context: html, text, full: html, text
    1dea84ee820d50f05255371bdaaf6d7b98f220ca Wed Mar 23 17:03:10 2022 -0700
    adding construction of bigBed file for chromAlias refs #29111
  • lines changed 5, context: html, text, full: html, text
    a2c648a9f1539f12cfab4a5642b20e3550e9cd2e Fri Mar 25 13:54:35 2022 -0700
    now using a bigBed file for chromAlias function refs #27228
  • lines changed 3, context: html, text, full: html, text
    13bfd800b82e7439df8f5dce583676890139d3c4 Mon Mar 28 09:56:25 2022 -0700
    create bpt during addMask refs #28961
• src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
  • lines changed 59, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.out
  • lines changed 2, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.psl
  • lines changed 5, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.bigRmskIn
  • lines changed 9, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.sizes
  • lines changed 1, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/hg/utils/rmskAlignToPsl/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    47b962229a3ebcd05377a52db7d389d48a5f38fa Fri Mar 25 09:08:31 2022 -0700
    added option to specify expected repeat sizes and discard PSLs that don't match
• src/lib/bbiAlias.c
  • lines changed 1, context: html, text, full: html, text
    5fbeef52986052068fcf6316a433908211fe4f65 Fri Mar 25 11:27:52 2022 -0700
    add a little comment to make it more clear how bbiAliasChromSize works
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    a0cb952a13f4567168f9be96c44b6cb4adf67f50 Wed Mar 23 11:09:14 2022 -0700
    Adding pairLastzWrapper.py to the makefile, refs #23122
• src/utils/qa/pairLastzWrapper.py
  • lines changed 188, context: html, text, full: html, text
    269136d8d81138891ee5df1ab47e5e6b42676bed Wed Mar 23 10:46:18 2022 -0700
    Adding a wrapper script for pairLastz.sh, refs #23122
  • lines changed 1, context: html, text, full: html, text
    4329d3be64083601aa9e9e4804d2c479bba780be Fri Mar 25 11:51:07 2022 -0700
    Updating the pairLastzWrapper.py shebang line to have python3, refs #23122
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    5bac348b99d46fa3896bda794d10569145a8380e Mon Mar 28 10:08:24 2022 -0700
    v429 preview2, refs #29124

• lines changed: 1687
• files changed: 56