All File Changes

v429_preview2 to v429_base (2022-03-28 to 2022-04-04) v429

• confs/hgwdev.hg.conf
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    463db8f9dc1fe5145d9889dda60d4344860dee21 Sun Apr 3 01:11:53 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/annoStreamDb.c
  • lines changed 26, context: html, text, full: html, text
    44b8e80672284df508a24fe193129c9673dc898d Fri Apr 1 11:43:20 2022 -0700
    Fix hgVai bug where position flag resets some memory initialized elsewhere, and also handle NULL mysql result better, refs Lou email
• src/hg/gar/garTable.pl
  • lines changed 19, context: html, text, full: html, text
    aaa182677fc86a82dd4cd7764cdb40a1476cedae Wed Mar 30 12:47:51 2022 -0700
    the selection menus now look like buttons with a down arrow icon and the column headers have an info icon refs #28930
  • lines changed 1, context: html, text, full: html, text
    4e9aedd9195104e098858f5908727498f3ef3e35 Wed Mar 30 15:04:15 2022 -0700
    fixup typo spelling error refs #28930
• src/hg/gar/garTable.sh
  • lines changed 2, context: html, text, full: html, text
    aaa182677fc86a82dd4cd7764cdb40a1476cedae Wed Mar 30 12:47:51 2022 -0700
    the selection menus now look like buttons with a down arrow icon and the column headers have an info icon refs #28930
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    495e22b6189fdf7a84ae089cdb8ac3c4017ad389 Thu Mar 31 14:50:11 2022 -0700
    Must make sure we encode descriptions when re-saving a session, refs #29086
• src/hg/hgTables/bam.c
  • lines changed 14, context: html, text, full: html, text
    3d865319000102f6164e546ddd9c959f67c664ce Wed Mar 30 13:09:30 2022 -0700
    add chromAlias support to bam support
• src/hg/hgTracks/bamTrack.c
  • lines changed 14, context: html, text, full: html, text
    3d865319000102f6164e546ddd9c959f67c664ce Wed Mar 30 13:09:30 2022 -0700
    add chromAlias support to bam support
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    e1f7896a08fb147d663f3a8339f1ad5aea037729 Tue Mar 29 17:04:52 2022 -0700
    make svgBarChart and multiRegionButtonTop be on by default
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 11, context: html, text, full: html, text
    0607b89d9588aa28b12dc406d22331e3e8b013d7 Fri Apr 1 09:09:51 2022 -0700
    sometimes the maf summary table deletes the version numbers from the "other" database. If we don't find the component with a dot, look for one without it
• src/hg/hgc/bamClick.c
  • lines changed 20, context: html, text, full: html, text
    3d865319000102f6164e546ddd9c959f67c664ce Wed Mar 30 13:09:30 2022 -0700
    add chromAlias support to bam support
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    e1f7896a08fb147d663f3a8339f1ad5aea037729 Tue Mar 29 17:04:52 2022 -0700
    make svgBarChart and multiRegionButtonTop be on by default
• src/hg/hgc/hgc.c
  • lines changed 33, context: html, text, full: html, text
    e469259cebde62bf0bf53f582f7f69ba9a22aebc Tue Mar 29 12:28:22 2022 -0700
    allow big* tracks with only a bigDataUrl to be used in Extended DNA coloring page
  • lines changed 2, context: html, text, full: html, text
    6c2bc6c25f4bffc4f9b31ae43ec71462faee80d9 Tue Mar 29 12:55:57 2022 -0700
    accept pgSnp custom tracks in extended DNA color dialog
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 9, context: html, text, full: html, text
    25c2212f3f5f510ad207b568f8652b1732d0d816 Mon Mar 28 15:03:20 2022 -0700
    Clarifying that BLAT supports queries of 4 types, refs #27193
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 1, context: html, text, full: html, text
    0da0030a65de00ed1a63da1213e9ca8c47cb82b4 Mon Mar 28 11:36:53 2022 -0700
    reworded a line that sounded awkward
• src/hg/htdocs/style/gar.css
  • lines changed 12, context: html, text, full: html, text
    d65e9081744ae28115fa8e5063a5d2e8938b3776 Wed Mar 30 12:06:58 2022 -0700
    reset the pull-down selection menus to look like buttons refs #28930
• src/hg/htdocs/training/index.html
  • lines changed 18, context: html, text, full: html, text
    f5a3c90fe99f1420a90522721ca27f792cde1f82 Mon Mar 28 12:06:21 2022 -0700
    added Protugal and Crete workshops
• src/hg/inc/featureBits.h
  • lines changed 1, context: html, text, full: html, text
    e469259cebde62bf0bf53f582f7f69ba9a22aebc Tue Mar 29 12:28:22 2022 -0700
    allow big* tracks with only a bigDataUrl to be used in Extended DNA coloring page
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    796395d2e9ad7e006411e29c451b394a4e760393 Mon Apr 4 10:14:35 2022 -0700
    New version number v429
• src/hg/lib/featureBits.c
  • lines changed 5, context: html, text, full: html, text
    e469259cebde62bf0bf53f582f7f69ba9a22aebc Tue Mar 29 12:28:22 2022 -0700
    allow big* tracks with only a bigDataUrl to be used in Extended DNA coloring page
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    03e01bc588d0e171fdb2487dc036e8c481aad4e8 Wed Mar 30 16:47:50 2022 -0700
    fix bug I introduced last year that breaks ByRange and Min and Max with bigBed filters.
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/build.txt
  • lines changed 8, context: html, text, full: html, text
    76ddee8cdcaad56a1fda557ad11ef437111c4d76 Tue Mar 15 19:19:07 2022 -0700
    added CAT+Liftoff genes
  • lines changed 7, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
  • lines changed 68, context: html, text, full: html, text
    a399d1ddab6d8f7456d94e7bcf4f3e3ef14ddbd3 Mon Mar 28 13:37:31 2022 -0700
    added human reference liftover chain tracks
  • lines changed 9, context: html, text, full: html, text
    4d85bbb2c1aee65ec5d504ebf123c23043da10a4 Mon Mar 28 16:23:38 2022 -0700
    move liftOver files to standard locations and simplify makefile
  • lines changed 31, context: html, text, full: html, text
    150df3f02a2b9f29e9c21d2de1d9db608fc8c574 Tue Mar 29 09:55:40 2022 -0700
    make naming of chain tracks consistent with browser; added mask file
  • lines changed 7, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 2, context: html, text, full: html, text
    94f37bab4351f8d08dcee2d168a7d12ba6621719 Tue Mar 29 15:46:31 2022 -0700
    moved liftOver track and renamed
  • lines changed 69, context: html, text, full: html, text
    79b2fe41306f412f04b9148e7ea23c997b97301f Tue Mar 29 22:24:11 2022 -0700
    added censat track
  • lines changed 53, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
  • lines changed 7, context: html, text, full: html, text
    a5e35bab38e9500347ce8262090777322be91560 Wed Mar 30 21:55:02 2022 -0700
    updated hg19 liftOver tracks to add in missing chroms
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/catLiftOffGenes.html
  • lines changed 104, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/catLiftOffGenesV1.html
  • lines changed 104, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/censat.html
  • lines changed 34, context: html, text, full: html, text
    79b2fe41306f412f04b9148e7ea23c997b97301f Tue Mar 29 22:24:11 2022 -0700
    added censat track
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/clinVar20220313.html
  • lines changed 14, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/dbSNP155.html
  • lines changed 14, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/gwasSNPs2022-03-08.html
  • lines changed 14, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgCactus.html
  • lines changed 44, context: html, text, full: html, text
    94f37bab4351f8d08dcee2d168a7d12ba6621719 Tue Mar 29 15:46:31 2022 -0700
    moved liftOver track and renamed
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgLiftOver.html
  • lines changed 89, context: html, text, full: html, text
    a399d1ddab6d8f7456d94e7bcf4f3e3ef14ddbd3 Mon Mar 28 13:37:31 2022 -0700
    added human reference liftover chain tracks
  • lines changed 4, context: html, text, full: html, text
    4d85bbb2c1aee65ec5d504ebf123c23043da10a4 Mon Mar 28 16:23:38 2022 -0700
    move liftOver files to standard locations and simplify makefile
  • lines changed 7, context: html, text, full: html, text
    150df3f02a2b9f29e9c21d2de1d9db608fc8c574 Tue Mar 29 09:55:40 2022 -0700
    make naming of chain tracks consistent with browser; added mask file
  • lines changed 1, context: html, text, full: html, text
    9608f328dbc9337ee107fa01a40b948657f07709 Tue Mar 29 10:12:14 2022 -0700
    updated liftover alignment labels
  • lines changed 4, context: html, text, full: html, text
    9f07e62e4e0365ac134e37a9aae3442cf5fe1dc9 Fri Apr 1 16:59:09 2022 -0700
    typo error for link fixed refs #29182
  • lines changed 1, context: html, text, full: html, text
    072c63e3652fb81f83a3db79363a0f841a488aae Fri Apr 1 17:13:40 2022 -0700
    type error for liftover-mask.bed reference refs #29182
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgUnique.html
  • lines changed 28, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
  • lines changed 36, context: html, text, full: html, text
    633d579bebb659ba2e74d036d06560dc37c574f4 Wed Mar 30 22:27:29 2022 -0700
    updated unique regions
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/sedefSegDups.html
  • lines changed 3, context: html, text, full: html, text
    deb2cc2117baca732f1ce86e6e63d10d0710a033 Wed Mar 16 17:05:19 2022 -0700
    update citation for sedefSegDups
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/makefile
  • lines changed 3, context: html, text, full: html, text
    76ddee8cdcaad56a1fda557ad11ef437111c4d76 Tue Mar 15 19:19:07 2022 -0700
    added CAT+Liftoff genes
  • lines changed 1, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
  • lines changed 1, context: html, text, full: html, text
    a399d1ddab6d8f7456d94e7bcf4f3e3ef14ddbd3 Mon Mar 28 13:37:31 2022 -0700
    added human reference liftover chain tracks
  • lines changed 29, context: html, text, full: html, text
    4d85bbb2c1aee65ec5d504ebf123c23043da10a4 Mon Mar 28 16:23:38 2022 -0700
    move liftOver files to standard locations and simplify makefile
  • lines changed 1, context: html, text, full: html, text
    150df3f02a2b9f29e9c21d2de1d9db608fc8c574 Tue Mar 29 09:55:40 2022 -0700
    make naming of chain tracks consistent with browser; added mask file
  • lines changed 7, context: html, text, full: html, text
    94f37bab4351f8d08dcee2d168a7d12ba6621719 Tue Mar 29 15:46:31 2022 -0700
    moved liftOver track and renamed
  • lines changed 2, context: html, text, full: html, text
    79b2fe41306f412f04b9148e7ea23c997b97301f Tue Mar 29 22:24:11 2022 -0700
    added censat track
  • lines changed 1, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/schema/cenSat.as
  • lines changed 14, context: html, text, full: html, text
    79b2fe41306f412f04b9148e7ea23c997b97301f Tue Mar 29 22:24:11 2022 -0700
    added censat track
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/catLiftOffGenes.trackDb.txt
  • lines changed 17, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/catLiftOffGenesV1.trackDb.txt
  • lines changed 17, context: html, text, full: html, text
    e6908b59adab1653c4fe5d149e4e5711bcc8b65e Wed Mar 16 08:04:34 2022 -0700
    indicate version number in catLiftOffGenes dataset
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/censat.trackDb.txt
  • lines changed 11, context: html, text, full: html, text
    79b2fe41306f412f04b9148e7ea23c997b97301f Tue Mar 29 22:24:11 2022 -0700
    added censat track
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    eadd2058507213bb801b09cfedff55a40ae5492c Tue Mar 29 22:34:41 2022 -0700
    add mouseover to censat
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/clinVar20220313.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/dbSNP155.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/gwasSNPs2022-03-08.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgCactus.trackDb.txt
  • lines changed 46, context: html, text, full: html, text
    94f37bab4351f8d08dcee2d168a7d12ba6621719 Tue Mar 29 15:46:31 2022 -0700
    moved liftOver track and renamed
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgLiftOver.trackDb.txt
  • lines changed 33, context: html, text, full: html, text
    a399d1ddab6d8f7456d94e7bcf4f3e3ef14ddbd3 Mon Mar 28 13:37:31 2022 -0700
    added human reference liftover chain tracks
  • lines changed 4, context: html, text, full: html, text
    150df3f02a2b9f29e9c21d2de1d9db608fc8c574 Tue Mar 29 09:55:40 2022 -0700
    make naming of chain tracks consistent with browser; added mask file
  • lines changed 3, context: html, text, full: html, text
    9608f328dbc9337ee107fa01a40b948657f07709 Tue Mar 29 10:12:14 2022 -0700
    updated liftover alignment labels
  • lines changed 7, context: html, text, full: html, text
    94f37bab4351f8d08dcee2d168a7d12ba6621719 Tue Mar 29 15:46:31 2022 -0700
    moved liftOver track and renamed
• src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgUnique.trackDb.txt
  • lines changed 34, context: html, text, full: html, text
    9a80954c855303d4a534f54661497d14a8f62d7c Wed Mar 30 21:26:31 2022 -0700
    added dbSNP155, clinVar20220313, and gwasSNPs2022-03-08 tracks
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
  • lines changed 76, context: html, text, full: html, text
    74a95a0342332cbd7594d930ef1a2fa4b7ceedfb Fri Apr 1 14:12:08 2022 -0700
    procedure for crisprAll refs #29123
• src/hg/makeDb/doc/hg19.txt
  • lines changed 36, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 19, context: html, text, full: html, text
    f59b87d2038e90c7969da0fa0cc3652d41720881 Wed Mar 30 12:34:29 2022 -0700
    create hg19/hg39 CHM13 liftover chains using NCBI names for now
• src/hg/makeDb/doc/hg38/chm13LiftOver.txt
  • lines changed 38, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 18, context: html, text, full: html, text
    f59b87d2038e90c7969da0fa0cc3652d41720881 Wed Mar 30 12:34:29 2022 -0700
    create hg19/hg39 CHM13 liftover chains using NCBI names for now
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 276, context: html, text, full: html, text
    12b6db960b81f9c254ca6f864052b7ef58e20e91 Wed Mar 30 15:09:57 2022 -0700
    chainNet lastz runs to CHM13, HG002 maternal, and HG002 paternal refs #28907
• src/hg/makeDb/trackDb/human/chainNetHuman.ra
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    c371f31291a175307f0bd092439a802edee30894 Wed Mar 30 10:37:22 2022 -0700
    adding in chainNet composite for alignments to CHM13 and the two HG002 assemblies refs #28907
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    7fa908f40df50ecd4d078811aea7c25c5556c63a Fri Apr 1 16:47:11 2022 -0700
    documentation for the human chainNets refs #29189
• src/hg/makeDb/trackDb/human/hg19/chm13LiftOver.html
  • lines changed 69, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 14, context: html, text, full: html, text
    118d97cafd3ac159446d7a01e53875b01c365177 Thu Mar 31 15:33:26 2022 -0700
    Sprucing up the desc pages for chain track, refs #29182
• src/hg/makeDb/trackDb/human/hg19/chm13LiftOver.ra
  • lines changed 10, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 3, context: html, text, full: html, text
    f59b87d2038e90c7969da0fa0cc3652d41720881 Wed Mar 30 12:34:29 2022 -0700
    create hg19/hg39 CHM13 liftover chains using NCBI names for now
  • lines changed 2, context: html, text, full: html, text
    5366458e3c57ce432a2d328482dabbde159528c8 Fri Apr 1 16:11:32 2022 -0700
    Fixing what was probably typo, was dispalying hg38 chains instead of hg19. Refs #29182
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
• src/hg/makeDb/trackDb/human/hg38/chm13LiftOver.html
  • lines changed 78, context: html, text, full: html, text
    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
  • lines changed 19, context: html, text, full: html, text
    118d97cafd3ac159446d7a01e53875b01c365177 Thu Mar 31 15:33:26 2022 -0700
    Sprucing up the desc pages for chain track, refs #29182
• src/hg/makeDb/trackDb/human/hg38/chm13LiftOver.ra
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    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
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    f59b87d2038e90c7969da0fa0cc3652d41720881 Wed Mar 30 12:34:29 2022 -0700
    create hg19/hg39 CHM13 liftover chains using NCBI names for now
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    3445474d3a3568bf41d3f9e9fce71fc54a795bd3 Tue Mar 29 15:42:24 2022 -0700
    add missing "table" record to knownGene which tells hgTables to use that table instead of the bigGenePred
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    e5f2b5cb689c5bd5c71872a400884d70cd4d2413 Tue Mar 29 13:05:59 2022 -0700
    Added liftover chains for T2T CHM13. Clicking on these currently fails due to chromAlias issues.
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    c371f31291a175307f0bd092439a802edee30894 Wed Mar 30 10:37:22 2022 -0700
    adding in chainNet composite for alignments to CHM13 and the two HG002 assemblies refs #28907
• src/hg/makeDb/trackDb/human/homoSapiensChainNet.html
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    addf10d08062993a60b45e52df8ddcdba57a8778 Fri Apr 1 16:46:52 2022 -0700
    documentation for the human chainNets refs #29189
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    6cda00dc26e57ab505aa0c21746960e0aaa5cc73 Fri Apr 1 16:54:51 2022 -0700
    listing the genomes refs #29189
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    b8501c7e5a045eb8434221824216c711f111dd2a Fri Apr 1 17:01:44 2022 -0700
    Fixing small typo, refs #29189
• src/hg/makeDb/trackDb/humanChainNet.html
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    eed5b92e1fea673976546c6cdfe47a9414a9c33a Thu Mar 31 15:49:42 2022 -0700
    Updating assembly to correct hg38, refs #29189
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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    00ed3e61b7e4a4ddca896ff1671ab0bd664a6e85 Tue Mar 29 16:04:50 2022 -0700
    rewind mm39 on dev back to VM27 for knownGene, fix problem with hgTables using the wrong table
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    00ed3e61b7e4a4ddca896ff1671ab0bd664a6e85 Tue Mar 29 16:04:50 2022 -0700
    rewind mm39 on dev back to VM27 for knownGene, fix problem with hgTables using the wrong table
• src/hg/makeDb/trackDb/rmsk.html
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    675d1eaac3a4f636444eb9e2056a1f1c5185b6c9 Fri Apr 1 16:30:36 2022 -0700
    Adding a note about rmsk process from MLQ #29181
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
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    c9f040b7cd79e62f2082a62fb0ae6ccbc90b02c6 Tue Mar 29 12:49:56 2022 -0700
    adding chainNet definition to CHM13 T2T GCA_009914755.4 assembly hub refs #28907
• src/hg/utils/automation/doAssemblyHub.pl
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    8b71be65ac62a68201a8681bc3e7bce756011487 Mon Mar 28 12:45:39 2022 -0700
    correct symlink for chromAlias.bb refs #27228
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    f587c6cd4ffa90b371583bbbf80373172b9ca885 Mon Mar 28 16:22:32 2022 -0700
    Added some more proposed recombinant lineages.
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    55553375e86d3efd4ab9dfcc153af6cf4b533b6c Mon Mar 28 20:34:31 2022 -0700
    Added AY.29.2, recombinant lineages X[G-L] and BA.2.[4-8] -- pango-designation releases v1.2.134 - v1.2.136.
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    3785ce567802bded5290ea2c462a80e82c2b72ca Tue Mar 29 15:07:38 2022 -0700
    Mask a couple sites for BA.1.1.1 that seem especially reversion-prone. Add proposed recombinant from pango-designation issue 472.
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    fe18535e3c8f3cb73f5e1255ab80365ea3d2d65c Tue Mar 29 16:45:43 2022 -0700
    Added BA.1.18 and BA.1.19 -- pango-designation v1.2.137
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    72fbe4500f9be4c2fc30cf70cd51663f64b56059 Thu Mar 31 22:39:33 2022 -0700
    Added AY.112.2, B.1.641 and renamed proposed472 to XM -- pango-designation releases v1.2.138-139
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    7d5aa04e69f02d055862f06cb8ed6244d41f18f3 Fri Apr 1 17:14:54 2022 -0700
    Added new lineages BA.1.17.2, BA.2.9, BA.2.10, BA.2.3.1, and renamed proposed480 to XN, proposed481 to XP, proposed468 to XQ, proposed469 to XR and proposed471 to XS -- pango-designation v1.2.140-141
• src/inc/srcVersion.h
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    796395d2e9ad7e006411e29c451b394a4e760393 Mon Apr 4 10:14:35 2022 -0700
    New version number v429
• src/utils/qa/hubPublicAutoUpdate
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    aa86873a1b9db21febf28de22752ee27a5778730 Wed Mar 30 15:53:42 2022 -0700
    Adding a -s flag to suppress and reduce cron emails, no RM
• src/utils/qa/weeklybld/buildEnv.csh
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    75dd61f05af43a6731247983b5204f08bd6a81cb Mon Apr 4 10:13:14 2022 -0700
    v429 final build, refs #29124

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