All File Changes

v434_base to v435_preview (2022-07-18 to 2022-07-25) v435

• src/hg/hgGene/hgGeneData/Human/links.ra
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    e1fb9f2edabe26eaca253ea878486b939d168a27 Wed Jul 20 10:16:48 2022 -0700
    Fixing linkout to MGI from knownGene refs #29774
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    280ab17935232874878663a960a3b5538063276f Wed Jul 20 15:32:04 2022 -0700
    fixing terrible braces error that I introduced in hgc code discovered by Luis, refs #29152
• src/hg/inc/hgFind.h
  • lines changed 2, context: html, text, full: html, text
    76367141415738bfc83da601aeeeaf05d1eee04f Fri Jul 22 11:43:03 2022 -0700
    When searching a bigBed track, search first the trix index if present, and then search on any bigBed indexes. Uniqify the results. Restores behaviour changed by my previous commit while still removing duplicates, refs #29685
• src/hg/js/hgGateway.js
  • lines changed 7, context: html, text, full: html, text
    cb4c22a814d2a23d93d63cd621333be7529a36b2 Fri Jul 22 15:24:08 2022 -0700
    Make gene selections on hgGateway automatically go to hgTracks
• src/hg/js/model/lib/cart.js
  • lines changed 6, context: html, text, full: html, text
    cb4c22a814d2a23d93d63cd621333be7529a36b2 Fri Jul 22 15:24:08 2022 -0700
    Make gene selections on hgGateway automatically go to hgTracks
• src/hg/lib/bigBedFind.c
  • lines changed 4, context: html, text, full: html, text
    8705123ad669501646271bdd1e341af235dcb1fd Fri Jul 22 09:37:38 2022 -0700
    Fix subtle duplicated item bug in bigBed trix searching
  • lines changed 23, context: html, text, full: html, text
    76367141415738bfc83da601aeeeaf05d1eee04f Fri Jul 22 11:43:03 2022 -0700
    When searching a bigBed track, search first the trix index if present, and then search on any bigBed indexes. Uniqify the results. Restores behaviour changed by my previous commit while still removing duplicates, refs #29685
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    76367141415738bfc83da601aeeeaf05d1eee04f Fri Jul 22 11:43:03 2022 -0700
    When searching a bigBed track, search first the trix index if present, and then search on any bigBed indexes. Uniqify the results. Restores behaviour changed by my previous commit while still removing duplicates, refs #29685
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 4, context: html, text, full: html, text
    2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
    adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 79, context: html, text, full: html, text
    6428d3411111567658e7496a9d131dcbe85034f6 Tue Jul 19 11:36:26 2022 -0700
    platypus to platypus per user request refs #29753
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 150, context: html, text, full: html, text
    38596ae2e82cc2e3d6e7b037aaa5bfc609e03177 Wed Jul 20 17:24:33 2022 -0700
    adding 150 human virus genome builds refs #29484
  • lines changed 101, context: html, text, full: html, text
    e027227ddfc859d20fdf629f9ea606b5a578861e Fri Jul 22 22:31:34 2022 -0700
    adding another set of viruses related to human diseases refs #29484
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 29, context: html, text, full: html, text
    2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
    adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 18, context: html, text, full: html, text
    2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
    adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
  • lines changed 2, context: html, text, full: html, text
    7a68602b325c40864c6937bc5803c4afd606bc9d Thu Jul 21 20:19:43 2022 -0700
    customize the track table for viral genomes refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 7, context: html, text, full: html, text
    8f226d9ae51d5aa0907e717fb310cab91a54cf87 Wed Jul 20 17:21:05 2022 -0700
    better choice of common names and manage lower valid track count for viruses refs #29484
• src/hg/makeDb/doc/chm13v2.0userData/build.txt
  • lines changed 9, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3ceca135069039ba2ce2290cc909128f3777dcc4 Fri Jul 22 23:40:38 2022 -0700
    this one GCF_000951615.1_common_carp_genome is in legacy refs #29545
• src/hg/makeDb/doc/hs1/t2t-supplied.txt
  • lines changed 18, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 222, context: html, text, full: html, text
    a15d57f02b4b49c9e3dbceaad6234e340ec96bbd Thu Jul 21 17:04:25 2022 -0700
    improve the legacy index page with a GenArk clade indication refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    fe31f12c7713e5cfa4612a64f70752388646c424 Thu Jul 21 09:25:50 2022 -0700
    catch up listing with zoo241 genomes refs #29545
  • lines changed 1, context: html, text, full: html, text
    5654588935d1aa4ea6cbc928d2b5706d275a6249 Fri Jul 22 23:41:56 2022 -0700
    this one GCA_000738955.1_M_pentadactyla-1.1.1 is in mammals not legacy yet refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    d017527e4dddb716147a243efe2bb38d1acff329 Thu Jul 21 09:27:24 2022 -0700
    catch up listing with zoo241 genomes refs #29545
  • lines changed 1, context: html, text, full: html, text
    41a463cd8f3d221e36fd583e4d58dd12993f0975 Fri Jul 22 23:40:10 2022 -0700
    this one GCA_004026985.1_MyoMyo_v1_BIUU is in legacy refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    035f7ea1c057b4923fc64f7bea14b3bae513ea2e Thu Jul 21 09:24:08 2022 -0700
    catch up listing with zoo241 genomes refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 152, context: html, text, full: html, text
    6cb40b8c7c2d15cf867031a5039a1ed1f198d04f Wed Jul 20 17:18:42 2022 -0700
    adding all human viruses from refseq about 150 refs #29484
  • lines changed 1, context: html, text, full: html, text
    837e1e89d23da949d16c0f9e6cd00eed3788642c Wed Jul 20 19:10:24 2022 -0700
    no need to have SARS-CoV-2 on this list refs #29484
  • lines changed 236, context: html, text, full: html, text
    50060dece064d88d993690dfbb67a802c7d3578e Fri Jul 22 22:51:33 2022 -0700
    adding another set of viruses related to human diseases refs #29484
• src/hg/makeDb/trackDb/human/dbSnp155Composite.html
  • lines changed 44, context: html, text, full: html, text
    18bc9c0ef9b603af3303c4c8c04d36a5b4d97361 Fri Jul 22 15:08:09 2022 -0700
    Updating the descriptions of the project studies for dbSNP 155, refs #27751
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    8bdfaf534e8af7dde7c68c3f5028ca00bc2d7efb Tue Jul 19 10:04:52 2022 -0700
    Adding new snowflake pennantIcont to indicate frozen data, and enabling it on decipher and clinvar. Refs #29694
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.ra
  • lines changed 1, context: html, text, full: html, text
    2b6066907bf54280eb7802af9edf9342fc77832d Wed Jul 20 10:46:27 2022 -0700
    Adding barChartMerge option, so merge button appears to help collapse the manhy many facet groups.
• src/hg/makeDb/trackDb/human/hs1/assembly.trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
    split of sections of trackDb to individual track includes refs #29762trackDb.ra
• src/hg/makeDb/trackDb/human/hs1/catLiftOffGenesV1.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/censat.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/clinVar20220313.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/cpgIslands.trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
    split of sections of trackDb to individual track includes refs #29762trackDb.ra
• src/hg/makeDb/trackDb/human/hs1/cytoBandMapped.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/dbSNP155.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/encode.trackDb.ra
  • lines changed 190, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/gc5Base.trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
    split of sections of trackDb to individual track includes refs #29762trackDb.ra
• src/hg/makeDb/trackDb/human/hs1/gwasSNPs2022-03-08.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/hgCactus.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/hgLiftOver.trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/hgUnique.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
  • lines changed 415, context: html, text, full: html, text
    3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
    split off sections of trackDb to individual track includes refs #29762
• src/hg/makeDb/trackDb/human/hs1/microsatellites.trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/ncbiRefSeq.trackDb.ra
  • lines changed 93, context: html, text, full: html, text
    3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
    split off sections of trackDb to individual track includes refs #29762
• src/hg/makeDb/trackDb/human/hs1/proseq.trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/rdnaModel.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/rnaseq.trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/sedefSegDups.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/sgdpCopyNumber.trackDb.ra
  • lines changed 348, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/simpleRepeat.trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
    split of sections of trackDb to individual track includes refs #29762trackDb.ra
• src/hg/makeDb/trackDb/human/hs1/t2tRepeatMasker.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    976c0e681fc3571f3a449ee2f7cb78400f11ce3e Fri Jul 22 11:39:18 2022 -0700
    moved t2t-supplied tracks out of bbi
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 596, context: html, text, full: html, text
    3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
    split off sections of trackDb to individual track includes refs #29762
• src/hg/makeDb/trackDb/human/hs1/windowMasker.trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
    split off sections of trackDb to individual track includes refs #29762
• src/hg/makeDb/trackDb/human/hs1/xenoRefGene.trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
    split off sections of trackDb to individual track includes refs #29762
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 27, context: html, text, full: html, text
    63016a5603d71b06864a89f83b97921feef7f1e6 Mon Jul 18 15:08:49 2022 -0700
    Removing whole genome queries for JASPAR and expanding the data access section, refs #29697
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    63016a5603d71b06864a89f83b97921feef7f1e6 Mon Jul 18 15:08:49 2022 -0700
    Removing whole genome queries for JASPAR and expanding the data access section, refs #29697
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 17, context: html, text, full: html, text
    d9dda4cb690fb3dddc3a34e6f0ac7093483f21f0 Mon Jul 25 09:03:30 2022 -0700
    adding trackDb for new revel overlaps track on hg19, using release alpha tdb tag, refs #29475
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8bdfaf534e8af7dde7c68c3f5028ca00bc2d7efb Tue Jul 19 10:04:52 2022 -0700
    Adding new snowflake pennantIcont to indicate frozen data, and enabling it on decipher and clinvar. Refs #29694
• src/hg/makeDb/trackDb/loadTracks
  • lines changed 2, context: html, text, full: html, text
    2b469974db57314e2aefab49529896e3ecc12081 Mon Jul 18 13:41:04 2022 -0700
    fix problem where description.html is not copied into place when building alpha or update in trackDb
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    ba64639bd0763cdd192865ff6e3d332c6e2c3066 Tue Jul 19 12:11:59 2022 -0700
    Staging fixing UniProt bugs on hgwbeta, refs #28560
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
  • lines changed 27, context: html, text, full: html, text
    f88c3be6f91a81ff6b7c43854c36a7b0694597f7 Tue Jul 19 08:16:57 2022 -0700
    Adapting Kim et all track short label after discussion with UniProt curator, no redmine (?)
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 24, context: html, text, full: html, text
    3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
    handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 3, context: html, text, full: html, text
    3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
    handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
  • lines changed 20, context: html, text, full: html, text
    5b5a242f38f695c23bc52e5388b941b8335307df Thu Jul 21 20:18:42 2022 -0700
    properly eliminate rmsk from trackDb when there are no items in the track refs #29545
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 32, context: html, text, full: html, text
    3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
    handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
• src/inc/bigBedCmdSupport.h
  • lines changed 13, context: html, text, full: html, text
    04b879361227c44e9602945464b83e5346b5dd4f Tue Jul 19 22:38:07 2022 -0700
    add option to output autoSql style header to bigBedNamedItems
• src/lib/bigBedCmdSupport.c
  • lines changed 24, context: html, text, full: html, text
    04b879361227c44e9602945464b83e5346b5dd4f Tue Jul 19 22:38:07 2022 -0700
    add option to output autoSql style header to bigBedNamedItems
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    04b879361227c44e9602945464b83e5346b5dd4f Tue Jul 19 22:38:07 2022 -0700
    add option to output autoSql style header to bigBedNamedItems
• src/utils/bedSingleCover.pl
  • lines changed 2, context: html, text, full: html, text
    75fb410e4222543ccdc30335f02247649e0d7186 Wed Jul 20 12:51:15 2022 -0700
    output nothing when nothing to output no redmine
• src/utils/bigBedNamedItems/bigBedNamedItems.c
  • lines changed 8, context: html, text, full: html, text
    04b879361227c44e9602945464b83e5346b5dd4f Tue Jul 19 22:38:07 2022 -0700
    add option to output autoSql style header to bigBedNamedItems
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 19, context: html, text, full: html, text
    04b879361227c44e9602945464b83e5346b5dd4f Tue Jul 19 22:38:07 2022 -0700
    add option to output autoSql style header to bigBedNamedItems
• src/utils/qa/imageComp.py
  • lines changed 13, context: html, text, full: html, text
    b2cf390e98648bbb8f4e919a0ad6d923aea3a24f Mon Jul 18 15:17:48 2022 -0700
    Code review edits, refs #29768
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    71ff2cf743374a55fe7fb1bbf2258597a8446666 Mon Jul 25 10:09:59 2022 -0700
    v435 preview1, refs #29716

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• files changed: 76