All File Changes

v435_preview to v435_preview2 (2022-07-25 to 2022-08-01) v435

• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    56ac43cdbbbee7f709fa9f6dc02fa8f71a8f5dac Sun Jul 31 01:11:24 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 35, context: html, text, full: html, text
    4db401fb2e91accfcf9ffcd3478b2f3d7881eb90 Wed Jul 27 06:50:50 2022 -0700
    fixing plus buttons and yet another bug with the copy button, refs #29583
  • lines changed 3, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 9, context: html, text, full: html, text
    ed1738b3b8296a6b7e7376336f054eae0b2c88c6 Wed Jul 27 03:09:02 2022 -0700
    adding clearer section header to genes faq, refs #29778
• src/hg/inc/hdb.h
  • lines changed 1, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/js/hgGateway.js
  • lines changed 7, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
• src/hg/js/hgHubConnect.js
  • lines changed 15, context: html, text, full: html, text
    4db401fb2e91accfcf9ffcd3478b2f3d7881eb90 Wed Jul 27 06:50:50 2022 -0700
    fixing plus buttons and yet another bug with the copy button, refs #29583
• src/hg/js/hgTracks.js
  • lines changed 14, context: html, text, full: html, text
    c65238ee792df4c552cb0716c4717a7b2ffbc3cf Wed Jul 27 05:27:24 2022 -0700
    fixing right-click problem onto highlights when the user clicks onto the left half of a bp, refs #29783
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/makeDb/dbDbToHubTxt/dbDbToHubTxt.c
  • lines changed 92, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/makeDb/dbDbToHubTxt/makefile
  • lines changed 3, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 3, context: html, text, full: html, text
    06d5e84beb82bba46586825f5f9447d5b570c132 Thu Jul 28 12:38:23 2022 -0700
    invertebrate genbank assembly can have as few as 11 tracks refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    2d4d3b7f9c58533f6deedb51ef61543b2d08166d Wed Jul 27 14:35:38 2022 -0700
    adding GCA_003013265.1_ASM301326v1 per user request refs #29545
• src/hg/makeDb/makefile
  • lines changed 3, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/makeDb/trackDb/dbDbToHubTxt
  • lines changed 51, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
  • lines changed 51, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/hg/makeDb/trackDb/human/hs1/assembly.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/cpgIslands.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/gc5Base.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/hubAndGenome.txt
  • lines changed 27, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
• src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
  • lines changed 64, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/ncbiRefSeq.trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/simpleRepeat.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/windowMasker.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/hs1/xenoRefGene.trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cfb6109e173c6023056e0afa30b46ecd2214bbf3 Wed Jul 27 15:07:14 2022 -0700
    renaming bbi and ixIxx file names to eliminate the GCA_009914755.4_T2T-CHM13v2.0 prefix on everything refs #29762
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 2, context: html, text, full: html, text
    14b689e5b1445efaa903e8715103cace098b3d7a Wed Jul 27 14:09:16 2022 -0700
    Feedback from CR refs #29797
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    14b689e5b1445efaa903e8715103cace098b3d7a Wed Jul 27 14:09:16 2022 -0700
    Feedback from CR refs #29797
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    14b689e5b1445efaa903e8715103cace098b3d7a Wed Jul 27 14:09:16 2022 -0700
    Feedback from CR refs #29797
• src/hg/makeDb/trackDb/maybeBuildHub
  • lines changed 3, context: html, text, full: html, text
    a30c400ad09e9ae41fbbf7636deed814a86e1edd Thu Jul 28 17:34:22 2022 -0700
    Build hub and genome stanzas for curated hubs from dbDb. Don't show curated assemblies as hubs on hgGateway or hgHubConnect.
  • lines changed 1, context: html, text, full: html, text
    50134b292a47af4ae93e22cc4f7d290c0a46262e Fri Jul 29 11:28:29 2022 -0700
    rewrite utility to take dbDb to assembly hubAndGenomes.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    045e9b0dd7f28ee6e922da51f4fc75b815e95b31 Mon Aug 1 10:04:34 2022 -0700
    v435 preview2, refs #29802

• lines changed: 413
• files changed: 32