File Changes for chmalee

v456_base to v457_preview (2023-10-30 to 2023-11-06) v457

• src/hg/cgilib/cartJson.c
  • lines changed 51, context: html, text, full: html, text
    401691176ea0ade97d1c643bc2ed4c382fee1ef2 Fri Nov 3 16:59:50 2023 -0700
    Fix multi-term searches when using genomePosCJ: 1. make sure to collapse hgps together and combine highlight strings and item highlight names, 2. make sure hgSearch checks the json data returned during its init function if there was an error from the search term, such as different chromosomes for a multi-term search, refs #22978
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    dad13f95ddaaa0f9c9b111fdc6454b0a3053c1c0 Tue Oct 31 10:56:18 2023 -0700
    Fix broken tables on hgc pages for tracks with the detailsDynamicTable setting, refs #32269,#32519
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    401691176ea0ade97d1c643bc2ed4c382fee1ef2 Fri Nov 3 16:59:50 2023 -0700
    Fix multi-term searches when using genomePosCJ: 1. make sure to collapse hgps together and combine highlight strings and item highlight names, 2. make sure hgSearch checks the json data returned during its init function if there was an error from the search term, such as different chromosomes for a multi-term search, refs #22978
• src/hg/js/hgc.js
  • lines changed 1, context: html, text, full: html, text
    dad13f95ddaaa0f9c9b111fdc6454b0a3053c1c0 Tue Oct 31 10:56:18 2023 -0700
    Fix broken tables on hgc pages for tracks with the detailsDynamicTable setting, refs #32269,#32519
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    c92b5b790779371b350dbee33d0d7383d3bd6f91 Thu Nov 2 10:58:21 2023 -0700
    Fix mouseover pop up positioning when the pop up would normally be off the top of the window, refs #32011
  • lines changed 56, context: html, text, full: html, text
    7d7ba731c432325f1b3c235402a5af54b23e1ec7 Fri Nov 3 14:59:07 2023 -0700
    Make user clicks into an input or select or contextmenu make tooltips go away. Also decrease fudgeFactor on mousemove so tooltips are a little more senstitive and turn off faster, refs Max email
• src/hg/lib/hdb.c
  • lines changed 10, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/lib/hgHgvs.c
  • lines changed 50, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
  • lines changed 2, context: html, text, full: html, text
    c3c923b6c7177c78d5dd26d21f0c623a528ae6fe Tue Oct 31 14:49:09 2023 -0700
    Fix one bug found by Angie for historical transcript querying, should be checking for empty result, not NotEmpty result. Also sort quick query when user does not include a transcript version to order the results by newest historical transcripts first
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 33, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 114, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 32, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
  • lines changed 2, context: html, text, full: html, text
    b8e4242557b46708572e17672d117b8a7de068a3 Thu Nov 2 15:25:22 2023 -0700
    Add link to gnomad for v4 vcf tracks, refs #32545
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 278, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 20, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.err
  • lines changed 2, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 1, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.