File Changes for angie

v399_preview to v399_preview2 (2020-05-18 to 2020-05-25) v399

• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    e13ac2383aa17a7f37bbea1526a8617af7b0f75d Tue May 19 09:58:20 2020 -0700
    Bugfix: itemLabel argument to printCustomUrlWithFields and printCustomUrlWithLabel was ignored. tangentially refs #25595 When a different itemLabel and itemName were passed into printCustomUrlWithFields, itemLabel was ignored for two reasons: 1. In printCustomUrlWithFields, itemName was passed into printCustomUrlWithLabel as both itemName and itemLabel arguments. 2. In printCustomUrlWithLabel, itemLabel was used only if it was the same as itemName, which kind of defeats the purpose of itemLabel.
• src/hg/hgc/vcfClick.c
  • lines changed 17, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 19, context: html, text, full: html, text
    2fb7246ce3bc2e617fd0194fa70fb11760ccf4e7 Mon May 18 14:44:05 2020 -0700
    hg19 description: Update the 'Note on chrM' to mention chrMT; add a bit more about p13 to 'Chromosome naming scheme'. refs #24648
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 23, context: html, text, full: html, text
    8301244fdedfac4e73bd039410be5b7c729abd70 Mon May 18 10:45:02 2020 -0700
    trackDb updates for release of hg19 p13+MT - thanks Ann for noticing we missed these earlier! refs #24648
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 32, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    8301244fdedfac4e73bd039410be5b7c729abd70 Mon May 18 10:45:02 2020 -0700
    trackDb updates for release of hg19 p13+MT - thanks Ann for noticing we missed these earlier! refs #24648
  • lines changed 17, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 18, context: html, text, full: html, text
    5bec29ddc58c05e2609f5c2409c93ce301e541fd Tue May 19 10:11:35 2020 -0700
    VCF details: replace hardcoded URLs for ExAC and gnomAD tracks with enhanced substitution variable support so urls can be specified by trackDb. refs #25595 vcfClick.c still has custom code for ExAC and gnomAD url labels in case the item ID is ".". trackDb now has alpha and beta,public stanzas for ExAC and GnomAD variants tracks because the new url setting is not correctly transformed with the current code release on beta/RR. The url settings have an extra "&ignore=$$" because of some logic in printCustomUrlWithLabel that suppresses the item name from being used as label if $$ is not included in the url setting. I don't agree with that logic, but adding "&ignore=$$" is an easy workaround that does not break the exac/gnomad website.