Commits for max

v454_preview to v454_preview2 (2023-09-04 to 2023-09-11) v454

2a1c7786e6c5a0d56d3499efe713f722bb78abfb Mon Sep 4 12:18:02 2023 -0700

• fixing word break bug on bigBed extra tables, refs #29652
  • src/hg/hgc/bigBedClick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/style/HGStyle.css - lines changed 4, context: html, text, full: html, text

1ac6479e16d76dbfce8121b3aa493c3d9122a39a Tue Sep 5 06:37:48 2023 -0700

• adding otto script for malacards to git repo and adding the missing cd command, refs #26446
  • src/hg/utils/otto/malacards/update.sh - lines changed 20, context: html, text, full: html, text

0f82da7969da1610cbaa96808797f4458c2d13a6 Tue Sep 5 07:27:44 2023 -0700

• switching to LC_ALL in usage help, refs #20910
  • src/lib/bbiWrite.c - lines changed 1, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 2, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 2, context: html, text, full: html, text

f59a0760e5064af60766ae929d73d7c9626a5bcf Wed Sep 6 01:36:24 2023 -0700

• tiny change to gnomad docs, refs #31989
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 1, context: html, text, full: html, text

1568d08d5e4dcf92808af8928bd1d9d80aef45d6 Wed Sep 6 04:41:52 2023 -0700

• another tiny change to gnomad docs, refs #31989
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 2, context: html, text, full: html, text

3936d80c4ab6899bbc757593729f1f3333d04ac7 Wed Sep 6 14:29:11 2023 +0200

• fixing browser grant number format, no redmine
  • src/hg/htdocs/goldenPath/credits.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/pubs.html - lines changed 1, context: html, text, full: html, text

42359030b483e8b6b4ec32c743b0fff0b52b3e17 Wed Sep 6 08:20:00 2023 -0700

• improving error message when no regions are output in tb, refs #32061
  • src/hg/hgTables/bedList.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/gffOut.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/seqOut.c - lines changed 5, context: html, text, full: html, text

527a3531a7db419bad01537556693e9424e0ee04 Fri Sep 8 05:00:23 2023 -0700

• removing the trackDb prefix for clinvar tracks, no redmine
  • src/hg/makeDb/trackDb/human/clinvar.ra - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.clinvar.ra - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text

cceb66c59fe9cdc9b97ea9218efbc1db474ad07b Fri Sep 8 05:06:43 2023 -0700

• creating an alpha version of the clinvar track. This is the only way to play with changes to the clinvar track without risking a leak of the changes to the RR via the otto push and without pausing the otto push, no redmine yet
  • src/hg/makeDb/trackDb/human/clinvar.alpha.ra - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text

2a1a263c3c172bdf671affee41e2aa71b00534b4 Fri Sep 8 06:12:43 2023 -0700

• clinvar has added a new mol consequence type, no redmine
  • src/hg/makeDb/trackDb/human/clinvar.alpha.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/clinvar.ra - lines changed 1, context: html, text, full: html, text