Commits for chmalee

v407_preview2 to v407_base (2020-11-09 to 2020-11-16) v407

702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800

• hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 44, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/expected/genomesConfigErrors.output.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/expected/supertrackChild.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/input/genomesConfigErrorsHub.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/input/misconfigGenomes.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/input/noErrors.araTha1.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/makefile - lines changed 5, context: html, text, full: html, text

488f5657d433c5446eba5d2b54f2812fea64fb3d Mon Nov 9 12:59:48 2020 -0800

• Removing gene filter from gnomAD variants track, refs #25010
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra - lines changed 2, context: html, text, full: html, text

f40b6f8e5a763bffbf364d8e64bcf252f8aef27d Mon Nov 9 13:20:57 2020 -0800

• Add vcfPhasedTrio to supported hgIntegrator track types, refs #25873
  • src/hg/lib/hAnno.c - lines changed 1, context: html, text, full: html, text

326e2863f25a00c91baa95df5d7e31d7ece175db Tue Nov 10 13:44:13 2020 -0800

• Adding URL searchability to hgPublicSessions using parameter 'search=blah', refs #18470
  • src/hg/hgPublicSessions/hgPublicSessions.c - lines changed 8, context: html, text, full: html, text

e2863d01dfb07e37992f4130c8cccb699370a398 Thu Nov 12 09:46:29 2020 -0800

• Fix boneheaded startsWith() mistake in vcfToBed
  • src/hg/utils/vcfToBed/vcfToBed.c - lines changed 5, context: html, text, full: html, text

5cdeda3ceacbf093b325e8ebd48e17c4ac03e6c6 Thu Nov 12 16:29:01 2020 -0800

• Quality of life improvements on VCF details page, put the info tag annotations in a collapsible table, and add a border to said table so it's easier to distinguish between different tags. Also fix a bug in INFO tabular tables where the trailing separator was causing extra table cells to print, refs #26451
  • src/hg/hgc/vcfClick.c - lines changed 21, context: html, text, full: html, text

302062e64efcf0d93b1955d4890e7456c5fdd524 Fri Nov 13 09:50:56 2020 -0800

• hgPublicSessions: Do not overwrite previous search if there is no 'search' variable on the URL, refs #18470
  • src/hg/hgPublicSessions/hgPublicSessions.c - lines changed 20, context: html, text, full: html, text

5afa332cc12c75f441ffaf7fa2d9a219ec1f219b Fri Nov 13 10:22:20 2020 -0800

• Remove the superfluous fields 'Reference Seq' and 'Variant Seq' from the genome in a bottle sv track, refs #24349
  • src/hg/utils/otto/dbVar/processNstd175.py - lines changed 2, context: html, text, full: html, text

4543dba7eee24c7463b60ae9fb5e5f6ac78a95ad Fri Nov 13 10:23:19 2020 -0800

• Forgot to commit updated autoSql for genome in a bottle sv track, refs #24349
  • src/hg/utils/otto/dbVar/giabSv.as - lines changed 2, context: html, text, full: html, text