Commits for chmalee

v454_base to v455_preview (2023-09-18 to 2023-09-25) v455

90052d845ed4c1e24963ad7cdc0161b29f50e1d3 Mon Sep 18 15:53:02 2023 -0700

• Fix bug that was printing 'matches to ucsc genes' when the pcr match was not to ucsc genes, just overlapping that position
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text

04a5652eeca73cbc1c426587576cf8d3b29a1f4c Mon Sep 18 15:57:17 2023 -0700

• Fix hgTracks and hgc crash when a users session has pcr results from both before we allowed multiple queries to stack and after, refs #32236
  • src/hg/cgilib/pcrResult.c - lines changed 12, context: html, text, full: html, text

67774b8e85d05089eb6482e1ea865c4298f4ac36 Tue Sep 19 09:41:09 2023 -0700

• When appending pcr results, if we would be writing to a file that is in a saved session, first copy the session pcr results into a new trash file, and then write our new results into that. This keeps the session unchanged, refs #32236
  • src/hg/hgPcr/hgPcr.c - lines changed 23, context: html, text, full: html, text

bbca1ee6f90a46e7a139434849dbf32bd206b522 Thu Sep 21 12:27:34 2023 -0700

• First cut of adding a historical refseq transcripts track, and getting hgvs searching to work with them, refs #26016
  • src/hg/lib/hgHgvs.c - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/ncbiRefSeq.txt - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 15, context: html, text, full: html, text

ae31cb7c9cb0b29fe6a23e7f96e3ad2b8d55f9d3 Thu Sep 21 16:46:47 2023 -0700

• Fill in missing bedList field for narrowPeak custom tracks, refs #32262
  • src/hg/lib/customFactory.c - lines changed 1, context: html, text, full: html, text

db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb Fri Sep 22 07:40:45 2023 -0700

• Move refSeqHistorical into hg38 trackDb instead of just the top level refSeqComposite, refs build email
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 15, context: html, text, full: html, text

ca8d3560aa51bc5d7a508359ebdb6fbedbc48b05 Fri Sep 22 13:19:15 2023 -0700

• Put special check for br tags in item titles behind hg.conf control now that we have new mouseover code. Eventually the else statement can be removed entirely, refs Jonathan email
  • src/hg/hgTracks/imageV2.c - lines changed 9, context: html, text, full: html, text

fbcacfcd4a8baadb31fca8b07c8f831580c31c82 Fri Sep 22 14:48:04 2023 -0700

• Fix hgvsToVcf tests now that we can have a track with old sequences, refs Galt email
  • src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.err - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf - lines changed 1, context: html, text, full: html, text