Commits for angie

v360_preview to v360_preview2 (2018-01-08 to 2018-01-16) v360

93d78cb9877d1b22ce6167fc1c0a18d27ca55c85 Tue Jan 9 13:38:10 2018 -0800

• hAnnoStreamerFromTrackDb was erring out if it didn't recognize a bigData track type for an assembly hub -- but even for assembly hubs, custom tracks are still sql-based, so let custom tracks past that check. refs #20798
  • src/hg/lib/hAnno.c - lines changed 1, context: html, text, full: html, text

62689a652c5741683e7042e753e32389c86d7003 Tue Jan 9 13:40:33 2018 -0800

• NCBI's latest RefSeq GFF3 now uses 'pseudogene' in some cases where it previously used 'gene'; treat it the same as before. refs #20108 note-18
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 4, context: html, text, full: html, text
  • src/inc/gff3.h - lines changed 1, context: html, text, full: html, text
  • src/lib/gff3.c - lines changed 1, context: html, text, full: html, text

ddc6aa1ff598414619b2b9a122017fbcf53c15e6 Tue Jan 9 15:33:05 2018 -0800

• Use ln -f and gzip -f to avoid file-already-exists errors from reruns.
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 17, context: html, text, full: html, text

4375c533fdfb3e651724f19d8173ab93f44b2233 Tue Jan 9 15:34:39 2018 -0800

• Regenerating hg38.ncbiRefSeq* tables and files from latest NCBI download file. refs #20108 note-14
  • src/hg/makeDb/doc/hg38/ncbiRefSeq.txt - lines changed 7, context: html, text, full: html, text

a9575f6e1eaeb3597910b1611fd8f718d58d759c Wed Jan 10 09:25:21 2018 -0800

• Don't compress ncbiRefSeqVersion.txt when cleaning up because there's a link to it from gbdb.
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 2, context: html, text, full: html, text

74f7bf30603c7dfe869afcbe63adb6ddd74e9898 Wed Jan 10 12:58:38 2018 -0800

• Link to NCBI's Genome Data Viewer (GDV) using GCA_ accessions from dbDb.sourceName instead of hardcoded GCF_ ids. refs #18671
  • src/hg/hgTracks/extTools.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/extTools.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/menu.c - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/hdb.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 23, context: html, text, full: html, text

79672605ddcba54a4c42b0b87ac243fc5d86d810 Wed Jan 10 14:04:37 2018 -0800

• Don't use (hgFixed.)trackVersion for NCBI RefSeq anymore -- tdb dataVersion is preferred now and included automatically by printDataVersion. refs #20108, #18997 note-141
  • src/hg/hgc/hgc.c - lines changed 27, context: html, text, full: html, text

25727d0f604cdf295c116beef0ad0ce47b5014a1 Wed Jan 10 14:40:42 2018 -0800

• Added index on track field to hubSearchText.sql. refs #20694 note-11
  • src/hg/lib/hubSearchText.sql - lines changed 1, context: html, text, full: html, text

03803eba90389888a329f1c2ddb16b61fdaac4b3 Wed Jan 10 17:06:08 2018 -0800

• In hgGateway's autocomplete search for assembly hubs, use the new & improved hubSearchText table instead of the no-longer-updated trix search files. refs #20694
  • src/hg/hgGateway/hgGateway.c - lines changed 75, context: html, text, full: html, text

15438197526bd4c53ebd64921edc05e266f28a93 Thu Jan 11 11:23:26 2018 -0800

• Apply the limitResults parameter to the number of matching terms collected in hgFind.matches, so a term with thousands of matching results doesn't lead to a cart so big that it's slow. refs #20809
  • src/hg/lib/hgFind.c - lines changed 8, context: html, text, full: html, text

36d99737da9468220abdd6926d3d60119e7c94be Thu Jan 11 12:18:19 2018 -0800

• Apply the limitResults parameter to hgFindSpec sql searches in doQuery. refs #20809 note-4
  • src/hg/lib/hgFind.c - lines changed 4, context: html, text, full: html, text