Commits for braney

v369_preview to v369_preview2 (2018-07-16 to 2018-07-23) v369

a2bcc20474a994fa100474209bebd017255d10c7 Wed Jul 18 10:41:49 2018 -0700

• changes to makeGencodeKnownGene to use the Ensembl id as the primary id instead of the uc id. Doc for building the proof of concept on grcHhh38
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh - lines changed 951, context: html, text, full: html, text
  • src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c - lines changed 34, context: html, text, full: html, text

7aa2c736ad6d5be50449b4765527e15a091812ee Wed Jul 18 10:46:26 2018 -0700

• needed to load fish blastTabs
  • src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh - lines changed 1, context: html, text, full: html, text

02b0a3f5b948147bfa8781fc7366f4668bae5845 Wed Jul 18 10:50:31 2018 -0700

• changes to SQL files to support new ucsc genes with ENST identifiers. Changes are backwards compatible.
  • src/hg/lib/kgColor.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/knownIsoforms.sql - lines changed 2, context: html, text, full: html, text

a2d849d0acd9e8921d1ff131d907ca867c858d11 Thu Jul 19 10:47:57 2018 -0700

• changes to support new new Gencode models in hgGene
  • src/hg/hgGene/hgGene.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgGene/hgGene.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgGene/synonym.c - lines changed 1, context: html, text, full: html, text

045e182a27b1059a13c90c5a1ed9fdc8a31b18f2 Thu Jul 19 14:45:08 2018 -0700

• more changes to enable using Ensembl id as primary id in knownGene.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 11, context: html, text, full: html, text

6791876ba30394c3aad18702708feb4bfb6ec761 Thu Jul 19 17:04:44 2018 -0700

• add bigBed numeric and filterBy filters
  • src/hg/hgTracks/bigBedFilter.h - lines changed 23, context: html, text, full: html, text
  • src/hg/hgTracks/bigBedTrack.c - lines changed 164, context: html, text, full: html, text
  • src/hg/hgTracks/encode.c - lines changed 115, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 8, context: html, text, full: html, text

fab970524dae1a360fed5951f1b69c8491cdc352 Fri Jul 20 10:01:47 2018 -0700

• make bigNarrowPeak support signalFilter on signalValue field. This means that arbitrary number filtering doesn't work on bigNarrowPeak
  • src/hg/hgTracks/encode.c - lines changed 3, context: html, text, full: html, text

6e842bcc421f0c27a6d13ab23615102963c8010d Fri Jul 20 10:14:43 2018 -0700

• change the name of a bigBed filter function
  • src/hg/hgTracks/bigBedFilter.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/encode.c - lines changed 4, context: html, text, full: html, text

d9ed1a589b8ab2d03412919fc2e8461cb18d7765 Fri Jul 20 12:56:28 2018 -0700

• a few more Gencode2 changes
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 39, context: html, text, full: html, text