Commits for braney

v342_preview2 to v342_base (2016-11-28 to 2016-12-05) v342

826153d8a963a91ca519e2dcac0c20e4793dc3e1 Mon Nov 28 12:49:38 2016 -0800

• change trash directory for blat bigPsl to "hgBlat"
  • src/hg/hgBlat/hgBlat.c - lines changed 3, context: html, text, full: html, text

cddf9961aaac4513b5cdaa7273eb652f51920f16 Mon Nov 28 14:32:38 2016 -0800

• added a note to make sure that predicted mRNA sequence is all upper case in UCSC knownGene track
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh - lines changed 1, context: html, text, full: html, text

128526c4704a9a40aa4dd26e4bdb3662c4daebb0 Mon Nov 28 17:57:25 2016 -0800

• for BLAT custom track support, call bedToBigBed in a way that disables its checking for overlapping exons, which BLAT is generating for some protein queries
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text

304efa5344d37ba0f66bef4965047eff35fd3fcd Tue Nov 29 12:46:32 2016 -0800

• fix bug in "View details of alignment in window" for blat tracks that I introduced in Februrary
  • src/hg/hgc/hgc.c - lines changed 9, context: html, text, full: html, text

4dd0e74f2da650f4f41ccfc29fc18df024e303d9 Tue Nov 29 18:03:37 2016 -0800

• get BLAT custom tracks to work on assembly hubs
  • src/hg/hgBlat/hgBlat.c - lines changed 17, context: html, text, full: html, text
  • src/inc/twoBit.h - lines changed 3, context: html, text, full: html, text
  • src/lib/twoBit.c - lines changed 15, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 17, context: html, text, full: html, text

30c398a790536f060e754cbb67226d30406f6912 Wed Nov 30 12:00:52 2016 -0800

• Always put Base Position, Short Match, and Restriction Enymes tracks into group map. Make group map if it doesn't exit #16170
  • src/hg/hgTracks/hgTracks.c - lines changed 24, context: html, text, full: html, text

6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800

• change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
  • src/hg/hgGene/hgGeneData/C_elegans/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/D_melanogaster/dm3/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Rat/rn4/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/links.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgPal/hgPal.c - lines changed 1, context: html, text, full: html, text

e60bbad4978e2942453c6177f35cbe9291bfb930 Wed Nov 30 15:36:51 2016 -0800

• make blat custom track names conform (mostly) with the requests in #2811
  • src/hg/hgBlat/hgBlat.c - lines changed 119, context: html, text, full: html, text