Commits for angie

v289_base to v290_preview (2013-09-09 to 2013-09-16) v290

• Adding bed4{New,Free,FreeList}.
  • src/inc/basicBed.h - lines changed 9, context: html, text, full: html, text
  • src/lib/basicBed.c - lines changed 37, context: html, text, full: html, text
• Correcting off-by-one intron number; adding recognition of stop_lost caused by inframe_deletion.
  • src/hg/lib/annoFormatVep.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 7, context: html, text, full: html, text
• Adding 'Artificial Example Variants' as an option for variant track.Since there is now at least one source of variants from which to choose,
  we no longer need to hide the rest of the UI until the user provides
  some variants.
  The variants are generated from genes in the user's cart position if
  possible. Variants are cached in trash files unique to database and
  cart position.
  refs #11110
  
  • src/hg/hgVai/hgVai.c - lines changed 341, context: html, text, full: html, text
• New and improved Database of Genomic Variants (DGV). It is now acomposite track as requested by the submitter, and the tables have
  more columns than the older dgv tables.
  The track description needs to be updated to make more clear what
  DGV gets from dbVar/DGVa and what it adds.
  refs #11200
  
  • src/hg/hgc/hgc.c - lines changed 118, context: html, text, full: html, text
  • src/hg/inc/dgvPlus.h - lines changed 84, context: html, text, full: html, text
  • src/hg/lib/dgvPlus.as - lines changed 26, context: html, text, full: html, text
  • src/hg/lib/dgvPlus.c - lines changed 255, context: html, text, full: html, text
  • src/hg/lib/dgvPlus.sql - lines changed 34, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg18.txt - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dgvPlus.html - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/automation/translateDgvPlus.pl - lines changed 59, context: html, text, full: html, text
• Wording change in header comment as suggested by b0b.
  • src/hg/lib/annoFormatVep.c - lines changed 1, context: html, text, full: html, text
• Updated DGV composite track description, borrowing some text fromhttp://dgv.tcag.ca/dgv/docs/201306-DGV_Newsletter.pdf .
  I will run this by Jeff MacDonald.
  refs #11200
  
  • src/hg/makeDb/trackDb/human/dgvPlus.html - lines changed 56, context: html, text, full: html, text
• Changing label of older DGV track for release=alpha.refs #11200
  
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 17, context: html, text, full: html, text