File Changes for angie

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

• src/hg/hgVai/hgVai.c
  • lines changed 341, 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/hgc/hgc.c
  • lines changed 118, 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/inc/dgvPlus.h
  • lines changed 84, 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/lib/annoFormatVep.c
  • lines changed 5, context: html, text, full: html, text
    Correcting off-by-one intron number; adding recognition of stop_lost caused by inframe_deletion.
  • lines changed 1, context: html, text, full: html, text
    Wording change in header comment as suggested by b0b.
• src/hg/lib/dgvPlus.as
  • lines changed 26, 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/lib/dgvPlus.c
  • lines changed 255, 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/lib/dgvPlus.sql
  • lines changed 34, 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/lib/gpFx.c
  • lines changed 7, context: html, text, full: html, text
    Correcting off-by-one intron number; adding recognition of stop_lost caused by inframe_deletion.
• src/hg/lib/makefile
  • lines changed 1, 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/makeDb/doc/hg18.txt
  • lines changed 73, 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/makeDb/doc/hg19.txt
  • lines changed 73, 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/makeDb/trackDb/human/dgvPlus.html
  • lines changed 103, 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
    
  • lines changed 56, 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/trackDb.ra
  • lines changed 40, 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
    
  • lines changed 17, context: html, text, full: html, text
    Changing label of older DGV track for release=alpha.refs #11200
    
• src/hg/utils/automation/translateDgvPlus.pl
  • lines changed 59, 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/inc/basicBed.h
  • lines changed 9, context: html, text, full: html, text
    Adding bed4{New,Free,FreeList}.
• src/lib/basicBed.c
  • lines changed 37, context: html, text, full: html, text
    Adding bed4{New,Free,FreeList}.