File Changes for angie

v276_preview2 to v276_base (2012-11-13 to 2012-11-20) v276

• src/hg/hgTracks/vcfTrack.c
  • lines changed 36, context: html, text, full: html, text
    VCF with mixed haploid status, for example on chrX where females are diploid andmales are haploid, was having gtHapIx assigned in two different ways, not good.
    Same formula for gtHapIx now applies to both diploid and haploid genotypes.
    We no longer have the invariant that the number of clustered haplotypes is the
    same as the max gtHapIx number, but it all works, trust me. :)
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/lib/dgv.as
  • lines changed 2, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/lib/dgv.sql
  • lines changed 3, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    Tweak to 10-year-old code: in hGetCtBedRange, when we need a placeholderfor a column in the sql query, use "0" instead of the startField. It's a
    tiny bit more efficient and hopefully less eye-catching for Jorge. :)
    Speaking of efficiency, the CGIs could use a position-only (bed3) version.
    
• src/hg/makeDb/doc/hg17.txt
  • lines changed 90, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 92, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 77, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
    for very specific patterns that wouldn't appear in any other track.
    
  • lines changed 13, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
    for very specific patterns that wouldn't appear in any other track.
    
• src/product/README.building.source
  • lines changed 3, context: html, text, full: html, text
    Feature #6336 (samtabix): The official git repository is now on genome-source.cse.ucsc.eduinstead of github.com.