angie: changes by file

branch to review (2009-09-02 to 2009-09-09) v214

• src/hg/encode/validateFiles/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Add to L instead of overwriting -- need common.mk's handling of USE_SSL.
• src/hg/hgGetAnn/tests/expected/chrRangeGenePred.gp
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
• src/hg/hgGetAnn/tests/expected/chrRangeGenePredColHeaders.gp
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
• src/hg/hgGetAnn/tests/expected/chrRangeGenePredTsvHeaders.gp
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.500 lines changed: 30, context: html, text, full: html, text
    Basic ui for type bam -- still need to add filtering on BAM flag bits.
• src/hg/hgTracks/bamTrack.c
  • 1.8 lines changed: 43, context: html, text, full: html, text
    Added basic filtering on hgTrackUi settings. Make paired-but-not-properly items a lighter shade.
• src/hg/lib/trackDbCustom.c
  • 1.70 lines changed: 2, context: html, text, full: html, text
    Added bam to packableType().
• src/hg/makeDb/doc/hg19.txt
  • 1.37 lines changed: 54, context: html, text, full: html, text
    Added snp130CodingDbSnp (used dbSNP's provisional SNP coord mapping from hg18).