bsuh: changes by file

branch to review (2010-05-25 to 2010-06-01) v233

• src/hg/encode/utils/tagAlignToSAM/tagAlignToSAM.py
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added one more comment
  • 1.4 lines changed: 10, context: html, text, full: html, text
    Added some comments to point to where people can add code to change the MAPQ policy
  • 1.3 lines changed: 9, context: html, text, full: html, text
    After some debate, we now always report MAPQ=255
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Fixed bug identified by Tim Durham @ Broad