angie: changes by file

review to branch (2010-01-26 to 2010-02-02) v224

• src/hg/hgc/hgc.c
  • 1.1595 lines changed: 11, context: html, text, full: html, text
    genericChainClick: fixed bug noticed by Katrina: we weren't checking the chainLinearGap trackDb setting, so when recalculating score-in-window, we used incorrect gap penalties unless the default loose penalties were used. Also, recalculating score-in-window had the unexpected side effect of clobbering the original chain's score when the whole chain fit in the window, because chainSubSetOnT was returning the original chain! I took out the score-in-window stuff for chains that fit in the window, and added a position link for the ref. genome (like we have on all of our other pages).
• src/hg/makeDb/trackDb/seaHare/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding correct alignment params for seaHare-human alignments.
• src/hg/makeDb/trackDb/seaHare/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Right now this is only needed for including trackDb.chainNet.ra -- would be cool for hgTrackDb to auto-include some filenames...