angie: changes by commit
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review to branch (2010-01-26 to 2010-02-02) v224
- 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/hgc/hgc.c 1.1595 - lines changed: 11, 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...
- src/hg/makeDb/trackDb/seaHare/trackDb.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.chainNet.ra 1.1 - lines changed: 0, context: html, text, full: html, text
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