Eric Banks b21889812d Removing some more usages of extended events. Not done yet, but almost there.		2012-03-30 01:51:37 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Removing some more usages of extended events. Not done yet, but almost there.	2012-03-30 01:51:37 -04:00
test	UG integration tests updated. A handful of sites are lost because there are only 5 indels and one starts at the beginning of the read so it no longer passes our min threshold (now consistent with GGA), but mostly the depth changes ever so slightly once in a while between extended and normal pileups (I think the normal pileups are correct). I have looked thoroughly in IGV at ALL differences and am happy with the new results. As an aside, the AD is now calculated more accurately for indels.	2012-03-30 01:35:49 -04:00